[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-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/11541607/PCPG-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PCPG-TP/11548818/transformed.cor.cli.txt"

nPatients in clinical file=132, in cluster file=162, common to both=129
[1]  28 129
[1] "AMP PEAK 1(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          21                          108 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          21                          108 
[1] "AMP PEAK 2(4Q25) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                         6                        123 
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                         6                        123 
[1] "AMP PEAK 3(4Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                          11                          118 
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                          11                          118 
[1] "AMP PEAK 4(11P15.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                            8                           121 
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                            8                           121 
[1] "AMP PEAK 5(12Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                           12                           117 
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                           12                           117 
[1] "AMP PEAK 6(14Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                            7                           122 
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                            7                           122 
[1] "AMP PEAK 7(17Q21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                            13                            116 
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                            13                            116 
[1] "DEL PEAK  1(1P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                         92                          37 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                         92                          37 
[1] "DEL PEAK  2(1Q42.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                            12                            117 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                            12                            117 
[1] "DEL PEAK  3(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           49                            80 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           49                            80 
[1] "DEL PEAK  4(3Q26.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           75                            54 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           75                            54 
[1] "DEL PEAK  5(4Q28.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                            8                           121 
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                            8                           121 
[1] "DEL PEAK  6(5Q15) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                         11                         118 
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                         11                         118 
[1] "DEL PEAK  7(6P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                            6                           123 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                            6                           123 
[1] "DEL PEAK  8(6Q16.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                           18                           111 
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                           18                           111 
[1] "DEL PEAK  9(8P22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                         20                         109 
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                         20                         109 
[1] "DEL PEAK 10(8Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                           10                           119 
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                           10                           119 
[1] "DEL PEAK 11(9P24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                           10                           119 
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                           10                           119 
[1] "DEL PEAK 12(9Q21.12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                            10                            119 
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                            10                            119 
[1] "DEL PEAK 13(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                            45                             84 
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                            45                             84 
[1] "DEL PEAK 14(11Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                            39                             90 
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                            39                             90 
[1] "DEL PEAK 15(12Q21.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                              5                             124 
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                              5                             124 
[1] "DEL PEAK 16(13Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                             5                            124 
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                             5                            124 
[1] "DEL PEAK 17(16Q21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           4                          125 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           4                          125 
[1] "DEL PEAK 18(17P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                            53                             76 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                            53                             76 
[1] "DEL PEAK 19(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                            36                             93 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                            36                             93 
[1] "DEL PEAK 20(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                             54                              75 
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                             54                              75 
[1] "DEL PEAK 21(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                           36                            93 
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                           36                            93 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DCCUPLOADDATE"                         
 [6] "GENDER"                                
 [7] "RADIATIONTHERAPY"                      
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCHNUMBER"                           

Input Data has 11 rows and 129 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF 
         957          883           69           29          179          240 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
        2485          852           38         1102          211           55 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
          22          766           70          134           24           29 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
        1178           28         2957         1249          246         2643 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 
         604           89          216         1013          724           32 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
          26          405           37          356          397          242 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
         191         2214          457           21          134           54 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
          NA           18          611          730          800          715 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
         441          346          909          912          601          527 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
         324          358          185          240          371         3180 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
        3087         2149         2040         2983          274         3013 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
          43            3         1558         1656         2222         3247 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
        3362         3269           NA          750          345         1509 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 
         132          765          242          317          770          432 
TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
         522           36          604          366          380          505 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
         538          779          324          840          678          136 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
         144          128         9219         3880          887           NA 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
        1000          182          531          992          795          234 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
         371           24         1131          730          737         1294 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
          34           57          595          652         1406          395 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
          NA           49          357          288         2161         1719 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
          41         2822          210 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=116,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'BATCH.NUMBER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
[1] "AGE"    "GENDER" "RACE"  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T"
[1] "PATHOLOGY.N"
Output Data has 129 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=56, 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    19   2
  AMP PEAK 1(1Q21.3) WILD-TYPE 106   2
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                          21                          108 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                           2                            2 
$`AMP PEAK 1(1Q21.3) MUTATED`
TCGA-P7-A5NY TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A686 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       31.46        33.30        23.80        13.32         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SR-A6MS TCGA-SR-A6MV 
       20.09        24.00       104.55       101.49        73.05       107.47 
TCGA-SR-A6MZ TCGA-WB-A80L TCGA-WB-A80P TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81G 
       11.34        22.29       303.09         5.98         7.69        24.23 
TCGA-WB-A81Q TCGA-WB-A81V TCGA-WB-A81W 
       24.82        71.05        56.52 

$`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         0.95         5.88         7.89        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         8.09        86.89        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 
        2.93         7.10         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         0.69 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
        4.41         1.78        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
        6.08         7.89        12.20        70.65        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
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         7.96        10.42        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        27.62         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        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81H 
       26.14        12.20         0.79        37.18        24.00        42.54 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        1.12         1.87        19.56        21.44        46.22        12.99 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.61        11.74         9.47         1.35        92.78         6.90 

  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                        0.59                         0.10 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                      303.09                       127.56 
  AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE 
                       24.23                        12.74 
[1] "0.6 - 303.1 (24.2)" "0.1 - 127.6 (12.7)"
[1] "hr=" "3.7"
D1V2, continuous
D1V3, binary
                              cls
clus                            0  1
  AMP PEAK 1(1Q21.3) MUTATED    7 14
  AMP PEAK 1(1Q21.3) WILD-TYPE 66 42
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q21.3) MUTATED      7   14
  AMP PEAK 1(1Q21.3) WILD-TYPE   66   42
        clus
vv       AMP PEAK 1(1Q21.3) MUTATED AMP PEAK 1(1Q21.3) WILD-TYPE
  FEMALE                          7                           66
  MALE                           14                           42
[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     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(1Q21.3) MUTATED                           0    20
  AMP PEAK 1(1Q21.3) WILD-TYPE                         9    92
D1V4, multiclass
                                  clus
vv                                 AMP PEAK 1(1Q21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                    20
                                  clus
vv                                 AMP PEAK 1(1Q21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      92
[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 119   4
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                         6                        123 
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                         0                          4 
$`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         0.69        98.07        27.62         1.87 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01         1.25         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         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-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D 
       13.32        11.70        13.05         7.96         6.28        72.79 
TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL 
       15.02         4.41         1.78         2.89         0.59        20.09 
TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR 
       24.00        26.30        23.51        14.50        11.38        29.88 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       73.05       106.75       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
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-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80L 
       12.49        16.60        17.69        25.61        10.65        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       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        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
       42.54         1.12        19.56        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       24.82         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                      0.69                       0.10 
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                     98.07                     303.09 
  AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE 
                    14.745                     15.020 
[1] "0.7 - 98.1 (14.7)"  "0.1 - 303.1 (15.0)"
[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 71 52
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(4Q25) MUTATED      2    4
  AMP PEAK 2(4Q25) WILD-TYPE   71   52
        clus
vv       AMP PEAK 2(4Q25) MUTATED AMP PEAK 2(4Q25) WILD-TYPE
  FEMALE                        2                         71
  MALE                          4                         52
[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     4
                            vv
clus                         BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(4Q25) MUTATED                           1     5
  AMP PEAK 2(4Q25) WILD-TYPE                         8   107
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                                                     4
  BLACK OR AFRICAN AMERICAN                                 8
  WHITE                                                   107
[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    11   0
  AMP PEAK 3(4Q31.1) WILD-TYPE 114   4
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                          11                          118 
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                           0                            4 
$`AMP PEAK 3(4Q31.1) MUTATED`
TCGA-PR-A5PF TCGA-PR-A5PH TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68G TCGA-SP-A6QI 
        7.89        28.01        13.32         1.22         0.69        98.07 
TCGA-TT-A6YN TCGA-W2-A7H5 TCGA-W2-A7HC TCGA-WB-A80K TCGA-WB-A80Q 
        7.96        14.20        12.03        27.62       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         0.95         5.88        81.70 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
        1.25        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         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         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-A689 
        7.10        33.30        23.80         1.05         0.85        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A7CZ 
       13.05         7.96         6.28        72.79        15.02         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       23.51        14.50        11.38        29.88        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       17.33        10.65        11.77         6.08         7.89        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK 
      104.55       101.49        70.65        67.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        54.44        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       107.47         3.12        24.66        11.34        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA 
        4.34        25.15        10.42        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 
       22.29         4.47         4.73         4.21       303.09        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        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       56.52         1.35        92.78         6.90 

  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                        0.69                         0.10 
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                      127.56                       303.09 
  AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE 
                       13.32                        16.88 
[1] "0.7 - 127.6 (13.3)" "0.1 - 303.1 (16.9)"
[1] "hr="     "7.5e+07"
D3V2, continuous
D3V3, binary
                              cls
clus                            0  1
  AMP PEAK 3(4Q31.1) MUTATED    5  6
  AMP PEAK 3(4Q31.1) WILD-TYPE 68 50
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(4Q31.1) MUTATED      5    6
  AMP PEAK 3(4Q31.1) WILD-TYPE   68   50
        clus
vv       AMP PEAK 3(4Q31.1) MUTATED AMP PEAK 3(4Q31.1) WILD-TYPE
  FEMALE                          5                           68
  MALE                            6                           50
[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     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(4Q31.1) MUTATED                           0    11
  AMP PEAK 3(4Q31.1) WILD-TYPE                         9   101
D3V4, multiclass
                                  clus
vv                                 AMP PEAK 3(4Q31.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 0
  WHITE                                                    11
                                  clus
vv                                 AMP PEAK 3(4Q31.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                     101
[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 117   4
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                            8                           121 
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                            0                             4 
$`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         7.89        81.70        11.70        72.79        70.65 
TCGA-TT-A6YN TCGA-WB-A80O 
        7.96         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-A6GS 
       31.46        29.03         0.95         5.88        28.01         1.25 
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         0.95        38.73         0.92        97.22 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       41.06         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-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
       13.05         7.96         6.28        15.02         0.69         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       23.51        14.50        11.38        29.88        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       17.33        10.65        11.77         6.08         7.89        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      104.55       101.49        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        54.44        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       107.47         3.12        24.66        11.34        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
        4.34        25.15        10.42        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        27.62        22.29         4.47         4.73 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       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 
       17.46        32.61        26.14         7.69        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R 
       19.56        21.44        46.22        12.99        24.82         1.61 
TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       11.74         9.47        71.05        56.52         1.35        92.78 
TCGA-XG-A823 
        6.90 

  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 
                        81.70                        303.09 
  AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE 
                         9.83                         16.60 
[1] "2.3 - 81.7 (9.8)"   "0.1 - 303.1 (16.6)"
[1] "hr="     "7.3e+07"
D4V2, continuous
D4V3, binary
                               cls
clus                             0  1
  AMP PEAK 4(11P15.2) MUTATED    6  2
  AMP PEAK 4(11P15.2) WILD-TYPE 67 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(11P15.2) MUTATED      6    2
  AMP PEAK 4(11P15.2) WILD-TYPE   67   54
        clus
vv       AMP PEAK 4(11P15.2) MUTATED AMP PEAK 4(11P15.2) WILD-TYPE
  FEMALE                           6                            67
  MALE                             2                            54
[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     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(11P15.2) MUTATED                           0     6
  AMP PEAK 4(11P15.2) WILD-TYPE                         9   106
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                                                        2
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      106
[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    12   0
  AMP PEAK 5(12Q13.3) WILD-TYPE 113   4
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                           12                           117 
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                            0                             4 
$`AMP PEAK 5(12Q13.3) MUTATED`
TCGA-QT-A5XJ TCGA-RT-A6YC TCGA-RW-A681 TCGA-RW-A68D TCGA-S7-A7X1 TCGA-SR-A6MP 
       36.23         8.09        23.80        72.79         7.89        51.22 
TCGA-SR-A6MT TCGA-SR-A6MZ TCGA-W2-A7H5 TCGA-W2-A7HB TCGA-W2-A7HD TCGA-WB-A821 
      106.75        11.34        14.20        19.86        12.49         1.35 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01         1.25         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
        0.92        97.22        41.06        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        7.10        33.30         1.05         0.85        13.32         1.22 
TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G 
       11.70        13.05         7.96         6.28        15.02         0.69 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89         0.59        20.09        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       26.30        23.51        14.50        11.38        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 
       19.76        17.33        10.65        11.77         6.08        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
       99.06         1.41         0.10        54.44        73.05       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK 
      107.47         3.12        24.66        49.61         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HC 
        7.96        10.42        25.32        17.16         1.18        12.03 
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        27.62        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       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        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
       56.52        92.78         6.90 

  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                         1.35                          0.10 
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                       106.75                        303.09 
  AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE 
                        17.03                         15.02 
[1] "1.4 - 106.8 (17.0)" "0.1 - 303.1 (15.0)"
[1] "hr="     "7.8e+07"
D5V2, continuous
D5V3, binary
                               cls
clus                             0  1
  AMP PEAK 5(12Q13.3) MUTATED    8  4
  AMP PEAK 5(12Q13.3) WILD-TYPE 65 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 5(12Q13.3) MUTATED      8    4
  AMP PEAK 5(12Q13.3) WILD-TYPE   65   52
        clus
vv       AMP PEAK 5(12Q13.3) MUTATED AMP PEAK 5(12Q13.3) WILD-TYPE
  FEMALE                           8                            65
  MALE                             4                            52
[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     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(12Q13.3) MUTATED                           1    10
  AMP PEAK 5(12Q13.3) WILD-TYPE                         8   102
D5V4, multiclass
                                  clus
vv                                 AMP PEAK 5(12Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     10
                                  clus
vv                                 AMP PEAK 5(12Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      102
[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     7   0
  AMP PEAK 6(14Q24.3) WILD-TYPE 118   4
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                            7                           122 
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                            0                             4 
$`AMP PEAK 6(14Q24.3) MUTATED`
TCGA-QT-A5XJ TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A5XO TCGA-RW-A681 TCGA-S7-A7WT 
       36.23         1.81        25.18         2.30        23.80        29.98 
TCGA-SR-A6MT 
      106.75 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XP 
       81.70        28.01         1.25         6.94         0.72         4.41 
TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA 
        0.79         0.95        38.73         0.92        97.22        41.06 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
        8.09        86.89        19.86         2.93         7.10        33.30 
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-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ 
        7.96         6.28        72.79        15.02         0.69         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WU TCGA-S7-A7WV 
       23.51        14.50        11.38        29.88        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
       10.65        11.77         6.08         7.89        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        54.44        73.05       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      107.47         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15         7.96        10.42        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        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       303.09       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        17.46        32.61        26.14         7.69        12.20 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
        0.79        37.18        24.00        24.23        42.54         1.12 
TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.87        19.56        21.44        46.22        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 
        1.61        11.74         9.47        71.05        56.52         1.35 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                         1.81                          0.10 
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                       106.75                        303.09 
  AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE 
                        25.18                         14.35 
[1] "1.8 - 106.8 (25.2)" "0.1 - 303.1 (14.3)"
[1] "hr="     "7.4e+07"
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK 6(14Q24.3) MUTATED    4  3
  AMP PEAK 6(14Q24.3) WILD-TYPE 69 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(14Q24.3) MUTATED      4    3
  AMP PEAK 6(14Q24.3) WILD-TYPE   69   53
        clus
vv       AMP PEAK 6(14Q24.3) MUTATED AMP PEAK 6(14Q24.3) WILD-TYPE
  FEMALE                           4                            69
  MALE                             3                            53
[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     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(14Q24.3) MUTATED                           3     4
  AMP PEAK 6(14Q24.3) WILD-TYPE                         6   108
D6V4, multiclass
                                  clus
vv                                 AMP PEAK 6(14Q24.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                      4
                                  clus
vv                                 AMP PEAK 6(14Q24.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    6
  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(7) Variable = AMP PEAK 7(17Q21.31) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 7(17Q21.31) MUTATED    11   2
  AMP PEAK 7(17Q21.31) WILD-TYPE 114   2
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                            13                            116 
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                             2                              2 
$`AMP PEAK 7(17Q21.31) MUTATED`
TCGA-P8-A5KC TCGA-PR-A5PF TCGA-PR-A5PH TCGA-RW-A681 TCGA-RW-A686 TCGA-RW-A688 
       29.03         7.89        28.01        23.80        13.32         1.22 
TCGA-RW-A8AZ TCGA-WB-A80K TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A81J TCGA-WB-A81Q 
        2.89        27.62       303.09       127.56         1.87        24.82 
TCGA-WB-A81W 
       56.52 

$`AMP PEAK 7(17Q21.31) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PG TCGA-QR-A6GS 
       31.46         2.27         0.95         5.88        81.70         1.25 
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         0.95        38.73         0.92        97.22 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       41.06         8.09        86.89        19.86         2.93         7.10 
TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B 
       33.30         1.05         0.85        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         0.69         4.41         1.78 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU 
        0.10        51.22        54.44        73.05       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      107.47         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15         7.96        10.42        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-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        10.65        22.29         4.47         4.73         4.21 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       24.23        42.54         1.12        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A821 
       12.99         1.61        11.74         9.47        71.05         1.35 
TCGA-WB-A822 TCGA-XG-A823 
       92.78         6.90 

  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 
                        303.09                         110.53 
  AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE 
                         24.82                          14.35 
[1] "1.2 - 303.1 (24.8)" "0.1 - 110.5 (14.3)"
[1] "hr=" "7.2"
D7V2, continuous
D7V3, binary
                                cls
clus                              0  1
  AMP PEAK 7(17Q21.31) MUTATED    3 10
  AMP PEAK 7(17Q21.31) WILD-TYPE 70 46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 7(17Q21.31) MUTATED      3   10
  AMP PEAK 7(17Q21.31) WILD-TYPE   70   46
        clus
vv       AMP PEAK 7(17Q21.31) MUTATED AMP PEAK 7(17Q21.31) WILD-TYPE
  FEMALE                            3                             70
  MALE                             10                             46
[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     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(17Q21.31) MUTATED                           0    13
  AMP PEAK 7(17Q21.31) WILD-TYPE                         9    99
D7V4, multiclass
                                  clus
vv                                 AMP PEAK 7(17Q21.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                      13
                                  clus
vv                                 AMP PEAK 7(17Q21.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                     9
  WHITE                                                        99
[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   90  2
  DEL PEAK  1(1P12) WILD-TYPE 35  2
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                         92                          37 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                          2                           2 
$`DEL PEAK  1(1P12) MUTATED`
TCGA-P7-A5NY TCGA-P8-A5KD TCGA-P8-A6RX TCGA-PR-A5PF TCGA-PR-A5PG TCGA-QR-A6GS 
       31.46         2.27         0.95         7.89        81.70         1.25 
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP 
       36.23         6.94         1.81         0.72         2.30         4.41 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RT-A6YA TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y 
        0.79        38.73        41.06        86.89        19.86         7.10 
TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 
       33.30        23.80         1.05         0.85         1.22        11.70 
TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ 
       13.05         7.96        72.79         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       20.09        24.00        26.30        11.38        29.88        29.98 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       51.22        54.44        73.05       106.75       110.53       107.47 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        11.34         4.34        25.15         7.96 
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-A7HF TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       17.69        10.65        27.62         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81D 
      303.09        29.16        17.46        26.14         7.69         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81K TCGA-WB-A81M 
       37.18        24.00        24.23        42.54        19.56        21.44 
TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       12.99         1.61        11.74         9.47        71.05        56.52 
TCGA-WB-A821 TCGA-WB-A822 
        1.35        92.78 

$`DEL PEAK  1(1P12) WILD-TYPE`
TCGA-P8-A5KC TCGA-P8-A6RY TCGA-PR-A5PH TCGA-QT-A5XN TCGA-QT-A7U0 TCGA-RM-A68W 
       29.03         5.88        28.01        25.18         0.95         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67X TCGA-RW-A686 TCGA-RW-A68C TCGA-RW-A68F 
       97.22         8.09         2.93        13.32         6.28        15.02 
TCGA-RW-A68G TCGA-RW-A7CZ TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WU TCGA-S7-A7WV 
        0.69         4.41        23.51        14.50        19.76        17.33 
TCGA-S7-A7WW TCGA-SQ-A6I6 TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HE 
       10.65         0.10        49.61        10.42        25.32        16.60 
TCGA-W2-A7HH TCGA-WB-A80L TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
       25.61        22.29       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        12.20         1.12         1.87        46.22        24.82 
TCGA-XG-A823 
        6.90 

  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                       0.59                        0.10 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                     303.09                      127.56 
  DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE 
                      15.68                       15.02 
[1] "0.6 - 303.1 (15.7)" "0.1 - 127.6 (15.0)"
[1] "hr=" "2.6"
D8V2, continuous
D8V3, binary
                             cls
clus                           0  1
  DEL PEAK  1(1P12) MUTATED   52 40
  DEL PEAK  1(1P12) WILD-TYPE 21 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  1(1P12) MUTATED     52   40
  DEL PEAK  1(1P12) WILD-TYPE   21   16
        clus
vv       DEL PEAK  1(1P12) MUTATED DEL PEAK  1(1P12) WILD-TYPE
  FEMALE                        52                          21
  MALE                          40                          16
[1] 2 2
[1] FALSE
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P12) MUTATED                                  1     4
  DEL PEAK  1(1P12) WILD-TYPE                                0     0
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P12) MUTATED                           6    78
  DEL PEAK  1(1P12) WILD-TYPE                         3    34
D8V4, multiclass
                                  clus
vv                                 DEL PEAK  1(1P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         1
  ASIAN                                                    4
  BLACK OR AFRICAN AMERICAN                                6
  WHITE                                                   78
                                  clus
vv                                 DEL PEAK  1(1P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     34
[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    12   0
  DEL PEAK  2(1Q42.13) WILD-TYPE 113   4
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                            12                            117 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                             0                              4 
$`DEL PEAK  2(1Q42.13) MUTATED`
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RW-A681 TCGA-RW-A68A TCGA-S7-A7WQ TCGA-S7-A7X1 
        0.79        38.73        23.80        13.05        11.38         7.89 
TCGA-SR-A6MT TCGA-TT-A6YJ TCGA-W2-A7H7 TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A821 
      106.75         4.34        17.16        37.18        24.00         1.35 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68W 
        0.72        25.18         2.30         4.41         0.95         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         8.09        86.89        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 
        7.10        33.30         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         0.69 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89         0.59        20.09        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       26.30        23.51        14.50        29.88        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QC 
       17.33        10.65        11.77         6.08        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        54.44        73.05       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK 
      107.47         3.12        24.66        11.34        49.61        25.15 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7HA TCGA-W2-A7HB 
        7.96        10.42        25.32        14.20         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 
       27.62        22.29         4.47         4.73         4.21       303.09 
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        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81G 
       32.61        26.14         7.69        12.20         0.79        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A822 TCGA-XG-A823 
       56.52        92.78         6.90 

  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                         303.09 
  DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE 
                        15.105                         15.020 
[1] "0.8 - 106.8 (15.1)" "0.1 - 303.1 (15.0)"
[1] "hr="     "7.6e+07"
D9V2, continuous
D9V3, binary
                                cls
clus                              0  1
  DEL PEAK  2(1Q42.13) MUTATED    5  7
  DEL PEAK  2(1Q42.13) WILD-TYPE 68 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1Q42.13) MUTATED      5    7
  DEL PEAK  2(1Q42.13) WILD-TYPE   68   49
        clus
vv       DEL PEAK  2(1Q42.13) MUTATED DEL PEAK  2(1Q42.13) WILD-TYPE
  FEMALE                            5                             68
  MALE                              7                             49
[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     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q42.13) MUTATED                           1    10
  DEL PEAK  2(1Q42.13) WILD-TYPE                         8   102
D9V4, multiclass
                                  clus
vv                                 DEL PEAK  2(1Q42.13) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   1
  WHITE                                                      10
                                  clus
vv                                 DEL PEAK  2(1Q42.13) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                     8
  WHITE                                                       102
[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   48  1
  DEL PEAK  3(3P24.1) WILD-TYPE 77  3
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                           49                            80 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK  3(3P24.1) MUTATED`
TCGA-P8-A6RX TCGA-PR-A5PF TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XN 
        0.95         7.89        36.23         6.94         1.81        25.18 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A689 
       97.22        41.06         2.93         7.10        33.30        11.70 
TCGA-RW-A68A TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A7CZ TCGA-S7-A7WL TCGA-S7-A7WM 
       13.05         6.28        72.79         4.41        20.09        24.00 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7X0 TCGA-S7-A7X1 
       14.50        11.38        29.88        29.98         6.08         7.89 
TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SQ-A6I6 TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
      101.49        67.07         0.10       106.75       110.53       107.47 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA 
        4.34        25.15        25.32        14.20        17.16         1.18 
TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
       17.69        10.65       303.09        29.16        19.59        32.88 
TCGA-WB-A815 TCGA-WB-A819 TCGA-WB-A81E TCGA-WB-A81K TCGA-WB-A81W TCGA-WB-A821 
        5.98         7.69        37.18        19.56        56.52         1.35 
TCGA-XG-A823 
        6.90 

$`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        28.01 
TCGA-QR-A6GS TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 
        1.25         0.72         2.30         4.41         0.79         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A681 
       38.73         0.92         8.09        86.89        19.86        23.80 
TCGA-RW-A684 TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68B TCGA-RW-A68F 
        1.05         0.85        13.32         1.22         7.96        15.02 
TCGA-RW-A68G TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO 
        0.69         1.78         2.89         0.59        26.30        23.51 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC 
       19.76        17.33        10.65        11.77        12.20       104.55 
TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MP 
       70.65        98.07         9.01        99.06         1.41        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
       54.44        73.05         3.12        24.66        11.34        49.61 
TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HE 
        7.96        10.42        19.86        12.03        12.49        16.60 
TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       25.61        27.62        22.29         4.47         4.73         4.21 
TCGA-WB-A80Q TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D 
      127.56        17.46        32.61        26.14        12.20         0.79 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M 
       24.00        24.23        42.54         1.12         1.87        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A822 
       71.05        92.78 

  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                         0.10                          0.59 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                       303.09                        127.56 
  DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE 
                       17.690                        13.155 
[1] "0.1 - 303.1 (17.7)" "0.6 - 127.6 (13.2)"
[1] "hr=" "2.2"
D10V2, continuous
D10V3, binary
                               cls
clus                             0  1
  DEL PEAK  3(3P24.1) MUTATED   31 18
  DEL PEAK  3(3P24.1) WILD-TYPE 42 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(3P24.1) MUTATED     31   18
  DEL PEAK  3(3P24.1) WILD-TYPE   42   38
        clus
vv       DEL PEAK  3(3P24.1) MUTATED DEL PEAK  3(3P24.1) WILD-TYPE
  FEMALE                          31                            42
  MALE                            18                            38
[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     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(3P24.1) MUTATED                           5    40
  DEL PEAK  3(3P24.1) WILD-TYPE                         4    72
D10V4, multiclass
                                  clus
vv                                 DEL PEAK  3(3P24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     40
                                  clus
vv                                 DEL PEAK  3(3P24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       72
[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   74  1
  DEL PEAK  4(3Q26.1) WILD-TYPE 51  3
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                           75                            54 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK  4(3Q26.1) MUTATED`
TCGA-P8-A5KD TCGA-P8-A6RX TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN 
        2.27         0.95        36.23         6.94         0.72        25.18 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67W TCGA-RW-A67X 
        2.30         4.41        97.22        41.06        19.86         2.93 
TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        7.10        33.30         0.85         1.22        11.70        13.05 
TCGA-RW-A68B TCGA-RW-A68C TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WP 
        7.96         6.28         4.41         1.78        20.09        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       11.38        29.88        11.77         6.08         7.89        12.20 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MT TCGA-SR-A6MU 
        1.41         0.10        51.22        54.44       106.75       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YK 
      107.47         3.12        24.66        11.34         4.34        25.15 
TCGA-TT-A6YN TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
        7.96        25.32        14.20        17.16         1.18        19.86 
TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80N 
       12.03        12.49        17.69        10.65         4.47         4.73 
TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A818 TCGA-WB-A819 
      303.09        29.16        32.88        17.46        26.14         7.69 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81W 
       24.00        24.23         1.61        11.74         9.47        56.52 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

$`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         7.89        81.70        28.01 
TCGA-QR-A6GS TCGA-QT-A5XL TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        1.25         1.81         0.79         0.95        38.73         0.92 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68D 
        8.09        86.89        23.80         1.05        13.32        72.79 
TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN 
       15.02         0.69         2.89         0.59        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-SP-A6QC 
       23.51        29.98        19.76        17.33        10.65       104.55 
TCGA-SR-A6MS TCGA-SR-A6N0 TCGA-TT-A6YO TCGA-W2-A7HE TCGA-W2-A7HH TCGA-WB-A80K 
       73.05        49.61        10.42        16.60        25.61        27.62 
TCGA-WB-A80L TCGA-WB-A80O TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A817 
       22.29         4.21       127.56        19.59         5.98        32.61 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       12.20         0.79        37.18        42.54         1.12         1.87 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81V 
       19.56        21.44        46.22        12.99        24.82        71.05 

  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                         0.10                          0.59 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                       303.09                        127.56 
  DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE 
                       12.200                        19.675 
[1] "0.1 - 303.1 (12.2)" "0.6 - 127.6 (19.7)"
[1] "hr=" "3.8"
D11V2, continuous
D11V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(3Q26.1) MUTATED   45 30
  DEL PEAK  4(3Q26.1) WILD-TYPE 28 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(3Q26.1) MUTATED     45   30
  DEL PEAK  4(3Q26.1) WILD-TYPE   28   26
        clus
vv       DEL PEAK  4(3Q26.1) MUTATED DEL PEAK  4(3Q26.1) WILD-TYPE
  FEMALE                          45                            28
  MALE                            30                            26
[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     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3Q26.1) MUTATED                           7    61
  DEL PEAK  4(3Q26.1) WILD-TYPE                         2    51
D11V4, multiclass
                                  clus
vv                                 DEL PEAK  4(3Q26.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     61
                                  clus
vv                                 DEL PEAK  4(3Q26.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                    2
  WHITE                                                       51
[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     8   0
  DEL PEAK  5(4Q28.3) WILD-TYPE 117   4
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                            8                           121 
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                            0                             4 
$`DEL PEAK  5(4Q28.3) MUTATED`
TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A68C TCGA-TT-A6YP 
        2.30         0.79        41.06         2.93         6.28        25.32 
TCGA-WB-A81J TCGA-WB-A821 
        1.87         1.35 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
        0.72        25.18         4.41         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 
       97.22         8.09        86.89        19.86         7.10        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         0.69         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       23.51        14.50        11.38        29.88        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       17.33        10.65        11.77         6.08         7.89        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ 
      106.75       110.53       107.47         3.12        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7H5 
       49.61         4.34        25.15         7.96        10.42        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        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       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        17.46        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q 
        1.12        19.56        21.44        46.22        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A822 
        1.61        11.74         9.47        71.05        56.52        92.78 
TCGA-XG-A823 
        6.90 

  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 
                        41.06                        303.09 
  DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE 
                        2.615                        17.160 
[1] "0.8 - 41.1 (2.6)"   "0.1 - 303.1 (17.2)"
[1] "hr="     "2.6e+07"
D12V2, continuous
D12V3, binary
                               cls
clus                             0  1
  DEL PEAK  5(4Q28.3) MUTATED    4  4
  DEL PEAK  5(4Q28.3) WILD-TYPE 69 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(4Q28.3) MUTATED      4    4
  DEL PEAK  5(4Q28.3) WILD-TYPE   69   52
        clus
vv       DEL PEAK  5(4Q28.3) MUTATED DEL PEAK  5(4Q28.3) WILD-TYPE
  FEMALE                           4                            69
  MALE                             4                            52
[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     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(4Q28.3) MUTATED                           1     7
  DEL PEAK  5(4Q28.3) WILD-TYPE                         8   105
D12V4, multiclass
                                  clus
vv                                 DEL PEAK  5(4Q28.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      7
                                  clus
vv                                 DEL PEAK  5(4Q28.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      105
[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    11   0
  DEL PEAK  6(5Q15) WILD-TYPE 114   4
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                         11                         118 
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                          0                           4 
$`DEL PEAK  6(5Q15) MUTATED`
TCGA-P8-A6RX TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-RW-A67Y TCGA-RW-A68C TCGA-SR-A6MQ 
        0.95        36.23         0.79         7.10         6.28        54.44 
TCGA-SR-A6MY TCGA-WB-A80M TCGA-WB-A81K TCGA-WB-A81S TCGA-WB-A81W 
       24.66         4.47        19.56        11.74        56.52 

$`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         7.89        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XN 
       28.01         1.25         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         0.95        38.73         0.92        97.22 
TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 
       41.06         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         0.69         4.41 
TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN 
        1.78         2.89         0.59        20.09        24.00        26.30 
TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU 
       23.51        14.50        11.38        29.88        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       17.33        10.65        11.77         6.08         7.89        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT 
       99.06         1.41         0.10        51.22        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      110.53       107.47         3.12        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 
       25.15         7.96        10.42        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-A80N TCGA-WB-A80O 
       25.61        10.65        27.62        22.29         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
      303.09       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 
       17.46        32.61        26.14         7.69        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J 
       37.18        24.00        24.23        42.54         1.12         1.87 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
       21.44        46.22        12.99        24.82         1.61         9.47 
TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05         1.35        92.78         6.90 

  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 
                      56.52                      303.09 
  DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE 
                      11.74                       15.81 
[1] "0.8 - 56.5 (11.7)"  "0.1 - 303.1 (15.8)"
[1] "hr="     "7.5e+07"
D13V2, continuous
D13V3, binary
                             cls
clus                           0  1
  DEL PEAK  6(5Q15) MUTATED    5  6
  DEL PEAK  6(5Q15) WILD-TYPE 68 50
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  6(5Q15) MUTATED      5    6
  DEL PEAK  6(5Q15) WILD-TYPE   68   50
        clus
vv       DEL PEAK  6(5Q15) MUTATED DEL PEAK  6(5Q15) WILD-TYPE
  FEMALE                         5                          68
  MALE                           6                          50
[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     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(5Q15) MUTATED                           1     9
  DEL PEAK  6(5Q15) WILD-TYPE                         8   103
D13V4, multiclass
                                  clus
vv                                 DEL PEAK  6(5Q15) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                    9
                                  clus
vv                                 DEL PEAK  6(5Q15) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                    103
[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     6   0
  DEL PEAK  7(6P12.3) WILD-TYPE 119   4
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                            6                           123 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                            0                             4 
$`DEL PEAK  7(6P12.3) MUTATED`
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-WB-A81S TCGA-XG-A823 
      110.53       107.47         4.34        10.42        11.74         6.90 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         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         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         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         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        2.89         0.59        20.09        24.00        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       14.50        11.38        29.88        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
       10.65        11.77         6.08         7.89        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
        1.41         0.10        51.22        54.44        73.05       106.75 
TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN 
        3.12        24.66        11.34        49.61        25.15         7.96 
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-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       22.29         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V 
       46.22        12.99        24.82         1.61         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       56.52         1.35        92.78 

  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                         4.34                          0.10 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                       110.53                        303.09 
  DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE 
                        11.08                         16.60 
[1] "4.3 - 110.5 (11.1)" "0.1 - 303.1 (16.6)"
[1] "hr="     "2.6e+07"
D14V2, continuous
D14V3, binary
                               cls
clus                             0  1
  DEL PEAK  7(6P12.3) MUTATED    6  0
  DEL PEAK  7(6P12.3) WILD-TYPE 67 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(6P12.3) MUTATED      6    0
  DEL PEAK  7(6P12.3) WILD-TYPE   67   56
        clus
vv       DEL PEAK  7(6P12.3) MUTATED DEL PEAK  7(6P12.3) WILD-TYPE
  FEMALE                           6                            67
  MALE                             0                            56
[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     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(6P12.3) MUTATED                           1     4
  DEL PEAK  7(6P12.3) WILD-TYPE                         8   108
D14V4, multiclass
                                  clus
vv                                 DEL PEAK  7(6P12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      4
                                  clus
vv                                 DEL PEAK  7(6P12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    8
  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(15) Variable = DEL PEAK  8(6Q16.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(6Q16.1) MUTATED    18   0
  DEL PEAK  8(6Q16.1) WILD-TYPE 107   4
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                           18                           111 
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                            0                             4 
$`DEL PEAK  8(6Q16.1) MUTATED`
TCGA-P8-A5KD TCGA-QT-A5XN TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WR TCGA-SR-A6MU 
        2.27        25.18        24.00        26.30        29.88       110.53 
TCGA-SR-A6MV TCGA-SR-A6MY TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-W2-A7HC TCGA-W2-A7UY 
      107.47        24.66         4.34        10.42        12.03        10.65 
TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A819 TCGA-WB-A81R TCGA-WB-A81S TCGA-XG-A823 
        4.21        29.16         7.69         1.61        11.74         6.90 

$`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         0.95         5.88         7.89        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         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         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         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         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WT TCGA-S7-A7WU 
       20.09        23.51        14.50        11.38        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 
       17.33        10.65        11.77         6.08         7.89        12.20 
TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ 
      104.55       101.49        70.65        67.07        98.07         9.01 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MX TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN 
      106.75         3.12        11.34        49.61        25.15         7.96 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HD 
       25.32        14.20        17.16         1.18        19.86        12.49 
TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        17.69        25.61        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 
        4.73       303.09       127.56        19.59        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       17.46        32.61        26.14        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81T TCGA-WB-A81V 
       21.44        46.22        12.99        24.82         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       56.52         1.35        92.78 

  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 
                       110.53                        303.09 
  DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE 
                       11.885                        16.600 
[1] "1.6 - 110.5 (11.9)" "0.1 - 303.1 (16.6)"
[1] "hr="     "8.4e+07"
D15V2, continuous
D15V3, binary
                               cls
clus                             0  1
  DEL PEAK  8(6Q16.1) MUTATED   14  4
  DEL PEAK  8(6Q16.1) WILD-TYPE 59 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(6Q16.1) MUTATED     14    4
  DEL PEAK  8(6Q16.1) WILD-TYPE   59   52
        clus
vv       DEL PEAK  8(6Q16.1) MUTATED DEL PEAK  8(6Q16.1) WILD-TYPE
  FEMALE                          14                            59
  MALE                             4                            52
[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     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(6Q16.1) MUTATED                           2    15
  DEL PEAK  8(6Q16.1) WILD-TYPE                         7    97
D15V4, multiclass
                                  clus
vv                                 DEL PEAK  8(6Q16.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     15
                                  clus
vv                                 DEL PEAK  8(6Q16.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    7
  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"

Clustering(16) Variable = DEL PEAK  9(8P22) MUTATION ANALYSIS
D16V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  9(8P22) MUTATED    19   1
  DEL PEAK  9(8P22) WILD-TYPE 106   3
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                         20                         109 
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                          1                           3 
$`DEL PEAK  9(8P22) MUTATED`
TCGA-PR-A5PF TCGA-PR-A5PG TCGA-QT-A5XN TCGA-RT-A6YA TCGA-RW-A68A TCGA-RW-A68D 
        7.89        81.70        25.18        41.06        13.05        72.79 
TCGA-S7-A7WL TCGA-S7-A7WR TCGA-S7-A7WT TCGA-SP-A6QI TCGA-SR-A6MP TCGA-SR-A6MT 
       20.09        29.88        29.98        98.07        51.22       106.75 
TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-WB-A80V TCGA-WB-A81D TCGA-WB-A81P TCGA-WB-A81Q 
       14.20        16.60        29.16         0.79        12.99        24.82 
TCGA-WB-A81R TCGA-WB-A81T 
        1.61         9.47 

$`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         0.95         5.88        28.01 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO 
        1.25        36.23         6.94         1.81         0.72         2.30 
TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 
        4.41         0.79         0.95        38.73         0.92        97.22 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A680 
        8.09        86.89        19.86         2.93         7.10        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-A68B TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 
        7.96         6.28        15.02         0.69         4.41         1.78 
TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        2.89         0.59        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       11.38        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS 
        9.01        99.06         1.41         0.10        54.44        73.05 
TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      110.53       107.47         3.12        24.66        11.34        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
        4.34        25.15         7.96        10.42        25.32        17.16 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7HH 
        1.18        19.86        12.03        12.49        17.69        25.61 
TCGA-W2-A7UY TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O 
       10.65        27.62        22.29         4.47         4.73         4.21 
TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 
      303.09       127.56        19.59        32.88         5.98        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81E TCGA-WB-A81F 
       32.61        26.14         7.69        12.20        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 
       46.22        11.74        71.05        56.52         1.35        92.78 
TCGA-XG-A823 
        6.90 

  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                       0.79                        0.10 
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                     106.75                      303.09 
  DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE 
                      25.00                       12.49 
[1] "0.8 - 106.8 (25.0)" "0.1 - 303.1 (12.5)"
[1] "hr=" "1.3"
D16V2, continuous
D16V3, binary
                             cls
clus                           0  1
  DEL PEAK  9(8P22) MUTATED   14  6
  DEL PEAK  9(8P22) WILD-TYPE 59 50
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  9(8P22) MUTATED     14    6
  DEL PEAK  9(8P22) WILD-TYPE   59   50
        clus
vv       DEL PEAK  9(8P22) MUTATED DEL PEAK  9(8P22) WILD-TYPE
  FEMALE                        14                          59
  MALE                           6                          50
[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     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(8P22) MUTATED                           1    18
  DEL PEAK  9(8P22) WILD-TYPE                         8    94
D16V4, multiclass
                                  clus
vv                                 DEL PEAK  9(8P22) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    1
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                   18
                                  clus
vv                                 DEL PEAK  9(8P22) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     94
[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     9   1
  DEL PEAK 10(8Q23.3) WILD-TYPE 116   3
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                           10                           119 
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                            1                             3 
$`DEL PEAK 10(8Q23.3) MUTATED`
TCGA-RW-A67W TCGA-RW-A68A TCGA-S7-A7WR TCGA-SR-A6MT TCGA-SR-A6MX TCGA-W2-A7H5 
       19.86        13.05        29.88       106.75         3.12        14.20 
TCGA-W2-A7H7 TCGA-W2-A7HD TCGA-WB-A80K TCGA-WB-A80V 
       17.16        12.49        27.62        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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         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         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V 
       38.73         0.92        97.22        41.06         8.09        86.89 
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-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         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 
       29.98        19.76        17.33        10.65        11.77         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG 
        7.89        12.20       104.55       101.49        70.65        67.07 
TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP 
       98.07         9.01        99.06         1.41         0.10        51.22 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MY TCGA-SR-A6MZ 
       54.44        73.05       110.53       107.47        24.66        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       49.61         4.34        25.15         7.96        10.42        25.32 
TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HE TCGA-W2-A7HF TCGA-W2-A7HH 
        1.18        19.86        12.03        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        22.29         4.47         4.73         4.21       303.09 
TCGA-WB-A80Q TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
      127.56        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       46.22        12.99        24.82         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  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                        303.09 
  DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE 
                        18.51                         14.50 
[1] "3.1 - 106.8 (18.5)" "0.1 - 303.1 (14.5)"
[1] "hr=" "3.3"
D17V2, continuous
D17V3, binary
                               cls
clus                             0  1
  DEL PEAK 10(8Q23.3) MUTATED    7  3
  DEL PEAK 10(8Q23.3) WILD-TYPE 66 53
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(8Q23.3) MUTATED      7    3
  DEL PEAK 10(8Q23.3) WILD-TYPE   66   53
        clus
vv       DEL PEAK 10(8Q23.3) MUTATED DEL PEAK 10(8Q23.3) WILD-TYPE
  FEMALE                           7                            66
  MALE                             3                            53
[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     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(8Q23.3) MUTATED                           0    10
  DEL PEAK 10(8Q23.3) WILD-TYPE                         9   102
D17V4, multiclass
                                  clus
vv                                 DEL PEAK 10(8Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  0
  WHITE                                                     10
                                  clus
vv                                 DEL PEAK 10(8Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    9
  WHITE                                                      102
[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     8   2
  DEL PEAK 11(9P24.2) WILD-TYPE 117   2
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                           10                           119 
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                            2                             2 
$`DEL PEAK 11(9P24.2) MUTATED`
TCGA-QT-A5XP TCGA-RT-A6YA TCGA-RW-A686 TCGA-RW-A8AZ TCGA-SP-A6QJ TCGA-SR-A6MV 
        4.41        41.06        13.32         2.89         9.01       107.47 
TCGA-W2-A7H5 TCGA-WB-A81J TCGA-WB-A81Q TCGA-WB-A81R 
       14.20         1.87        24.82         1.61 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         6.94         1.81 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
        0.72        25.18         2.30         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
        0.92        97.22         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-A688 
        7.10        33.30        23.80         1.05         0.85         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-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        0.69         4.41         1.78         0.59        20.09        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       26.30        23.51        14.50        11.38        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       19.76        17.33        10.65        11.77         6.08         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       12.20       104.55       101.49        70.65        67.07        98.07 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS 
       99.06         1.41         0.10        51.22        54.44        73.05 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 
      106.75       110.53         3.12        24.66        11.34        49.61 
TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
        4.34        25.15         7.96        10.42        25.32        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        27.62        22.29         4.47         4.73 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 
        4.21       303.09       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        17.46        32.61        26.14         7.69        12.20 
TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I 
        0.79        37.18        24.00        24.23        42.54         1.12 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81T 
       19.56        21.44        46.22        12.99        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  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 
                       107.47                        303.09 
  DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE 
                       11.165                        17.160 
[1] "1.6 - 107.5 (11.2)" "0.1 - 303.1 (17.2)"
[1] "hr=" "14" 
D18V2, continuous
D18V3, binary
                               cls
clus                             0  1
  DEL PEAK 11(9P24.2) MUTATED    6  4
  DEL PEAK 11(9P24.2) WILD-TYPE 67 52
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(9P24.2) MUTATED      6    4
  DEL PEAK 11(9P24.2) WILD-TYPE   67   52
        clus
vv       DEL PEAK 11(9P24.2) MUTATED DEL PEAK 11(9P24.2) WILD-TYPE
  FEMALE                           6                            67
  MALE                             4                            52
[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     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(9P24.2) MUTATED                           1     9
  DEL PEAK 11(9P24.2) WILD-TYPE                         8   103
D18V4, multiclass
                                  clus
vv                                 DEL PEAK 11(9P24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      9
                                  clus
vv                                 DEL PEAK 11(9P24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                    8
  WHITE                                                      103
[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     9   1
  DEL PEAK 12(9Q21.12) WILD-TYPE 116   3
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                            10                            119 
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                             1                              3 
$`DEL PEAK 12(9Q21.12) MUTATED`
TCGA-QT-A5XJ TCGA-QT-A5XP TCGA-RT-A6YA TCGA-S7-A7WL TCGA-SP-A6QJ TCGA-SR-A6MP 
       36.23         4.41        41.06        20.09         9.01        51.22 
TCGA-SR-A6MV TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-WB-A81Q 
      107.47        14.20        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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01         1.25         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W 
       25.18         2.30         0.79         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A67Y 
       97.22         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-A7WM 
        0.69         4.41         1.78         2.89         0.59        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT 
       26.30        23.51        14.50        11.38        29.88        29.98 
TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 
       19.76        17.33        10.65        11.77         6.08         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI 
       12.20       104.55       101.49        70.65        67.07        98.07 
TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT 
       99.06         1.41         0.10        54.44        73.05       106.75 
TCGA-SR-A6MU TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ 
      110.53         3.12        24.66        11.34        49.61         4.34 
TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7HA TCGA-W2-A7HB 
       25.15         7.96        10.42        25.32         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 
       27.62        22.29         4.47         4.73         4.21       303.09 
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        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T 
       21.44        46.22        12.99         1.61        11.74         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                          4.41                           0.10 
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                        107.47                         303.09 
  DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE 
                        22.455                         13.320 
[1] "4.4 - 107.5 (22.5)" "0.1 - 303.1 (13.3)"
[1] "hr=" "3"  
D19V2, continuous
D19V3, binary
                                cls
clus                              0  1
  DEL PEAK 12(9Q21.12) MUTATED    7  3
  DEL PEAK 12(9Q21.12) WILD-TYPE 66 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(9Q21.12) MUTATED      7    3
  DEL PEAK 12(9Q21.12) WILD-TYPE   66   53
        clus
vv       DEL PEAK 12(9Q21.12) MUTATED DEL PEAK 12(9Q21.12) WILD-TYPE
  FEMALE                            7                             66
  MALE                              3                             53
[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     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(9Q21.12) MUTATED                           2     8
  DEL PEAK 12(9Q21.12) WILD-TYPE                         7   104
D19V4, multiclass
                                  clus
vv                                 DEL PEAK 12(9Q21.12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                       8
                                  clus
vv                                 DEL PEAK 12(9Q21.12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                       104
[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   45  0
  DEL PEAK 13(11P15.4) WILD-TYPE 80  4
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                            45                             84 
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                             0                              4 
$`DEL PEAK 13(11P15.4) MUTATED`
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-QT-A5XL TCGA-QT-A5XN TCGA-QT-A7U0 TCGA-RM-A68T 
        0.95         5.88         1.81        25.18         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A68A 
        0.92        41.06         2.93        23.80         1.05        13.05 
TCGA-RW-A68C TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A7CZ TCGA-S7-A7WP TCGA-S7-A7WQ 
        6.28        72.79        15.02         4.41        14.50        11.38 
TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SP-A6QD 
       29.98        19.76        10.65         6.08         7.89       101.49 
TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YP 
      106.75       110.53       107.47        49.61        25.15        25.32 
TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A814 TCGA-WB-A816 
       14.20        17.16        10.65         4.47        32.88        17.46 
TCGA-WB-A81I TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81S TCGA-WB-A81V TCGA-WB-A81W 
        1.12        19.56        21.44        11.74        71.05        56.52 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

$`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         7.89        81.70        28.01 
TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XO TCGA-QT-A5XP 
        1.25        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        97.22         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 
        0.69         1.78         2.89         0.59        20.09        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WR TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 
       26.30        23.51        29.88        17.33        11.77        12.20 
TCGA-SP-A6QC TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      104.55        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MX 
        1.41         0.10        51.22        54.44        73.05         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-W2-A7HA 
       24.66        11.34         4.34         7.96        10.42         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-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       27.62        22.29         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A815 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 
       29.16        19.59         5.98        32.61        26.14         7.69 
TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H 
       12.20         0.79        37.18        24.00        24.23        42.54 
TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
        1.87        46.22        12.99        24.82         1.61         9.47 

  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 
                        110.53                         303.09 
  DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE 
                         15.02                          14.96 
[1] "0.9 - 110.5 (15.0)" "0.1 - 303.1 (15.0)"
[1] "hr="     "3.6e+08"
D20V2, continuous
D20V3, binary
                                cls
clus                              0  1
  DEL PEAK 13(11P15.4) MUTATED   24 21
  DEL PEAK 13(11P15.4) WILD-TYPE 49 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(11P15.4) MUTATED     24   21
  DEL PEAK 13(11P15.4) WILD-TYPE   49   35
        clus
vv       DEL PEAK 13(11P15.4) MUTATED DEL PEAK 13(11P15.4) WILD-TYPE
  FEMALE                           24                             49
  MALE                             21                             35
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(11P15.4) MUTATED                                  0     1
  DEL PEAK 13(11P15.4) WILD-TYPE                                1     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(11P15.4) MUTATED                           3    40
  DEL PEAK 13(11P15.4) WILD-TYPE                         6    72
D20V4, multiclass
                                  clus
vv                                 DEL PEAK 13(11P15.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      40
                                  clus
vv                                 DEL PEAK 13(11P15.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                     6
  WHITE                                                        72
[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   38  1
  DEL PEAK 14(11Q22.1) WILD-TYPE 87  3
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                            39                             90 
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                             1                              3 
$`DEL PEAK 14(11Q22.1) MUTATED`
TCGA-P8-A6RX TCGA-P8-A6RY TCGA-PR-A5PF TCGA-QR-A6GS TCGA-QT-A5XL TCGA-QT-A5XO 
        0.95         5.88         7.89         1.25         1.81         2.30 
TCGA-QT-A69Q TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA TCGA-RW-A67X TCGA-RW-A681 
        0.79        38.73         0.92        41.06         2.93        23.80 
TCGA-RW-A689 TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-S7-A7WL 
       11.70         6.28        15.02         4.41         2.89        20.09 
TCGA-S7-A7WP TCGA-S7-A7WQ TCGA-S7-A7WU TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 
       14.50        11.38        19.76        10.65         6.08         7.89 
TCGA-SR-A6MT TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7UY 
      106.75        49.61         4.34        10.42        25.32        10.65 
TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A81D TCGA-WB-A81P TCGA-WB-A81S TCGA-WB-A81V 
       32.88         5.98         0.79        12.99        11.74        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-XG-A823 
       56.52         1.35         6.90 

$`DEL PEAK 14(11Q22.1) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A5KD TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QT-A5XJ 
       31.46        29.03         2.27        81.70        28.01        36.23 
TCGA-QT-A5XK TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A7U0 TCGA-RT-A6Y9 
        6.94         0.72        25.18         4.41         0.95        97.22 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67Y TCGA-RW-A680 TCGA-RW-A684 
        8.09        86.89        19.86         7.10        33.30         1.05 
TCGA-RW-A685 TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68D 
        0.85        13.32         1.22        13.05         7.96        72.79 
TCGA-RW-A68G TCGA-RW-A7D0 TCGA-RX-A8JQ TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO 
        0.69         1.78         0.59        24.00        26.30        23.51 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WV TCGA-S7-A7WX TCGA-S7-A7X2 TCGA-SP-A6QC 
       29.88        29.98        17.33        11.77        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK 
      101.49        70.65        67.07        98.07         9.01        99.06 
TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU 
        1.41         0.10        51.22        54.44        73.05       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YK TCGA-TT-A6YN 
      107.47         3.12        24.66        11.34        25.15         7.96 
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-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        17.69        25.61        27.62        22.29         4.47 
TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A80Y 
        4.73         4.21       303.09       127.56        29.16        19.59 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81E 
       17.46        32.61        26.14         7.69        12.20        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A822 
       21.44        46.22        24.82         1.61         9.47        92.78 

  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                         303.09 
  DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE 
                         10.42                          19.86 
[1] "0.8 - 106.8 (10.4)" "0.1 - 303.1 (19.9)"
[1] "hr=" "1.1"
D21V2, continuous
D21V3, binary
                                cls
clus                              0  1
  DEL PEAK 14(11Q22.1) MUTATED   23 16
  DEL PEAK 14(11Q22.1) WILD-TYPE 50 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.1) MUTATED     23   16
  DEL PEAK 14(11Q22.1) WILD-TYPE   50   40
        clus
vv       DEL PEAK 14(11Q22.1) MUTATED DEL PEAK 14(11Q22.1) WILD-TYPE
  FEMALE                           23                             50
  MALE                             16                             40
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(11Q22.1) MUTATED                                  0     0
  DEL PEAK 14(11Q22.1) WILD-TYPE                                1     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(11Q22.1) MUTATED                           4    34
  DEL PEAK 14(11Q22.1) WILD-TYPE                         5    78
D21V4, multiclass
                                  clus
vv                                 DEL PEAK 14(11Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      34
                                  clus
vv                                 DEL PEAK 14(11Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                     5
  WHITE                                                        78
[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     5   0
  DEL PEAK 15(12Q21.33) WILD-TYPE 120   4
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                              5                             124 
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                              0                               4 
$`DEL PEAK 15(12Q21.33) MUTATED`
TCGA-RT-A6YC TCGA-SP-A6QJ TCGA-SR-A6MV TCGA-TT-A6YJ TCGA-WB-A81S 
        8.09         9.01       107.47         4.34        11.74 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL 
       81.70        28.01         1.25        36.23         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         0.95 
TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RW-A67V TCGA-RW-A67W 
       38.73         0.92        97.22        41.06        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-A68A TCGA-RW-A68B TCGA-RW-A68C 
       13.32         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP 
        0.59        20.09        24.00        26.30        23.51        14.50 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW 
       11.38        29.88        29.98        19.76        17.33        10.65 
TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       11.77         6.08         7.89        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       70.65        67.07        98.07        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MX 
       51.22        54.44        73.05       106.75       110.53         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       24.66        11.34        49.61        25.15         7.96        10.42 
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-A7HE TCGA-W2-A7HF TCGA-W2-A7HH TCGA-W2-A7UY TCGA-WB-A80K 
       12.49        16.60        17.69        25.61        10.65        27.62 
TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       22.29         4.47         4.73         4.21       303.09       127.56 
TCGA-WB-A80V TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A815 TCGA-WB-A816 TCGA-WB-A817 
       29.16        19.59        32.88         5.98        17.46        32.61 
TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
       26.14         7.69        12.20         0.79        37.18        24.00 
TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M 
       24.23        42.54         1.12         1.87        19.56        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V 
       46.22        12.99        24.82         1.61         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       56.52         1.35        92.78         6.90 

  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 
                         107.47                          303.09 
  DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE 
                           9.01                           16.88 
[1] "4.3 - 107.5 (9.0)"  "0.1 - 303.1 (16.9)"
[1] "hr="     "2.6e+07"
D22V2, continuous
D22V3, binary
                                 cls
clus                               0  1
  DEL PEAK 15(12Q21.33) MUTATED    4  1
  DEL PEAK 15(12Q21.33) WILD-TYPE 69 55
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(12Q21.33) MUTATED      4    1
  DEL PEAK 15(12Q21.33) WILD-TYPE   69   55
        clus
vv       DEL PEAK 15(12Q21.33) MUTATED DEL PEAK 15(12Q21.33) WILD-TYPE
  FEMALE                             4                              69
  MALE                               1                              55
[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     4
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(12Q21.33) MUTATED                           0     4
  DEL PEAK 15(12Q21.33) WILD-TYPE                         9   108
D22V4, multiclass
                                  clus
vv                                 DEL PEAK 15(12Q21.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    0
  WHITE                                                        4
                                  clus
vv                                 DEL PEAK 15(12Q21.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          4
  BLACK OR AFRICAN AMERICAN                                      9
  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(23) Variable = DEL PEAK 16(13Q22.3) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(13Q22.3) MUTATED     5   0
  DEL PEAK 16(13Q22.3) WILD-TYPE 120   4
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                             5                            124 
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                             0                              4 
$`DEL PEAK 16(13Q22.3) MUTATED`
TCGA-PR-A5PF TCGA-RW-A68A TCGA-S7-A7WX TCGA-SP-A6QF TCGA-W2-A7H5 
        7.89        13.05        11.77        70.65        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         0.95         5.88        81.70 
TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       28.01         1.25        36.23         6.94         1.81         0.72 
TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-QT-A7U0 TCGA-RM-A68T 
       25.18         2.30         4.41         0.79         0.95        38.73 
TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W 
        0.92        97.22        41.06         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-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         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 
       29.88        29.98        19.76        17.33        10.65         6.08 
TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QG TCGA-SP-A6QI 
        7.89        12.20       104.55       101.49        67.07        98.07 
TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
        9.01        99.06         1.41         0.10        51.22        54.44 
TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       73.05       106.75       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO 
       11.34        49.61         4.34        25.15         7.96        10.42 
TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC TCGA-W2-A7HD 
       25.32        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        27.62        22.29 
TCGA-WB-A80M TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V 
        4.47         4.73         4.21       303.09       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        17.46        32.61        26.14 
TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
        7.69        12.20         0.79        37.18        24.00        24.23 
TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81N 
       42.54         1.12         1.87        19.56        21.44        46.22 
TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       12.99        24.82         1.61        11.74         9.47        71.05 
TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       56.52         1.35        92.78         6.90 

  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                          7.89                           0.10 
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                         70.65                         303.09 
  DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE 
                         13.05                          16.88 
[1] "7.9 - 70.7 (13.1)"  "0.1 - 303.1 (16.9)"
[1] "hr="     "2.6e+07"
D23V2, continuous
D23V3, binary
                                cls
clus                              0  1
  DEL PEAK 16(13Q22.3) MUTATED    3  2
  DEL PEAK 16(13Q22.3) WILD-TYPE 70 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(13Q22.3) MUTATED      3    2
  DEL PEAK 16(13Q22.3) WILD-TYPE   70   54
        clus
vv       DEL PEAK 16(13Q22.3) MUTATED DEL PEAK 16(13Q22.3) WILD-TYPE
  FEMALE                            3                             70
  MALE                              2                             54
[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     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(13Q22.3) MUTATED                           0     4
  DEL PEAK 16(13Q22.3) WILD-TYPE                         9   108
D23V4, multiclass
                                  clus
vv                                 DEL PEAK 16(13Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   0
  WHITE                                                       4
                                  clus
vv                                 DEL PEAK 16(13Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                     9
  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(24) Variable = DEL PEAK 17(16Q21) MUTATION ANALYSIS
D24V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 17(16Q21) MUTATED     4   0
  DEL PEAK 17(16Q21) WILD-TYPE 121   4
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           4                          125 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                           0                            4 
$`DEL PEAK 17(16Q21) MUTATED`
TCGA-QT-A5XJ TCGA-QT-A69Q TCGA-SR-A6MT TCGA-WB-A81S 
       36.23         0.79       106.75        11.74 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01         1.25         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         0.95        38.73         0.92 
TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X 
       97.22        41.06         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         0.69         4.41         1.78         2.89         0.59 
TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WQ 
       20.09        24.00        26.30        23.51        14.50        11.38 
TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7WX 
       29.88        29.98        19.76        17.33        10.65        11.77 
TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD TCGA-SP-A6QF 
        6.08         7.89        12.20       104.55       101.49        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SQ-A6I6 
       67.07        98.07         9.01        99.06         1.41         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX 
       51.22        54.44        73.05       110.53       107.47         3.12 
TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN 
       24.66        11.34        49.61         4.34        25.15         7.96 
TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB 
       10.42        25.32        14.20        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 
       27.62        22.29         4.47         4.73         4.21       303.09 
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        17.46 
TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81E 
       32.61        26.14         7.69        12.20         0.79        37.18 
TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K 
       24.00        24.23        42.54         1.12         1.87        19.56 
TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T 
       21.44        46.22        12.99        24.82         1.61         9.47 
TCGA-WB-A81V TCGA-WB-A81W TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
       71.05        56.52         1.35        92.78         6.90 

  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                       303.09 
  DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE 
                      23.985                       15.020 
[1] "0.8 - 106.8 (24.0)" "0.1 - 303.1 (15.0)"
[1] "hr="     "2.6e+07"
D24V2, continuous
D24V3, binary
                              cls
clus                            0  1
  DEL PEAK 17(16Q21) MUTATED    3  1
  DEL PEAK 17(16Q21) WILD-TYPE 70 55
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 17(16Q21) MUTATED      3    1
  DEL PEAK 17(16Q21) WILD-TYPE   70   55
        clus
vv       DEL PEAK 17(16Q21) MUTATED DEL PEAK 17(16Q21) WILD-TYPE
  FEMALE                          3                           70
  MALE                            1                           55
[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     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(16Q21) MUTATED                           1     3
  DEL PEAK 17(16Q21) WILD-TYPE                         8   109
D24V4, multiclass
                                  clus
vv                                 DEL PEAK 17(16Q21) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     0
  BLACK OR AFRICAN AMERICAN                                 1
  WHITE                                                     3
                                  clus
vv                                 DEL PEAK 17(16Q21) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                   8
  WHITE                                                     109
[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   51  2
  DEL PEAK 18(17P13.2) WILD-TYPE 74  2
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                            53                             76 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                             2                              2 
$`DEL PEAK 18(17P13.2) MUTATED`
TCGA-PR-A5PG TCGA-QR-A6GS TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RW-A67X 
       81.70         1.25        25.18         4.41         0.79         2.93 
TCGA-RW-A67Y TCGA-RW-A681 TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A 
        7.10        23.80         0.85         1.22        11.70        13.05 
TCGA-RW-A68C TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM 
        6.28        15.02         0.69         1.78        20.09        24.00 
TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WT TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X1 
       11.38        29.88        29.98        10.65        11.77         7.89 
TCGA-S7-A7X2 TCGA-SP-A6QD TCGA-SP-A6QJ TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MQ 
       12.20       101.49         9.01         0.10        51.22        54.44 
TCGA-SR-A6MT TCGA-TT-A6YJ TCGA-TT-A6YK TCGA-TT-A6YN TCGA-W2-A7HA TCGA-W2-A7HC 
      106.75         4.34        25.15         7.96         1.18        12.03 
TCGA-W2-A7UY TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80V TCGA-WB-A80Y 
       10.65         4.73         4.21       303.09        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A818 TCGA-WB-A81J TCGA-WB-A81M TCGA-WB-A81N TCGA-WB-A81P 
        5.98        26.14         1.87        21.44        46.22        12.99 
TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81W TCGA-WB-A822 
       24.82        11.74         9.47        56.52        92.78 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XO 
       28.01        36.23         6.94         1.81         0.72         2.30 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YA TCGA-RT-A6YC 
        0.95        38.73         0.92        97.22        41.06         8.09 
TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A680 TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68B 
       86.89        19.86        33.30         1.05        13.32         7.96 
TCGA-RW-A68D TCGA-RW-A7CZ TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO 
       72.79         4.41         2.89         0.59        26.30        23.51 
TCGA-S7-A7WP TCGA-S7-A7WU TCGA-S7-A7WV TCGA-S7-A7X0 TCGA-SP-A6QC TCGA-SP-A6QF 
       14.50        19.76        17.33         6.08       104.55        70.65 
TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QK TCGA-SQ-A6I4 TCGA-SR-A6MS TCGA-SR-A6MU 
       67.07        98.07        99.06         1.41        73.05       110.53 
TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YO 
      107.47         3.12        24.66        11.34        49.61        10.42 
TCGA-TT-A6YP TCGA-W2-A7H5 TCGA-W2-A7H7 TCGA-W2-A7HB TCGA-W2-A7HD TCGA-W2-A7HE 
       25.32        14.20        17.16        19.86        12.49        16.60 
TCGA-W2-A7HF TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80Q 
       17.69        25.61        27.62        22.29         4.47       127.56 
TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D 
       32.88        17.46        32.61         7.69        12.20         0.79 
TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81K 
       37.18        24.00        24.23        42.54         1.12        19.56 
TCGA-WB-A81R TCGA-WB-A81V TCGA-WB-A821 TCGA-XG-A823 
        1.61        71.05         1.35         6.90 

  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                          0.10                           0.59 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                        303.09                         127.56 
  DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE 
                        11.770                         18.625 
[1] "0.1 - 303.1 (11.8)" "0.6 - 127.6 (18.6)"
[1] "hr=" "1.6"
D25V2, continuous
D25V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(17P13.2) MUTATED   28 25
  DEL PEAK 18(17P13.2) WILD-TYPE 45 31
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(17P13.2) MUTATED     28   25
  DEL PEAK 18(17P13.2) WILD-TYPE   45   31
        clus
vv       DEL PEAK 18(17P13.2) MUTATED DEL PEAK 18(17P13.2) WILD-TYPE
  FEMALE                           28                             45
  MALE                             25                             31
[1] 2 2
[1] FALSE
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(17P13.2) MUTATED                                  1     1
  DEL PEAK 18(17P13.2) WILD-TYPE                                0     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(17P13.2) MUTATED                           2    47
  DEL PEAK 18(17P13.2) WILD-TYPE                         7    65
D25V4, multiclass
                                  clus
vv                                 DEL PEAK 18(17P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            1
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      47
                                  clus
vv                                 DEL PEAK 18(17P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              0
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                     7
  WHITE                                                        65
[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   34  2
  DEL PEAK 19(17Q11.2) WILD-TYPE 91  2
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                            36                             93 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                             2                              2 
$`DEL PEAK 19(17Q11.2) MUTATED`
TCGA-QR-A6GS TCGA-QT-A5XN TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6YA TCGA-RW-A67W 
        1.25        25.18         4.41         0.79        41.06        19.86 
TCGA-RW-A67X TCGA-RW-A67Y TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68C 
        2.93         7.10         0.85         1.22        11.70         6.28 
TCGA-RW-A7D0 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX 
        1.78        20.09        24.00        11.38        29.88        11.77 
TCGA-S7-A7X1 TCGA-SQ-A6I6 TCGA-SR-A6MP TCGA-SR-A6MT TCGA-TT-A6YJ TCGA-W2-A7UY 
        7.89         0.10        51.22       106.75         4.34        10.65 
TCGA-WB-A80N TCGA-WB-A80Y TCGA-WB-A818 TCGA-WB-A81D TCGA-WB-A81E TCGA-WB-A81F 
        4.73        19.59        26.14         0.79        37.18        24.00 
TCGA-WB-A81H TCGA-WB-A81J TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S 
       42.54         1.87        46.22        12.99        24.82        11.74 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XL TCGA-QT-A5XM 
       81.70        28.01        36.23         6.94         1.81         0.72 
TCGA-QT-A5XO TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC 
        2.30         0.95        38.73         0.92        97.22         8.09 
TCGA-RW-A67V TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A686 TCGA-RW-A68A 
       86.89        33.30        23.80         1.05        13.32        13.05 
TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A8AZ 
        7.96        72.79        15.02         0.69         4.41         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU 
        0.59        26.30        23.51        14.50        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X2 TCGA-SP-A6QC TCGA-SP-A6QD 
       17.33        10.65         6.08        12.20       104.55       101.49 
TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
       70.65        67.07        98.07         9.01        99.06         1.41 
TCGA-SR-A6MQ TCGA-SR-A6MS TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MX TCGA-SR-A6MY 
       54.44        73.05       110.53       107.47         3.12        24.66 
TCGA-SR-A6MZ TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP 
       11.34        49.61        25.15         7.96        10.42        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-WB-A80K TCGA-WB-A80L TCGA-WB-A80M 
       16.60        17.69        25.61        27.62        22.29         4.47 
TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q TCGA-WB-A80V TCGA-WB-A814 TCGA-WB-A815 
        4.21       303.09       127.56        29.16        32.88         5.98 
TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81G TCGA-WB-A81I 
       17.46        32.61         7.69        12.20        24.23         1.12 
TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81V TCGA-WB-A81W 
       19.56        21.44         1.61         9.47        71.05        56.52 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                          0.10                           0.59 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                        106.75                         303.09 
  DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE 
                         11.72                          17.33 
[1] "0.1 - 106.8 (11.7)" "0.6 - 303.1 (17.3)"
[1] "hr=" "3"  
D26V2, continuous
D26V3, binary
                                cls
clus                              0  1
  DEL PEAK 19(17Q11.2) MUTATED   21 15
  DEL PEAK 19(17Q11.2) WILD-TYPE 52 41
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(17Q11.2) MUTATED     21   15
  DEL PEAK 19(17Q11.2) WILD-TYPE   52   41
        clus
vv       DEL PEAK 19(17Q11.2) MUTATED DEL PEAK 19(17Q11.2) WILD-TYPE
  FEMALE                           21                             52
  MALE                             15                             41
[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     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(17Q11.2) MUTATED                           2    33
  DEL PEAK 19(17Q11.2) WILD-TYPE                         7    79
D26V4, multiclass
                                  clus
vv                                 DEL PEAK 19(17Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      33
                                  clus
vv                                 DEL PEAK 19(17Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              1
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                     7
  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(27) Variable = DEL PEAK 20(22Q13.31) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 20(22Q13.31) MUTATED   51  3
  DEL PEAK 20(22Q13.31) WILD-TYPE 74  1
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                             54                              75 
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                              3                               1 
$`DEL PEAK 20(22Q13.31) MUTATED`
TCGA-P8-A5KD TCGA-P8-A6RY TCGA-PR-A5PF TCGA-PR-A5PH TCGA-QT-A5XK TCGA-QT-A5XL 
        2.27         5.88         7.89        28.01         6.94         1.81 
TCGA-QT-A5XO TCGA-QT-A5XP TCGA-QT-A69Q TCGA-RT-A6Y9 TCGA-RW-A67Y TCGA-RW-A681 
        2.30         4.41         0.79        97.22         7.10        23.80 
TCGA-RW-A686 TCGA-S7-A7WL TCGA-S7-A7WM TCGA-S7-A7WQ TCGA-S7-A7WR TCGA-S7-A7WX 
       13.32        20.09        24.00        11.38        29.88        11.77 
TCGA-S7-A7X2 TCGA-SP-A6QF TCGA-SP-A6QG TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I6 
       12.20        70.65        67.07         9.01        99.06         0.10 
TCGA-SR-A6MP TCGA-SR-A6MQ TCGA-SR-A6MX TCGA-SR-A6MY TCGA-SR-A6MZ TCGA-TT-A6YK 
       51.22        54.44         3.12        24.66        11.34        25.15 
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-A7UY TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80V TCGA-WB-A80Y 
       17.69        10.65         4.73         4.21        29.16        19.59 
TCGA-WB-A815 TCGA-WB-A818 TCGA-WB-A819 TCGA-WB-A81A TCGA-WB-A81D TCGA-WB-A81H 
        5.98        26.14         7.69        12.20         0.79        42.54 
TCGA-WB-A81N TCGA-WB-A81Q TCGA-WB-A81R TCGA-WB-A81T TCGA-WB-A81W TCGA-XG-A823 
       46.22        24.82         1.61         9.47        56.52         6.90 

$`DEL PEAK 20(22Q13.31) WILD-TYPE`
TCGA-P7-A5NY TCGA-P8-A5KC TCGA-P8-A6RX TCGA-PR-A5PG TCGA-QR-A6GS TCGA-QT-A5XJ 
       31.46        29.03         0.95        81.70         1.25        36.23 
TCGA-QT-A5XM TCGA-QT-A5XN TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6YA 
        0.72        25.18         0.95        38.73         0.92        41.06 
TCGA-RT-A6YC TCGA-RW-A67V TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A684 
        8.09        86.89        19.86         2.93        33.30         1.05 
TCGA-RW-A685 TCGA-RW-A688 TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68B TCGA-RW-A68C 
        0.85         1.22        11.70        13.05         7.96         6.28 
TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ 
       72.79        15.02         0.69         4.41         1.78         2.89 
TCGA-RX-A8JQ TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU 
        0.59        26.30        23.51        14.50        29.98        19.76 
TCGA-S7-A7WV TCGA-S7-A7WW TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-SP-A6QC TCGA-SP-A6QD 
       17.33        10.65         6.08         7.89       104.55       101.49 
TCGA-SP-A6QI TCGA-SQ-A6I4 TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV 
       98.07         1.41        73.05       106.75       110.53       107.47 
TCGA-SR-A6N0 TCGA-TT-A6YJ TCGA-TT-A6YN TCGA-TT-A6YO TCGA-TT-A6YP TCGA-W2-A7H7 
       49.61         4.34         7.96        10.42        25.32        17.16 
TCGA-W2-A7HH TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80M TCGA-WB-A80P TCGA-WB-A80Q 
       25.61        27.62        22.29         4.47       303.09       127.56 
TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81G 
       32.88        17.46        32.61        37.18        24.00        24.23 
TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81K TCGA-WB-A81M TCGA-WB-A81P TCGA-WB-A81S 
        1.12         1.87        19.56        21.44        12.99        11.74 
TCGA-WB-A81V TCGA-WB-A821 TCGA-WB-A822 
       71.05         1.35        92.78 

  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                           0.10                            0.59 
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                          99.06                          303.09 
  DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE 
                          12.20                           19.56 
[1] "0.1 - 99.1 (12.2)"  "0.6 - 303.1 (19.6)"
[1] "hr=" "4.7"
D27V2, continuous
D27V3, binary
                                 cls
clus                               0  1
  DEL PEAK 20(22Q13.31) MUTATED   31 23
  DEL PEAK 20(22Q13.31) WILD-TYPE 42 33
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(22Q13.31) MUTATED     31   23
  DEL PEAK 20(22Q13.31) WILD-TYPE   42   33
        clus
vv       DEL PEAK 20(22Q13.31) MUTATED DEL PEAK 20(22Q13.31) WILD-TYPE
  FEMALE                            31                              42
  MALE                              23                              33
[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     1
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(22Q13.31) MUTATED                           4    46
  DEL PEAK 20(22Q13.31) WILD-TYPE                         5    66
D27V4, multiclass
                                  clus
vv                                 DEL PEAK 20(22Q13.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       46
                                  clus
vv                                 DEL PEAK 20(22Q13.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               0
  ASIAN                                                          1
  BLACK OR AFRICAN AMERICAN                                      5
  WHITE                                                         66
[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   35  1
  DEL PEAK 21(XP21.1) WILD-TYPE 90  3
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                           36                            93 
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK 21(XP21.1) MUTATED`
TCGA-QT-A5XJ TCGA-QT-A5XK TCGA-QT-A5XN TCGA-QT-A5XO TCGA-QT-A69Q TCGA-RT-A6YA 
       36.23         6.94        25.18         2.30         0.79        41.06 
TCGA-RW-A67Y TCGA-RW-A689 TCGA-RW-A68A TCGA-RW-A68C TCGA-S7-A7WQ TCGA-S7-A7WR 
        7.10        11.70        13.05         6.28        11.38        29.88 
TCGA-SP-A6QG TCGA-SQ-A6I6 TCGA-SR-A6MQ TCGA-SR-A6MX TCGA-SR-A6MY TCGA-TT-A6YJ 
       67.07         0.10        54.44         3.12        24.66         4.34 
TCGA-TT-A6YN TCGA-TT-A6YP TCGA-W2-A7H7 TCGA-W2-A7HA TCGA-W2-A7HB TCGA-W2-A7HC 
        7.96        25.32        17.16         1.18        19.86        12.03 
TCGA-W2-A7HD TCGA-W2-A7HF TCGA-W2-A7UY TCGA-WB-A80M TCGA-WB-A80V TCGA-WB-A815 
       12.49        17.69        10.65         4.47        29.16         5.98 
TCGA-WB-A819 TCGA-WB-A81E TCGA-WB-A81F TCGA-WB-A81K TCGA-WB-A81R TCGA-WB-A81W 
        7.69        37.18        24.00        19.56         1.61        56.52 

$`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         0.95         5.88         7.89 
TCGA-PR-A5PG TCGA-PR-A5PH TCGA-QR-A6GS TCGA-QT-A5XL TCGA-QT-A5XM TCGA-QT-A5XP 
       81.70        28.01         1.25         1.81         0.72         4.41 
TCGA-QT-A7U0 TCGA-RM-A68T TCGA-RM-A68W TCGA-RT-A6Y9 TCGA-RT-A6YC TCGA-RW-A67V 
        0.95        38.73         0.92        97.22         8.09        86.89 
TCGA-RW-A67W TCGA-RW-A67X TCGA-RW-A680 TCGA-RW-A681 TCGA-RW-A684 TCGA-RW-A685 
       19.86         2.93        33.30        23.80         1.05         0.85 
TCGA-RW-A686 TCGA-RW-A688 TCGA-RW-A68B TCGA-RW-A68D TCGA-RW-A68F TCGA-RW-A68G 
       13.32         1.22         7.96        72.79        15.02         0.69 
TCGA-RW-A7CZ TCGA-RW-A7D0 TCGA-RW-A8AZ TCGA-RX-A8JQ TCGA-S7-A7WL TCGA-S7-A7WM 
        4.41         1.78         2.89         0.59        20.09        24.00 
TCGA-S7-A7WN TCGA-S7-A7WO TCGA-S7-A7WP TCGA-S7-A7WT TCGA-S7-A7WU TCGA-S7-A7WV 
       26.30        23.51        14.50        29.98        19.76        17.33 
TCGA-S7-A7WW TCGA-S7-A7WX TCGA-S7-A7X0 TCGA-S7-A7X1 TCGA-S7-A7X2 TCGA-SP-A6QC 
       10.65        11.77         6.08         7.89        12.20       104.55 
TCGA-SP-A6QD TCGA-SP-A6QF TCGA-SP-A6QI TCGA-SP-A6QJ TCGA-SP-A6QK TCGA-SQ-A6I4 
      101.49        70.65        98.07         9.01        99.06         1.41 
TCGA-SR-A6MP TCGA-SR-A6MS TCGA-SR-A6MT TCGA-SR-A6MU TCGA-SR-A6MV TCGA-SR-A6MZ 
       51.22        73.05       106.75       110.53       107.47        11.34 
TCGA-SR-A6N0 TCGA-TT-A6YK TCGA-TT-A6YO TCGA-W2-A7H5 TCGA-W2-A7HE TCGA-W2-A7HH 
       49.61        25.15        10.42        14.20        16.60        25.61 
TCGA-WB-A80K TCGA-WB-A80L TCGA-WB-A80N TCGA-WB-A80O TCGA-WB-A80P TCGA-WB-A80Q 
       27.62        22.29         4.73         4.21       303.09       127.56 
TCGA-WB-A80Y TCGA-WB-A814 TCGA-WB-A816 TCGA-WB-A817 TCGA-WB-A818 TCGA-WB-A81A 
       19.59        32.88        17.46        32.61        26.14        12.20 
TCGA-WB-A81D TCGA-WB-A81G TCGA-WB-A81H TCGA-WB-A81I TCGA-WB-A81J TCGA-WB-A81M 
        0.79        24.23        42.54         1.12         1.87        21.44 
TCGA-WB-A81N TCGA-WB-A81P TCGA-WB-A81Q TCGA-WB-A81S TCGA-WB-A81T TCGA-WB-A81V 
       46.22        12.99        24.82        11.74         9.47        71.05 
TCGA-WB-A821 TCGA-WB-A822 TCGA-XG-A823 
        1.35        92.78         6.90 

  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                         0.10                          0.59 
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                        67.07                        303.09 
  DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE 
                        12.26                         17.33 
[1] "0.1 - 67.1 (12.3)"  "0.6 - 303.1 (17.3)"
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
                               cls
clus                             0  1
  DEL PEAK 21(XP21.1) MUTATED   22 14
  DEL PEAK 21(XP21.1) WILD-TYPE 51 42
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 21(XP21.1) MUTATED     22   14
  DEL PEAK 21(XP21.1) WILD-TYPE   51   42
        clus
vv       DEL PEAK 21(XP21.1) MUTATED DEL PEAK 21(XP21.1) WILD-TYPE
  FEMALE                          22                            51
  MALE                            14                            42
[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     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(XP21.1) MUTATED                           5    28
  DEL PEAK 21(XP21.1) WILD-TYPE                         4    84
D28V4, multiclass
                                  clus
vv                                 DEL PEAK 21(XP21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           1
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     28
                                  clus
vv                                 DEL PEAK 21(XP21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                    4
  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"
