[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"        "-oTDLBC-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/DLBC-TP/11541278/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/11544213/transformed.cor.cli.txt"

nPatients in clinical file=35, in cluster file=48, common to both=35
[1] "Reduce the number of clustering variables from 41 to 37."
[1] 37 35
[1] "AMP PEAK  1(1Q24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                           11                            24 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                           11                            24 
[1] "AMP PEAK  2(2P16.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                            9                            26 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                            9                            26 
[1] "AMP PEAK  3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           10                            25 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                           10                            25 
[1] "AMP PEAK  4(3Q29) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                          9                          26 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                          9                          26 
[1] "AMP PEAK  5(5P13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            4                            31 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            4                            31 
[1] "AMP PEAK  6(7P22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                           11                            24 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                           11                            24 
[1] "AMP PEAK  7(7Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                           10                            25 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                           10                            25 
[1] "AMP PEAK  8(8Q24.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                             8                             27 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                             8                             27 
[1] "AMP PEAK  9(12Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                             9                             26 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                             9                             26 
[1] "AMP PEAK 11(16P12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                             8                             27 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                             8                             27 
[1] "AMP PEAK 12(18Q21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                            11                             24 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                            11                             24 
[1] "AMP PEAK 13(19Q13.43) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                              7                              28 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                              7                              28 
[1] "AMP PEAK 14(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            6                            29 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            6                            29 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             8                             27 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             8                             27 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           10                            25 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           10                            25 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          9                          26 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          9                          26 
[1] "DEL PEAK  4(2Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            6                            29 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            6                            29 
[1] "DEL PEAK  5(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             3                             32 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             3                             32 
[1] "DEL PEAK  6(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                            8                            27 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                            8                            27 
[1] "DEL PEAK  8(6P21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             4                             31 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             4                             31 
[1] "DEL PEAK  9(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                           12                            23 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                           12                            23 
[1] "DEL PEAK 10(6Q22.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                            10                             25 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                            10                             25 
[1] "DEL PEAK 11(6Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                            8                            27 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                            8                            27 
[1] "DEL PEAK 13(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                            7                            28 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                            7                            28 
[1] "DEL PEAK 14(8Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            7                            28 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            7                            28 
[1] "DEL PEAK 15(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           13                            22 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           13                            22 
[1] "DEL PEAK 16(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              5                              30 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              5                              30 
[1] "DEL PEAK 17(12P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             7                             28 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             7                             28 
[1] "DEL PEAK 18(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             3                             32 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             3                             32 
[1] "DEL PEAK 19(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                             9                             26 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                             9                             26 
[1] "DEL PEAK 20(16P13.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              4                              31 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              4                              31 
[1] "DEL PEAK 21(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             5                             30 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             5                             30 
[1] "DEL PEAK 22(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                             6                             29 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                             6                             29 
[1] "DEL PEAK 23(17Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             3                             32 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             3                             32 
[1] "DEL PEAK 24(19P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             3                             32 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             3                             32 
[1] "DEL PEAK 25(19Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             3                             32 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             3                             32 
[1] "DEL PEAK 26(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              5                              30 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              5                              30 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "NEOPLASM.DISEASESTAGE"                 
 [6] "PATHOLOGY.T.STAGE"                     
 [7] "PATHOLOGY.N.STAGE"                     
 [8] "PATHOLOGY.M.STAGE"                     
 [9] "DCCUPLOADDATE"                         
[10] "GENDER"                                
[11] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[12] "RADIATIONTHERAPY"                      
[13] "HISTOLOGICALTYPE"                      
[14] "RADIATIONS.RADIATION.REGIMENINDICATION"
[15] "RACE"                                  
[16] "ETHNICITY"                             
[17] "BATCHNUMBER"                           

Input Data has 17 rows and 35 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
         132          132          456            6            6          410 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FA-A86F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
          22           25           NA         1081          946          965 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
         751          126          832          679          298           NA 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
         791          385          139           NA         1581         1441 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
          NA           NA         3227         5980         4578         2983 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
        1099         1299         1334         1739          788 
Variable 1:'AGE':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'NEOPLASM.DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PATHOLOGY.T.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 7:'PATHOLOGY.N.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 8:'PATHOLOGY.M.STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 9:'DCCUPLOADDAY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 12:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 13:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=5,	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 35 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=26, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q24.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1Q24.2) MUTATED   10  0
  AMP PEAK  1(1Q24.2) WILD-TYPE 19  5
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                           10                            24 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                            0                             5 
$`AMP PEAK  1(1Q24.2) MUTATED`
TCGA-FA-A4BB TCGA-FA-A7Q1 TCGA-FF-8047 TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6325 
        4.34         0.72         4.14        26.01         4.57        51.98 
TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60        98.07        43.86        57.17 

$`AMP PEAK  1(1Q24.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F 
        4.34        14.99         0.20         0.20        13.48         0.82 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 
        9.80        10.29        12.66        41.16        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-RQ-A68N 
       19.56       106.09       150.51        36.13        42.71        25.91 

  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                         0.72                          0.20 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                       196.60                        211.23 
  AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE 
                       34.935                        25.300 
[1] "0.7 - 196.6 (34.9)" "0.2 - 211.2 (25.3)"
[1] "hr="     "9.6e+08"
D1V2, continuous
D1V3, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q24.2) MUTATED    6  5
  AMP PEAK  1(1Q24.2) WILD-TYPE 12 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.2) MUTATED      6    5
  AMP PEAK  1(1Q24.2) WILD-TYPE   12   12
        clus
vv       AMP PEAK  1(1Q24.2) MUTATED AMP PEAK  1(1Q24.2) WILD-TYPE
  FEMALE                           6                            12
  MALE                             5                            12
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q24.2) MUTATED       4                         0     7
  AMP PEAK  1(1Q24.2) WILD-TYPE    14                         1     9
D1V4, multiclass
                           clus
vv                          AMP PEAK  1(1Q24.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               7
                           clus
vv                          AMP PEAK  1(1Q24.2) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                 9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(2P16.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(2P16.1) MUTATED    7  2
  AMP PEAK  2(2P16.1) WILD-TYPE 22  3
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                            9                            25 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                            2                             3 
$`AMP PEAK  2(2P16.1) MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8061 
       14.99         0.72         0.82        35.54        31.73        27.35 
TCGA-FM-8000 TCGA-G8-6907 TCGA-G8-6909 
        4.57        19.56       106.09 

$`AMP PEAK  2(2P16.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8042 
        4.34         4.34         0.20         0.20        13.48        31.10 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
       24.69         4.14        22.32         9.80        10.29        26.01 
TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6914 
       12.66        41.16        51.98        47.38       211.23       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                         0.72                          0.20 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                       106.09                        211.23 
  AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE 
                        19.56                         26.01 
[1] "0.7 - 106.1 (19.6)" "0.2 - 211.2 (26.0)"
[1] "hr=" "4.1"
D2V2, continuous
D2V3, binary
                               cls
clus                             0  1
  AMP PEAK  2(2P16.1) MUTATED    6  3
  AMP PEAK  2(2P16.1) WILD-TYPE 12 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(2P16.1) MUTATED      6    3
  AMP PEAK  2(2P16.1) WILD-TYPE   12   14
        clus
vv       AMP PEAK  2(2P16.1) MUTATED AMP PEAK  2(2P16.1) WILD-TYPE
  FEMALE                           6                            12
  MALE                             3                            14
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2P16.1) MUTATED       6                         0     3
  AMP PEAK  2(2P16.1) WILD-TYPE    12                         1    13
D2V4, multiclass
                           clus
vv                          AMP PEAK  2(2P16.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          AMP PEAK  2(2P16.1) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(3Q27.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(3Q27.3) MUTATED    9  0
  AMP PEAK  3(3Q27.3) WILD-TYPE 20  5
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                            9                            25 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                            0                             5 
$`AMP PEAK  3(3Q27.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-G8-6914 
       14.99         0.20         0.82        31.10        26.01       196.60 
TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-RQ-A68N 
       36.13        43.86        25.91 

$`AMP PEAK  3(3Q27.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         0.20        13.48         0.72        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       10.29        12.66         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 
      211.23        19.56       106.09       150.51        98.07        42.71 
TCGA-GR-A4D9 
       57.17 

  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                          0.2                           0.2 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                       196.60                        211.23 
  AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE 
                        26.01                         24.69 
[1] "0.2 - 196.6 (26.0)" "0.2 - 211.2 (24.7)"
[1] "hr="     "2.9e+08"
D3V2, continuous
D3V3, binary
                               cls
clus                             0  1
  AMP PEAK  3(3Q27.3) MUTATED    6  4
  AMP PEAK  3(3Q27.3) WILD-TYPE 12 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(3Q27.3) MUTATED      6    4
  AMP PEAK  3(3Q27.3) WILD-TYPE   12   13
        clus
vv       AMP PEAK  3(3Q27.3) MUTATED AMP PEAK  3(3Q27.3) WILD-TYPE
  FEMALE                           6                            12
  MALE                             4                            13
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q27.3) MUTATED       6                         0     4
  AMP PEAK  3(3Q27.3) WILD-TYPE    12                         1    12
D3V4, multiclass
                           clus
vv                          AMP PEAK  3(3Q27.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               4
                           clus
vv                          AMP PEAK  3(3Q27.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(3Q29) MUTATION ANALYSIS
D4V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  4(3Q29) MUTATED    8  0
  AMP PEAK  4(3Q29) WILD-TYPE 21  5
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                          8                          26 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                          0                           5 
$`AMP PEAK  4(3Q29) MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D4 
        0.20         0.82        31.10        26.01       196.60        36.13 
TCGA-GR-A4D6 TCGA-RQ-A68N 
       43.86        25.91 

$`AMP PEAK  4(3Q29) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-7353 
       47.38       211.23        19.56       106.09       150.51        98.07 
TCGA-GR-A4D5 TCGA-GR-A4D9 
       42.71        57.17 

  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                        0.2                         0.2 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                     196.60                      211.23 
  AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE 
                     28.555                      23.505 
[1] "0.2 - 196.6 (28.6)" "0.2 - 211.2 (23.5)"
[1] "hr="     "2.8e+08"
D4V2, continuous
D4V3, binary
                             cls
clus                           0  1
  AMP PEAK  4(3Q29) MUTATED    6  3
  AMP PEAK  4(3Q29) WILD-TYPE 12 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  4(3Q29) MUTATED      6    3
  AMP PEAK  4(3Q29) WILD-TYPE   12   14
        clus
vv       AMP PEAK  4(3Q29) MUTATED AMP PEAK  4(3Q29) WILD-TYPE
  FEMALE                         6                          12
  MALE                           3                          14
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3Q29) MUTATED       5                         0     4
  AMP PEAK  4(3Q29) WILD-TYPE    13                         1    12
D4V4, multiclass
                           clus
vv                          AMP PEAK  4(3Q29) MUTATED
  ASIAN                                             5
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             4
                           clus
vv                          AMP PEAK  4(3Q29) WILD-TYPE
  ASIAN                                              13
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(5P13.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(5P13.1) MUTATED    3  1
  AMP PEAK  5(5P13.1) WILD-TYPE 26  4
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            4                            30 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                            1                             4 
$`AMP PEAK  5(5P13.1) MUTATED`
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-G8-6909 
        0.72         0.82        35.54       106.09 

$`AMP PEAK  5(5P13.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 
       51.98        47.38       211.23        19.56       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       98.07        36.13        42.71        43.86        57.17        25.91 

  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                         0.72                          0.20 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                       106.09                        211.23 
  AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE 
                        18.18                         25.96 
[1] "0.7 - 106.1 (18.2)" "0.2 - 211.2 (26.0)"
[1] "hr=" "2.4"
D5V2, continuous
D5V3, binary
                               cls
clus                             0  1
  AMP PEAK  5(5P13.1) MUTATED    3  1
  AMP PEAK  5(5P13.1) WILD-TYPE 15 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5P13.1) MUTATED      3    1
  AMP PEAK  5(5P13.1) WILD-TYPE   15   16
        clus
vv       AMP PEAK  5(5P13.1) MUTATED AMP PEAK  5(5P13.1) WILD-TYPE
  FEMALE                           3                            15
  MALE                             1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(5P13.1) MUTATED       3                         0     1
  AMP PEAK  5(5P13.1) WILD-TYPE    15                         1    15
D5V4, multiclass
                           clus
vv                          AMP PEAK  5(5P13.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               1
                           clus
vv                          AMP PEAK  5(5P13.1) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(7P22.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(7P22.3) MUTATED   11  0
  AMP PEAK  6(7P22.3) WILD-TYPE 18  5
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                           11                            23 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                            0                             5 
$`AMP PEAK  6(7P22.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CW TCGA-FM-8000 
       14.99         0.20         0.82        31.10        26.01         4.57 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      196.60       150.51        98.07        36.13        43.86 

$`AMP PEAK  6(7P22.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         0.20        13.48         0.72        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       10.29        12.66        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
       19.56       106.09        42.71        57.17        25.91 

  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                          0.2                           0.2 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                       196.60                        211.23 
  AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE 
                        31.10                         24.69 
[1] "0.2 - 196.6 (31.1)" "0.2 - 211.2 (24.7)"
[1] "hr="     "1.1e+09"
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK  6(7P22.3) MUTATED    7  4
  AMP PEAK  6(7P22.3) WILD-TYPE 11 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7P22.3) MUTATED      7    4
  AMP PEAK  6(7P22.3) WILD-TYPE   11   13
        clus
vv       AMP PEAK  6(7P22.3) MUTATED AMP PEAK  6(7P22.3) WILD-TYPE
  FEMALE                           7                            11
  MALE                             4                            13
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7P22.3) MUTATED       6                         0     5
  AMP PEAK  6(7P22.3) WILD-TYPE    12                         1    11
D6V4, multiclass
                           clus
vv                          AMP PEAK  6(7P22.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               5
                           clus
vv                          AMP PEAK  6(7P22.3) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(7Q21.3) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(7Q21.3) MUTATED   10  0
  AMP PEAK  7(7Q21.3) WILD-TYPE 19  5
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                           10                            24 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                            0                             5 
$`AMP PEAK  7(7Q21.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-A7CQ TCGA-FF-A7CW 
       14.99         0.20         0.82        31.10         9.80        26.01 
TCGA-FM-8000 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
        4.57        98.07        36.13        43.86 

$`AMP PEAK  7(7Q21.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         0.20        13.48         0.72        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR 
       31.73        24.69         4.14        27.35        22.32        10.29 
TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       12.66        41.16        51.98        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
      106.09       196.60       150.51        42.71        57.17        25.91 

  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                          0.2                           0.2 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                        98.07                        211.23 
  AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE 
                        20.50                         26.63 
[1] "0.2 - 98.1 (20.5)"  "0.2 - 211.2 (26.6)"
[1] "hr="     "2.7e+08"
D7V2, continuous
D7V3, binary
                               cls
clus                             0  1
  AMP PEAK  7(7Q21.3) MUTATED    6  4
  AMP PEAK  7(7Q21.3) WILD-TYPE 12 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  7(7Q21.3) MUTATED      6    4
  AMP PEAK  7(7Q21.3) WILD-TYPE   12   13
        clus
vv       AMP PEAK  7(7Q21.3) MUTATED AMP PEAK  7(7Q21.3) WILD-TYPE
  FEMALE                           6                            12
  MALE                             4                            13
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(7Q21.3) MUTATED       7                         0     3
  AMP PEAK  7(7Q21.3) WILD-TYPE    11                         1    13
D7V4, multiclass
                           clus
vv                          AMP PEAK  7(7Q21.3) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          AMP PEAK  7(7Q21.3) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(8Q24.23) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(8Q24.23) MUTATED    7  0
  AMP PEAK  8(8Q24.23) WILD-TYPE 22  5
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                             7                             27 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                             0                              5 
$`AMP PEAK  8(8Q24.23) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-A7CQ 
        0.20         0.72        35.54        31.10        31.73         9.80 
TCGA-GR-7353 
       98.07 

$`AMP PEAK  8(8Q24.23) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A82F 
        4.34         4.34        14.99         0.20        13.48         0.82 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CR TCGA-FF-A7CW 
       24.69         4.14        27.35        22.32        10.29        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66         4.57        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       106.09       196.60       150.51        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       43.86        57.17        25.91 

  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                           0.2                            0.2 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                         98.07                         211.23 
  AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE 
                         31.10                          25.91 
[1] "0.2 - 98.1 (31.1)"  "0.2 - 211.2 (25.9)"
[1] "hr="     "2.4e+08"
D8V2, continuous
D8V3, binary
                                cls
clus                              0  1
  AMP PEAK  8(8Q24.23) MUTATED    6  2
  AMP PEAK  8(8Q24.23) WILD-TYPE 12 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(8Q24.23) MUTATED      6    2
  AMP PEAK  8(8Q24.23) WILD-TYPE   12   15
        clus
vv       AMP PEAK  8(8Q24.23) MUTATED AMP PEAK  8(8Q24.23) WILD-TYPE
  FEMALE                            6                             12
  MALE                              2                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(8Q24.23) MUTATED       6                         0     2
  AMP PEAK  8(8Q24.23) WILD-TYPE    12                         1    14
D8V4, multiclass
                           clus
vv                          AMP PEAK  8(8Q24.23) MUTATED
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          AMP PEAK  8(8Q24.23) WILD-TYPE
  ASIAN                                                 12
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(12Q21.1) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(12Q21.1) MUTATED    8  1
  AMP PEAK  9(12Q21.1) WILD-TYPE 21  4
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                             9                             25 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                             1                              4 
$`AMP PEAK  9(12Q21.1) MUTATED`
TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 
       14.99        13.48         0.72         0.82        35.54        31.73 
TCGA-FF-A7CR TCGA-GR-A4D5 TCGA-RQ-A68N 
       10.29        42.71        25.91 

$`AMP PEAK  9(12Q21.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8046 
        4.34         4.34         0.20         0.20        31.10        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FF-A7CX 
        4.14        27.35        22.32         9.80        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
        4.57        41.16        51.98        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      106.09       196.60       150.51        98.07        36.13        43.86 
TCGA-GR-A4D9 
       57.17 

  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                          0.72                           0.20 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                         42.71                         211.23 
  AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE 
                         14.99                          27.35 
[1] "0.7 - 42.7 (15.0)"  "0.2 - 211.2 (27.4)"
[1] "hr=" "2.3"
D9V2, continuous
D9V3, binary
                                cls
clus                              0  1
  AMP PEAK  9(12Q21.1) MUTATED    6  3
  AMP PEAK  9(12Q21.1) WILD-TYPE 12 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12Q21.1) MUTATED      6    3
  AMP PEAK  9(12Q21.1) WILD-TYPE   12   14
        clus
vv       AMP PEAK  9(12Q21.1) MUTATED AMP PEAK  9(12Q21.1) WILD-TYPE
  FEMALE                            6                             12
  MALE                              3                             14
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(12Q21.1) MUTATED       7                         0     2
  AMP PEAK  9(12Q21.1) WILD-TYPE    11                         1    14
D9V4, multiclass
                           clus
vv                          AMP PEAK  9(12Q21.1) MUTATED
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          AMP PEAK  9(12Q21.1) WILD-TYPE
  ASIAN                                                 11
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 11(16P12.2) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(16P12.2) MUTATED    7  1
  AMP PEAK 11(16P12.2) WILD-TYPE 22  4
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                             8                             26 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                             1                              4 
$`AMP PEAK 11(16P12.2) MUTATED`
TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8043 TCGA-FM-8000 TCGA-G8-6909 
       14.99         0.72         0.82        31.73         4.57       106.09 
TCGA-GR-A4D4 TCGA-RQ-A68N 
       36.13        25.91 

$`AMP PEAK 11(16P12.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34         0.20         0.20        13.48        35.54 
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.10        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       10.29        26.01        12.66        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 
      211.23        19.56       196.60       150.51        98.07        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 
       43.86        57.17 

  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                          0.72                           0.20 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                        106.09                         211.23 
  AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE 
                         20.45                          26.68 
[1] "0.7 - 106.1 (20.4)" "0.2 - 211.2 (26.7)"
[1] "hr=" "1.5"
D10V2, continuous
D10V3, binary
                                cls
clus                              0  1
  AMP PEAK 11(16P12.2) MUTATED    5  3
  AMP PEAK 11(16P12.2) WILD-TYPE 13 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(16P12.2) MUTATED      5    3
  AMP PEAK 11(16P12.2) WILD-TYPE   13   14
        clus
vv       AMP PEAK 11(16P12.2) MUTATED AMP PEAK 11(16P12.2) WILD-TYPE
  FEMALE                            5                             13
  MALE                              3                             14
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(16P12.2) MUTATED       4                         0     4
  AMP PEAK 11(16P12.2) WILD-TYPE    14                         1    12
D10V4, multiclass
                           clus
vv                          AMP PEAK 11(16P12.2) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                4
                           clus
vv                          AMP PEAK 11(16P12.2) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 12(18Q21.2) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(18Q21.2) MUTATED   10  1
  AMP PEAK 12(18Q21.2) WILD-TYPE 19  4
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                            11                             23 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                             1                              4 
$`AMP PEAK 12(18Q21.2) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8043 
       14.99         0.20        13.48         0.82        31.10        31.73 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-G8-6914 TCGA-GR-A4D6 
        9.80        10.29        26.01       196.60        43.86 

$`AMP PEAK 12(18Q21.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8046 
        4.34         4.34         0.20         0.72        35.54        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        4.14        27.35        22.32        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-GR-7351 
       51.98        47.38       211.23        19.56       106.09       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
       98.07        36.13        42.71        57.17        25.91 

  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                           0.2                            0.2 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                        196.60                         211.23 
  AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE 
                         14.99                          27.35 
[1] "0.2 - 196.6 (15.0)" "0.2 - 211.2 (27.4)"
[1] "hr=" "1"  
D11V2, continuous
D11V3, binary
                                cls
clus                              0  1
  AMP PEAK 12(18Q21.2) MUTATED    6  5
  AMP PEAK 12(18Q21.2) WILD-TYPE 12 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(18Q21.2) MUTATED      6    5
  AMP PEAK 12(18Q21.2) WILD-TYPE   12   12
        clus
vv       AMP PEAK 12(18Q21.2) MUTATED AMP PEAK 12(18Q21.2) WILD-TYPE
  FEMALE                            6                             12
  MALE                              5                             12
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(18Q21.2) MUTATED      10                         0     1
  AMP PEAK 12(18Q21.2) WILD-TYPE     8                         1    15
D11V4, multiclass
                           clus
vv                          AMP PEAK 12(18Q21.2) MUTATED
  ASIAN                                               10
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                1
                           clus
vv                          AMP PEAK 12(18Q21.2) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 13(19Q13.43) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 13(19Q13.43) MUTATED    4  2
  AMP PEAK 13(19Q13.43) WILD-TYPE 25  3
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                              6                              28 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                              2                               3 
$`AMP PEAK 13(19Q13.43) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-A7CR TCGA-G8-6909 
        0.20        13.48         0.82        35.54        10.29       106.09 

$`AMP PEAK 13(19Q13.43) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FF-8042 
        4.34         4.34        14.99         0.20         0.72        31.10 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.73        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       26.01        12.66         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
      211.23        19.56       196.60       150.51        98.07        36.13 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       42.71        43.86        57.17        25.91 

  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                            0.2                             0.2 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                         106.09                          211.23 
  AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE 
                         11.885                          26.680 
[1] "0.2 - 106.1 (11.9)" "0.2 - 211.2 (26.7)"
[1] "hr=" "6.2"
D12V2, continuous
D12V3, binary
                                 cls
clus                               0  1
  AMP PEAK 13(19Q13.43) MUTATED    5  2
  AMP PEAK 13(19Q13.43) WILD-TYPE 13 15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(19Q13.43) MUTATED      5    2
  AMP PEAK 13(19Q13.43) WILD-TYPE   13   15
        clus
vv       AMP PEAK 13(19Q13.43) MUTATED AMP PEAK 13(19Q13.43) WILD-TYPE
  FEMALE                             5                              13
  MALE                               2                              15
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(19Q13.43) MUTATED       5                         0     2
  AMP PEAK 13(19Q13.43) WILD-TYPE    13                         1    14
D12V4, multiclass
                           clus
vv                          AMP PEAK 13(19Q13.43) MUTATED
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 2
                           clus
vv                          AMP PEAK 13(19Q13.43) WILD-TYPE
  ASIAN                                                  13
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 14(XQ27.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 14(XQ27.3) MUTATED    6  0
  AMP PEAK 14(XQ27.3) WILD-TYPE 23  5
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            6                            28 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                            0                             5 
$`AMP PEAK 14(XQ27.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-RQ-A68N 
       14.99         0.20        35.54        31.10        31.73        25.91 

$`AMP PEAK 14(XQ27.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34         0.20        13.48         0.72         0.82 
TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       24.69         4.14        27.35        22.32         9.80        10.29 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       26.01        12.66         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       106.09       196.60       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       36.13        42.71        43.86        57.17 

  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                          0.2                           0.2 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                        35.54                        211.23 
  AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE 
                       28.505                        25.350 
[1] "0.2 - 35.5 (28.5)"  "0.2 - 211.2 (25.4)"
[1] "hr="     "9.3e+07"
D13V2, continuous
D13V3, binary
                               cls
clus                             0  1
  AMP PEAK 14(XQ27.3) MUTATED    3  3
  AMP PEAK 14(XQ27.3) WILD-TYPE 15 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 14(XQ27.3) MUTATED      3    3
  AMP PEAK 14(XQ27.3) WILD-TYPE   15   14
        clus
vv       AMP PEAK 14(XQ27.3) MUTATED AMP PEAK 14(XQ27.3) WILD-TYPE
  FEMALE                           3                            15
  MALE                             3                            14
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(XQ27.3) MUTATED       5                         0     1
  AMP PEAK 14(XQ27.3) WILD-TYPE    13                         1    15
D13V4, multiclass
                           clus
vv                          AMP PEAK 14(XQ27.3) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               1
                           clus
vv                          AMP PEAK 14(XQ27.3) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.32) MUTATED    7  1
  DEL PEAK  1(1P36.32) WILD-TYPE 22  4
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             8                             26 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             1                              4 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6909 
        0.20         0.72         0.82         4.57        51.98       106.09 
TCGA-GR-7353 TCGA-RQ-A68N 
       98.07        25.91 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34        14.99         0.20        13.48        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6326 
        9.80        10.29        26.01        12.66        41.16        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 
      211.23        19.56       196.60       150.51        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 
       43.86        57.17 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                           0.2                            0.2 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        106.09                         211.23 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                         15.24                          26.68 
[1] "0.2 - 106.1 (15.2)" "0.2 - 211.2 (26.7)"
[1] "hr=" "1.2"
D14V2, continuous
D14V3, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    4  4
  DEL PEAK  1(1P36.32) WILD-TYPE 14 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      4    4
  DEL PEAK  1(1P36.32) WILD-TYPE   14   13
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                            4                             14
  MALE                              4                             13
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED       3                         0     5
  DEL PEAK  1(1P36.32) WILD-TYPE    15                         1    11
D14V4, multiclass
                           clus
vv                          DEL PEAK  1(1P36.32) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                5
                           clus
vv                          DEL PEAK  1(1P36.32) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.1) MUTATED    8  2
  DEL PEAK  2(1P13.1) WILD-TYPE 21  3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                           10                            24 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            2                             3 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-G8-6325 
        0.20         0.20        13.48         9.80        10.29        51.98 
TCGA-G8-6909 TCGA-GR-7353 TCGA-GR-A4D6 TCGA-RQ-A68N 
      106.09        98.07        43.86        25.91 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 
        4.34         4.34        14.99         0.72         0.82        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       31.10        31.73        24.69         4.14        27.35        22.32 
TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 
       26.01        12.66         4.57        41.16        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
       19.56       196.60       150.51        36.13        42.71        57.17 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                         0.20                          0.72 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       106.09                        211.23 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                       19.695                        26.680 
[1] "0.2 - 106.1 (19.7)" "0.7 - 211.2 (26.7)"
[1] "hr=" "2.6"
D15V2, continuous
D15V3, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    3  7
  DEL PEAK  2(1P13.1) WILD-TYPE 15 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      3    7
  DEL PEAK  2(1P13.1) WILD-TYPE   15   10
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                           3                            15
  MALE                             7                            10
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.1) MUTATED       6                         0     4
  DEL PEAK  2(1P13.1) WILD-TYPE    12                         1    12
D15V4, multiclass
                           clus
vv                          DEL PEAK  2(1P13.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               4
                           clus
vv                          DEL PEAK  2(1P13.1) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D16V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(1Q43) MUTATED    8  0
  DEL PEAK  3(1Q43) WILD-TYPE 21  5
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          8                          26 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          0                           5 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-A7CW 
        0.20         0.20        31.10        31.73         4.14        26.01 
TCGA-GR-A4D9 TCGA-RQ-A68N 
       57.17        25.91 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        14.99        13.48         0.72         0.82 
TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       35.54        24.69        27.35        22.32         9.80        10.29 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66         4.57        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 
       19.56       106.09       196.60       150.51        98.07        36.13 
TCGA-GR-A4D5 TCGA-GR-A4D6 
       42.71        43.86 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       0.20                        0.72 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      57.17                      211.23 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      25.96                       26.02 
[1] "0.2 - 57.2 (26.0)"  "0.7 - 211.2 (26.0)"
[1] "hr="     "2.6e+08"
D16V2, continuous
D16V3, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    6  3
  DEL PEAK  3(1Q43) WILD-TYPE 12 14
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      6    3
  DEL PEAK  3(1Q43) WILD-TYPE   12   14
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                         6                          12
  MALE                           3                          14
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q43) MUTATED       6                         0     3
  DEL PEAK  3(1Q43) WILD-TYPE    12                         1    13
D16V4, multiclass
                           clus
vv                          DEL PEAK  3(1Q43) MUTATED
  ASIAN                                             6
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             3
                           clus
vv                          DEL PEAK  3(1Q43) WILD-TYPE
  ASIAN                                              12
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = DEL PEAK  4(2Q23.1) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q23.1) MUTATED    5  1
  DEL PEAK  4(2Q23.1) WILD-TYPE 24  4
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            6                            28 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            1                             4 
$`DEL PEAK  4(2Q23.1) MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6324 TCGA-GR-7351 TCGA-RQ-A68N 
        0.20        31.73         4.14        41.16       150.51        25.91 

$`DEL PEAK  4(2Q23.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
        0.82        35.54        31.10        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6325 
        9.80        10.29        26.01        12.66         4.57        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7353 
       47.38       211.23        19.56       106.09       196.60        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       36.13        42.71        43.86        57.17 

  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                       150.51                        211.23 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                        28.82                         25.35 
[1] "0.2 - 150.5 (28.8)" "0.2 - 211.2 (25.4)"
[1] "hr=" "1.4"
D17V2, continuous
D17V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    5  1
  DEL PEAK  4(2Q23.1) WILD-TYPE 13 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      5    1
  DEL PEAK  4(2Q23.1) WILD-TYPE   13   16
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  FEMALE                           5                            13
  MALE                             1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q23.1) MUTATED       3                         1     2
  DEL PEAK  4(2Q23.1) WILD-TYPE    15                         0    14
D17V4, multiclass
                           clus
vv                          DEL PEAK  4(2Q23.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               2
                           clus
vv                          DEL PEAK  4(2Q23.1) WILD-TYPE
  ASIAN                                                15
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = DEL PEAK  5(3P21.31) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  5(3P21.31) MUTATED    1  1
  DEL PEAK  5(3P21.31) WILD-TYPE 28  4
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             2                             32 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                             1                              4 
$`DEL PEAK  5(3P21.31) MUTATED`
TCGA-FA-8693 TCGA-FF-A7CR 
        4.34        10.29 

$`DEL PEAK  5(3P21.31) WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34        14.99         0.20         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        0.82        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       27.35        22.32         9.80        26.01        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        36.13        42.71        43.86 
TCGA-GR-A4D9 TCGA-RQ-A68N 
       57.17        25.91 

  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                          4.34                           0.20 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                         10.29                         211.23 
  DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE 
                         7.315                         26.680 
[1] "4.3 - 10.3 (7.3)"   "0.2 - 211.2 (26.7)"
[1] "Remove cluster labels:"       "DEL PEAK  5(3P21.31) MUTATED"
D18V2, continuous
D18V3, binary
                                cls
clus                              0  1
  DEL PEAK  5(3P21.31) MUTATED    1  2
  DEL PEAK  5(3P21.31) WILD-TYPE 17 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  5(3P21.31) MUTATED      1    2
  DEL PEAK  5(3P21.31) WILD-TYPE   17   15
        clus
vv       DEL PEAK  5(3P21.31) MUTATED DEL PEAK  5(3P21.31) WILD-TYPE
  FEMALE                            1                             17
  MALE                              2                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P21.31) MUTATED       1                         0     2
  DEL PEAK  5(3P21.31) WILD-TYPE    17                         1    14
D18V4, multiclass
                           clus
vv                          DEL PEAK  5(3P21.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK  5(3P21.31) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = DEL PEAK  6(4Q35.1) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q35.1) MUTATED    6  1
  DEL PEAK  6(4Q35.1) WILD-TYPE 23  4
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                            7                            27 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                            1                             4 
$`DEL PEAK  6(4Q35.1) MUTATED`
TCGA-FA-A6HN TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-A7CQ TCGA-FF-A7CR 
        0.20        31.10        31.73         4.14         9.80        10.29 
TCGA-GR-7353 
       98.07 

$`DEL PEAK  6(4Q35.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CW 
        0.82        35.54        24.69        27.35        22.32        26.01 
TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       12.66         4.57        41.16        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       106.09       196.60       150.51        36.13        42.71 
TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       43.86        57.17        25.91 

  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                        98.07                        211.23 
  DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE 
                        10.29                         26.01 
[1] "0.2 - 98.1 (10.3)"  "0.2 - 211.2 (26.0)"
[1] "hr=" "3.4"
D19V2, continuous
D19V3, binary
                               cls
clus                             0  1
  DEL PEAK  6(4Q35.1) MUTATED    4  4
  DEL PEAK  6(4Q35.1) WILD-TYPE 14 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q35.1) MUTATED      4    4
  DEL PEAK  6(4Q35.1) WILD-TYPE   14   13
        clus
vv       DEL PEAK  6(4Q35.1) MUTATED DEL PEAK  6(4Q35.1) WILD-TYPE
  FEMALE                           4                            14
  MALE                             4                            13
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q35.1) MUTATED       6                         0     2
  DEL PEAK  6(4Q35.1) WILD-TYPE    12                         1    14
D19V4, multiclass
                           clus
vv                          DEL PEAK  6(4Q35.1) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               2
                           clus
vv                          DEL PEAK  6(4Q35.1) WILD-TYPE
  ASIAN                                                12
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = DEL PEAK  8(6P21.32) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  8(6P21.32) MUTATED    4  0
  DEL PEAK  8(6P21.32) WILD-TYPE 25  5
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             4                             30 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                             0                              5 
$`DEL PEAK  8(6P21.32) MUTATED`
TCGA-FA-A4BB TCGA-FA-A7DS TCGA-GR-A4D5 TCGA-RQ-A68N 
        4.34        13.48        42.71        25.91 

$`DEL PEAK  8(6P21.32) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34        14.99         0.20         0.20         0.72         0.82 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       35.54        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 
       22.32         9.80        10.29        26.01        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        98.07        36.13        43.86        57.17 

  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                          4.34                           0.20 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                         42.71                         211.23 
  DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE 
                        19.695                         26.680 
[1] "4.3 - 42.7 (19.7)"  "0.2 - 211.2 (26.7)"
[1] "hr="     "7.8e+07"
D20V2, continuous
D20V3, binary
                                cls
clus                              0  1
  DEL PEAK  8(6P21.32) MUTATED    2  2
  DEL PEAK  8(6P21.32) WILD-TYPE 16 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  8(6P21.32) MUTATED      2    2
  DEL PEAK  8(6P21.32) WILD-TYPE   16   15
        clus
vv       DEL PEAK  8(6P21.32) MUTATED DEL PEAK  8(6P21.32) WILD-TYPE
  FEMALE                            2                             16
  MALE                              2                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(6P21.32) MUTATED       1                         0     3
  DEL PEAK  8(6P21.32) WILD-TYPE    17                         1    13
D20V4, multiclass
                           clus
vv                          DEL PEAK  8(6P21.32) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                3
                           clus
vv                          DEL PEAK  8(6P21.32) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = DEL PEAK  9(6Q14.1) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(6Q14.1) MUTATED   11  1
  DEL PEAK  9(6Q14.1) WILD-TYPE 18  4
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                           12                            22 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                            1                             4 
$`DEL PEAK  9(6Q14.1) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-A7CW 
       14.99         0.20         0.82        31.10        24.69        26.01 
TCGA-FF-A7CX TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
       12.66        51.98       211.23        42.71        57.17        25.91 

$`DEL PEAK  9(6Q14.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8041 
        4.34         4.34         0.20        13.48         0.72        35.54 
TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR 
       31.73         4.14        27.35        22.32         9.80        10.29 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 
        4.57        41.16        47.38        19.56       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      150.51        98.07        36.13        43.86 

  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE 
                       25.960                        24.835 
[1] "0.2 - 211.2 (26.0)" "0.2 - 196.6 (24.8)"
[1] "hr="   "1e+09"
D21V2, continuous
D21V3, binary
                               cls
clus                             0  1
  DEL PEAK  9(6Q14.1) MUTATED    5  7
  DEL PEAK  9(6Q14.1) WILD-TYPE 13 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6Q14.1) MUTATED      5    7
  DEL PEAK  9(6Q14.1) WILD-TYPE   13   10
        clus
vv       DEL PEAK  9(6Q14.1) MUTATED DEL PEAK  9(6Q14.1) WILD-TYPE
  FEMALE                           5                            13
  MALE                             7                            10
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(6Q14.1) MUTATED       7                         0     5
  DEL PEAK  9(6Q14.1) WILD-TYPE    11                         1    11
D21V4, multiclass
                           clus
vv                          DEL PEAK  9(6Q14.1) MUTATED
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               5
                           clus
vv                          DEL PEAK  9(6Q14.1) WILD-TYPE
  ASIAN                                                11
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = DEL PEAK 10(6Q22.32) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 10(6Q22.32) MUTATED    7  3
  DEL PEAK 10(6Q22.32) WILD-TYPE 22  2
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                            10                             24 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                             3                              2 
$`DEL PEAK 10(6Q22.32) MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-A7CR TCGA-FF-A7CX TCGA-G8-6325 TCGA-G8-6906 
        0.20         0.82        10.29        12.66        51.98       211.23 
TCGA-G8-6909 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
      106.09        42.71        57.17        25.91 

$`DEL PEAK 10(6Q22.32) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 
       35.54        31.10        31.73        24.69         4.14        27.35 
TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 
       22.32         9.80        26.01         4.57        41.16        47.38 
TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       19.56       196.60       150.51        98.07        36.13        43.86 

  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                           0.2                            0.2 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                        211.23                         196.60 
  DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE 
                         34.31                          25.35 
[1] "0.2 - 211.2 (34.3)" "0.2 - 196.6 (25.4)"
[1] "hr=" "1.6"
D22V2, continuous
D22V3, binary
                                cls
clus                              0  1
  DEL PEAK 10(6Q22.32) MUTATED    4  6
  DEL PEAK 10(6Q22.32) WILD-TYPE 14 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.32) MUTATED      4    6
  DEL PEAK 10(6Q22.32) WILD-TYPE   14   11
        clus
vv       DEL PEAK 10(6Q22.32) MUTATED DEL PEAK 10(6Q22.32) WILD-TYPE
  FEMALE                            4                             14
  MALE                              6                             11
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q22.32) MUTATED       4                         0     6
  DEL PEAK 10(6Q22.32) WILD-TYPE    14                         1    10
D22V4, multiclass
                           clus
vv                          DEL PEAK 10(6Q22.32) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          DEL PEAK 10(6Q22.32) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = DEL PEAK 11(6Q23.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(6Q23.3) MUTATED    6  2
  DEL PEAK 11(6Q23.3) WILD-TYPE 23  3
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                            8                            26 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                            2                             3 
$`DEL PEAK 11(6Q23.3) MUTATED`
TCGA-FA-A82F TCGA-FF-A7CX TCGA-G8-6325 TCGA-G8-6906 TCGA-G8-6909 TCGA-GR-A4D5 
        0.82        12.66        51.98       211.23       106.09        42.71 
TCGA-GR-A4D9 TCGA-RQ-A68N 
       57.17        25.91 

$`DEL PEAK 11(6Q23.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        0.72        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 
       27.35        22.32         9.80        10.29        26.01         4.57 
TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
       41.16        47.38        19.56       196.60       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D6 
       36.13        43.86 

  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                         0.82                          0.20 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE 
                       47.345                        23.505 
[1] "0.8 - 211.2 (47.3)" "0.2 - 196.6 (23.5)"
[1] "hr=" "1.9"
D23V2, continuous
D23V3, binary
                               cls
clus                             0  1
  DEL PEAK 11(6Q23.3) MUTATED    3  5
  DEL PEAK 11(6Q23.3) WILD-TYPE 15 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q23.3) MUTATED      3    5
  DEL PEAK 11(6Q23.3) WILD-TYPE   15   12
        clus
vv       DEL PEAK 11(6Q23.3) MUTATED DEL PEAK 11(6Q23.3) WILD-TYPE
  FEMALE                           3                            15
  MALE                             5                            12
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q23.3) MUTATED       2                         0     6
  DEL PEAK 11(6Q23.3) WILD-TYPE    16                         1    10
D23V4, multiclass
                           clus
vv                          DEL PEAK 11(6Q23.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               6
                           clus
vv                          DEL PEAK 11(6Q23.3) WILD-TYPE
  ASIAN                                                16
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = DEL PEAK 13(8P23.2) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(8P23.2) MUTATED    6  0
  DEL PEAK 13(8P23.2) WILD-TYPE 23  5
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                            6                            28 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                            0                             5 
$`DEL PEAK 13(8P23.2) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8047 TCGA-GR-A4D6 TCGA-RQ-A68N 
        0.20         0.72         0.82         4.14        43.86        25.91 

$`DEL PEAK 13(8P23.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34        14.99         0.20        13.48        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.10        31.73        24.69        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
       98.07        36.13        42.71        57.17 

  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                        43.86                        211.23 
  DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE 
                        2.480                        29.225 
[1] "0.2 - 43.9 (2.5)"   "0.2 - 211.2 (29.2)"
[1] "hr="     "7.6e+07"
D24V2, continuous
D24V3, binary
                               cls
clus                             0  1
  DEL PEAK 13(8P23.2) MUTATED    6  1
  DEL PEAK 13(8P23.2) WILD-TYPE 12 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8P23.2) MUTATED      6    1
  DEL PEAK 13(8P23.2) WILD-TYPE   12   16
        clus
vv       DEL PEAK 13(8P23.2) MUTATED DEL PEAK 13(8P23.2) WILD-TYPE
  FEMALE                           6                            12
  MALE                             1                            16
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(8P23.2) MUTATED       5                         0     2
  DEL PEAK 13(8P23.2) WILD-TYPE    13                         1    14
D24V4, multiclass
                           clus
vv                          DEL PEAK 13(8P23.2) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               2
                           clus
vv                          DEL PEAK 13(8P23.2) WILD-TYPE
  ASIAN                                                13
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = DEL PEAK 14(8Q12.1) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(8Q12.1) MUTATED    5  1
  DEL PEAK 14(8Q12.1) WILD-TYPE 24  4
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            6                            28 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                            1                             4 
$`DEL PEAK 14(8Q12.1) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8047 TCGA-FF-A7CR TCGA-GR-7353 TCGA-RQ-A68N 
        0.20        13.48         4.14        10.29        98.07        25.91 

$`DEL PEAK 14(8Q12.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        14.99         0.20         0.72         0.82 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        31.73        24.69        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        9.80        26.01        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       36.13        42.71        43.86        57.17 

  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                        98.07                        211.23 
  DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE 
                       11.885                        29.225 
[1] "0.2 - 98.1 (11.9)"  "0.2 - 211.2 (29.2)"
[1] "hr=" "3.9"
D25V2, continuous
D25V3, binary
                               cls
clus                             0  1
  DEL PEAK 14(8Q12.1) MUTATED    4  3
  DEL PEAK 14(8Q12.1) WILD-TYPE 14 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8Q12.1) MUTATED      4    3
  DEL PEAK 14(8Q12.1) WILD-TYPE   14   14
        clus
vv       DEL PEAK 14(8Q12.1) MUTATED DEL PEAK 14(8Q12.1) WILD-TYPE
  FEMALE                           4                            14
  MALE                             3                            14
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8Q12.1) MUTATED       4                         0     3
  DEL PEAK 14(8Q12.1) WILD-TYPE    14                         1    13
D25V4, multiclass
                           clus
vv                          DEL PEAK 14(8Q12.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          DEL PEAK 14(8Q12.1) WILD-TYPE
  ASIAN                                                14
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = DEL PEAK 15(9P21.3) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(9P21.3) MUTATED   11  2
  DEL PEAK 15(9P21.3) WILD-TYPE 18  3
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                           13                            21 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                            2                             3 
$`DEL PEAK 15(9P21.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-A7CQ 
       14.99        13.48         0.72        31.10         4.14         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-A4D6 TCGA-GR-A4D9 
       10.29        26.01        51.98       211.23        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

$`DEL PEAK 15(9P21.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8041 
        4.34         4.34         0.20         0.20         0.82        35.54 
TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CX TCGA-FM-8000 
       31.73        24.69        27.35        22.32        12.66         4.57 
TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       41.16        47.38        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
       98.07        36.13        42.71 

  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                         0.72                          0.20 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE 
                        25.91                         27.35 
[1] "0.7 - 211.2 (25.9)" "0.2 - 196.6 (27.4)"
[1] "hr=" "1.5"
D26V2, continuous
D26V3, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P21.3) MUTATED    6  7
  DEL PEAK 15(9P21.3) WILD-TYPE 12 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P21.3) MUTATED      6    7
  DEL PEAK 15(9P21.3) WILD-TYPE   12   10
        clus
vv       DEL PEAK 15(9P21.3) MUTATED DEL PEAK 15(9P21.3) WILD-TYPE
  FEMALE                           6                            12
  MALE                             7                            10
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P21.3) MUTATED       9                         0     4
  DEL PEAK 15(9P21.3) WILD-TYPE     9                         1    12
D26V4, multiclass
                           clus
vv                          DEL PEAK 15(9P21.3) MUTATED
  ASIAN                                               9
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               4
                           clus
vv                          DEL PEAK 15(9P21.3) WILD-TYPE
  ASIAN                                                 9
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = DEL PEAK 16(10Q23.31) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(10Q23.31) MUTATED    4  1
  DEL PEAK 16(10Q23.31) WILD-TYPE 25  4
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              5                              29 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                              1                               4 
$`DEL PEAK 16(10Q23.31) MUTATED`
TCGA-FA-A7Q1 TCGA-G8-6907 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
        0.72        19.56        98.07        36.13        43.86 

$`DEL PEAK 16(10Q23.31) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        0.82        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 
        4.57        41.16        51.98        47.38       211.23       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-A4D5 TCGA-GR-A4D9 TCGA-RQ-A68N 
      196.60       150.51        42.71        57.17        25.91 

  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                           0.72                            0.20 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                          98.07                          211.23 
  DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE 
                          36.13                           25.91 
[1] "0.7 - 98.1 (36.1)"  "0.2 - 211.2 (25.9)"
[1] "hr=" "2.3"
D27V2, continuous
D27V3, binary
                                 cls
clus                               0  1
  DEL PEAK 16(10Q23.31) MUTATED    4  1
  DEL PEAK 16(10Q23.31) WILD-TYPE 14 16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(10Q23.31) MUTATED      4    1
  DEL PEAK 16(10Q23.31) WILD-TYPE   14   16
        clus
vv       DEL PEAK 16(10Q23.31) MUTATED DEL PEAK 16(10Q23.31) WILD-TYPE
  FEMALE                             4                              14
  MALE                               1                              16
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q23.31) MUTATED       2                         0     3
  DEL PEAK 16(10Q23.31) WILD-TYPE    16                         1    13
D27V4, multiclass
                           clus
vv                          DEL PEAK 16(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 3
                           clus
vv                          DEL PEAK 16(10Q23.31) WILD-TYPE
  ASIAN                                                  16
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  13
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = DEL PEAK 17(12P13.2) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(12P13.2) MUTATED    7  0
  DEL PEAK 17(12P13.2) WILD-TYPE 22  5
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             7                             27 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                             0                              5 
$`DEL PEAK 17(12P13.2) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FF-8043 TCGA-FF-A7CQ TCGA-GR-A4D4 TCGA-GR-A4D6 
        0.20        13.48        31.73         9.80        36.13        43.86 
TCGA-RQ-A68N 
       25.91 

$`DEL PEAK 17(12P13.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        14.99         0.20         0.72         0.82 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D9 
       98.07        42.71        57.17 

  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                           0.2                            0.2 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                         43.86                         211.23 
  DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE 
                         25.91                          26.01 
[1] "0.2 - 43.9 (25.9)"  "0.2 - 211.2 (26.0)"
[1] "hr="     "2.4e+08"
D28V2, continuous
D28V3, binary
                                cls
clus                              0  1
  DEL PEAK 17(12P13.2) MUTATED    5  2
  DEL PEAK 17(12P13.2) WILD-TYPE 13 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(12P13.2) MUTATED      5    2
  DEL PEAK 17(12P13.2) WILD-TYPE   13   15
        clus
vv       DEL PEAK 17(12P13.2) MUTATED DEL PEAK 17(12P13.2) WILD-TYPE
  FEMALE                            5                             13
  MALE                              2                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(12P13.2) MUTATED       5                         0     2
  DEL PEAK 17(12P13.2) WILD-TYPE    13                         1    14
D28V4, multiclass
                           clus
vv                          DEL PEAK 17(12P13.2) MUTATED
  ASIAN                                                5
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK 17(12P13.2) WILD-TYPE
  ASIAN                                                 13
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK 18(13Q14.2) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(13Q14.2) MUTATED    2  1
  DEL PEAK 18(13Q14.2) WILD-TYPE 27  4
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             3                             31 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                             1                              4 
$`DEL PEAK 18(13Q14.2) MUTATED`
TCGA-FF-8043 TCGA-G8-6907 TCGA-GR-A4D4 
       31.73        19.56        36.13 

$`DEL PEAK 18(13Q14.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 
        0.72         0.82        35.54        31.10        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 
        4.57        41.16        51.98        47.38       211.23       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      196.60       150.51        98.07        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                         19.56                           0.20 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                         36.13                         211.23 
  DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE 
                         31.73                          25.91 
[1] "19.6 - 36.1 (31.7)" "0.2 - 211.2 (25.9)"
[1] "hr=" "6.6"
D29V2, continuous
D29V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(13Q14.2) MUTATED    3  0
  DEL PEAK 18(13Q14.2) WILD-TYPE 15 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(13Q14.2) MUTATED      3    0
  DEL PEAK 18(13Q14.2) WILD-TYPE   15   17
        clus
vv       DEL PEAK 18(13Q14.2) MUTATED DEL PEAK 18(13Q14.2) WILD-TYPE
  FEMALE                            3                             15
  MALE                              0                             17
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(13Q14.2) MUTATED       1                         0     2
  DEL PEAK 18(13Q14.2) WILD-TYPE    17                         1    14
D29V4, multiclass
                           clus
vv                          DEL PEAK 18(13Q14.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK 18(13Q14.2) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = DEL PEAK 19(15Q21.1) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(15Q21.1) MUTATED    7  1
  DEL PEAK 19(15Q21.1) WILD-TYPE 22  4
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                             8                             26 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                             1                              4 
$`DEL PEAK 19(15Q21.1) MUTATED`
TCGA-FA-8693 TCGA-FA-A6HO TCGA-FF-8043 TCGA-G8-6907 TCGA-GR-7351 TCGA-GR-7353 
        4.34         0.20        31.73        19.56       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D6 
       36.13        43.86 

$`DEL PEAK 19(15Q21.1) WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34        14.99         0.20        13.48         0.72         0.82 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
       35.54        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 
        9.80        10.29        26.01        12.66         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-A4D5 
       51.98        47.38       211.23       106.09       196.60        42.71 
TCGA-GR-A4D9 TCGA-RQ-A68N 
       57.17        25.91 

  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                           0.2                            0.2 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                        150.51                         211.23 
  DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE 
                         33.93                          25.30 
[1] "0.2 - 150.5 (33.9)" "0.2 - 211.2 (25.3)"
[1] "hr=" "1.1"
D30V2, continuous
D30V3, binary
                                cls
clus                              0  1
  DEL PEAK 19(15Q21.1) MUTATED    7  2
  DEL PEAK 19(15Q21.1) WILD-TYPE 11 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(15Q21.1) MUTATED      7    2
  DEL PEAK 19(15Q21.1) WILD-TYPE   11   15
        clus
vv       DEL PEAK 19(15Q21.1) MUTATED DEL PEAK 19(15Q21.1) WILD-TYPE
  FEMALE                            7                             11
  MALE                              2                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(15Q21.1) MUTATED       3                         0     6
  DEL PEAK 19(15Q21.1) WILD-TYPE    15                         1    10
D30V4, multiclass
                           clus
vv                          DEL PEAK 19(15Q21.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                6
                           clus
vv                          DEL PEAK 19(15Q21.1) WILD-TYPE
  ASIAN                                                 15
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = DEL PEAK 20(16P13.13) MUTATION ANALYSIS
D31V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 20(16P13.13) MUTATED    4  0
  DEL PEAK 20(16P13.13) WILD-TYPE 25  5
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              4                              30 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                              0                               5 
$`DEL PEAK 20(16P13.13) MUTATED`
TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8043 TCGA-FM-8000 
        0.20        35.54        31.73         4.57 

$`DEL PEAK 20(16P13.13) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
        0.82        31.10        24.69         4.14        27.35        22.32 
TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-G8-6324 TCGA-G8-6325 
        9.80        10.29        26.01        12.66        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       98.07        36.13        42.71        43.86        57.17        25.91 

  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                            0.2                             0.2 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                          35.54                          211.23 
  DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE 
                          18.15                           25.96 
[1] "0.2 - 35.5 (18.1)"  "0.2 - 211.2 (26.0)"
[1] "hr="     "7.6e+07"
D31V2, continuous
D31V3, binary
                                 cls
clus                               0  1
  DEL PEAK 20(16P13.13) MUTATED    4  0
  DEL PEAK 20(16P13.13) WILD-TYPE 14 17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(16P13.13) MUTATED      4    0
  DEL PEAK 20(16P13.13) WILD-TYPE   14   17
        clus
vv       DEL PEAK 20(16P13.13) MUTATED DEL PEAK 20(16P13.13) WILD-TYPE
  FEMALE                             4                              14
  MALE                               0                              17
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(16P13.13) MUTATED       3                         0     1
  DEL PEAK 20(16P13.13) WILD-TYPE    15                         1    15
D31V4, multiclass
                           clus
vv                          DEL PEAK 20(16P13.13) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 1
                           clus
vv                          DEL PEAK 20(16P13.13) WILD-TYPE
  ASIAN                                                  15
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK 21(16Q23.1) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(16Q23.1) MUTATED    5  0
  DEL PEAK 21(16Q23.1) WILD-TYPE 24  5
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             5                             29 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                             0                              5 
$`DEL PEAK 21(16Q23.1) MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 
        0.20         0.20        31.73         4.14        36.13 

$`DEL PEAK 21(16Q23.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A7DS TCGA-FA-A7Q1 TCGA-FA-A82F 
        4.34         4.34        14.99        13.48         0.72         0.82 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       35.54        31.10        24.69        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       98.07        42.71        43.86        57.17        25.91 

  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                          0.20                           0.72 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                         36.13                         211.23 
  DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE 
                          4.14                          26.01 
[1] "0.2 - 36.1 (4.1)"   "0.7 - 211.2 (26.0)"
[1] "hr="     "7.6e+07"
D32V2, continuous
D32V3, binary
                                cls
clus                              0  1
  DEL PEAK 21(16Q23.1) MUTATED    4  1
  DEL PEAK 21(16Q23.1) WILD-TYPE 14 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(16Q23.1) MUTATED      4    1
  DEL PEAK 21(16Q23.1) WILD-TYPE   14   16
        clus
vv       DEL PEAK 21(16Q23.1) MUTATED DEL PEAK 21(16Q23.1) WILD-TYPE
  FEMALE                            4                             14
  MALE                              1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(16Q23.1) MUTATED       4                         0     1
  DEL PEAK 21(16Q23.1) WILD-TYPE    14                         1    15
D32V4, multiclass
                           clus
vv                          DEL PEAK 21(16Q23.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                1
                           clus
vv                          DEL PEAK 21(16Q23.1) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK 22(17P13.1) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(17P13.1) MUTATED    6  0
  DEL PEAK 22(17P13.1) WILD-TYPE 23  5
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                             6                             28 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                             0                              5 
$`DEL PEAK 22(17P13.1) MUTATED`
TCGA-FA-A6HO TCGA-FA-A82F TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D4 TCGA-RQ-A68N 
        0.20         0.82        31.73         4.14        36.13        25.91 

$`DEL PEAK 22(17P13.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34        14.99         0.20        13.48         0.72 
TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       35.54        31.10        24.69        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       10.29        26.01        12.66         4.57        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       47.38       211.23        19.56       106.09       196.60       150.51 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       98.07        42.71        43.86        57.17 

  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                           0.2                            0.2 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                         36.13                         211.23 
  DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE 
                        15.025                         26.680 
[1] "0.2 - 36.1 (15.0)"  "0.2 - 211.2 (26.7)"
[1] "hr="     "8.2e+07"
D33V2, continuous
D33V3, binary
                                cls
clus                              0  1
  DEL PEAK 22(17P13.1) MUTATED    5  1
  DEL PEAK 22(17P13.1) WILD-TYPE 13 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(17P13.1) MUTATED      5    1
  DEL PEAK 22(17P13.1) WILD-TYPE   13   16
        clus
vv       DEL PEAK 22(17P13.1) MUTATED DEL PEAK 22(17P13.1) WILD-TYPE
  FEMALE                            5                             13
  MALE                              1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(17P13.1) MUTATED       4                         0     2
  DEL PEAK 22(17P13.1) WILD-TYPE    14                         1    14
D33V4, multiclass
                           clus
vv                          DEL PEAK 22(17P13.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK 22(17P13.1) WILD-TYPE
  ASIAN                                                 14
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK 23(17Q24.1) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(17Q24.1) MUTATED    2  1
  DEL PEAK 23(17Q24.1) WILD-TYPE 27  4
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             3                             31 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                             1                              4 
$`DEL PEAK 23(17Q24.1) MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-G8-6907 
       14.99         4.57        19.56 

$`DEL PEAK 23(17Q24.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS TCGA-FA-A7Q1 
        4.34         4.34         0.20         0.20        13.48         0.72 
TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        0.82        35.54        31.10        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX 
       27.35        22.32         9.80        10.29        26.01        12.66 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 
       41.16        51.98        47.38       211.23       106.09       196.60 
TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
      150.51        98.07        36.13        42.71        43.86        57.17 
TCGA-RQ-A68N 
       25.91 

  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                          4.57                           0.20 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                         19.56                         211.23 
  DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE 
                         14.99                          27.35 
[1] "4.6 - 19.6 (15.0)"  "0.2 - 211.2 (27.4)"
[1] "hr=" "15" 
D34V2, continuous
D34V3, binary
                                cls
clus                              0  1
  DEL PEAK 23(17Q24.1) MUTATED    2  1
  DEL PEAK 23(17Q24.1) WILD-TYPE 16 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(17Q24.1) MUTATED      2    1
  DEL PEAK 23(17Q24.1) WILD-TYPE   16   16
        clus
vv       DEL PEAK 23(17Q24.1) MUTATED DEL PEAK 23(17Q24.1) WILD-TYPE
  FEMALE                            2                             16
  MALE                              1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(17Q24.1) MUTATED       1                         0     2
  DEL PEAK 23(17Q24.1) WILD-TYPE    17                         1    14
D34V4, multiclass
                           clus
vv                          DEL PEAK 23(17Q24.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK 23(17Q24.1) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK 24(19P13.2) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(19P13.2) MUTATED    3  0
  DEL PEAK 24(19P13.2) WILD-TYPE 26  5
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             3                             31 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                             0                              5 
$`DEL PEAK 24(19P13.2) MUTATED`
TCGA-FF-A7CX TCGA-GR-A4D4 TCGA-RQ-A68N 
       12.66        36.13        25.91 

$`DEL PEAK 24(19P13.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8046 
        0.72         0.82        35.54        31.10        31.73        24.69 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW 
        4.14        27.35        22.32         9.80        10.29        26.01 
TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
        4.57        41.16        51.98        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 
      106.09       196.60       150.51        98.07        42.71        43.86 
TCGA-GR-A4D9 
       57.17 

  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                         12.66                           0.20 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                         36.13                         211.23 
  DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE 
                         25.91                          26.01 
[1] "12.7 - 36.1 (25.9)" "0.2 - 211.2 (26.0)"
[1] "hr="     "7.9e+07"
D35V2, continuous
D35V3, binary
                                cls
clus                              0  1
  DEL PEAK 24(19P13.2) MUTATED    1  2
  DEL PEAK 24(19P13.2) WILD-TYPE 17 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(19P13.2) MUTATED      1    2
  DEL PEAK 24(19P13.2) WILD-TYPE   17   15
        clus
vv       DEL PEAK 24(19P13.2) MUTATED DEL PEAK 24(19P13.2) WILD-TYPE
  FEMALE                            1                             17
  MALE                              2                             15
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(19P13.2) MUTATED       1                         0     2
  DEL PEAK 24(19P13.2) WILD-TYPE    17                         1    14
D35V4, multiclass
                           clus
vv                          DEL PEAK 24(19P13.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK 24(19P13.2) WILD-TYPE
  ASIAN                                                 17
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK 25(19Q13.2) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(19Q13.2) MUTATED    3  0
  DEL PEAK 25(19Q13.2) WILD-TYPE 26  5
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             3                             31 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                             0                              5 
$`DEL PEAK 25(19Q13.2) MUTATED`
TCGA-FF-8042 TCGA-FF-A7CX TCGA-GR-A4D9 
       31.10        12.66        57.17 

$`DEL PEAK 25(19Q13.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FA-A7DS 
        4.34         4.34        14.99         0.20         0.20        13.48 
TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8046 TCGA-FF-8047 
        0.72         0.82        35.54        31.73        24.69         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FM-8000 
       27.35        22.32         9.80        10.29        26.01         4.57 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
       41.16        51.98        47.38       211.23        19.56       106.09 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      196.60       150.51        98.07        36.13        42.71        43.86 
TCGA-RQ-A68N 
       25.91 

  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                         12.66                           0.20 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                         57.17                         211.23 
  DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE 
                         31.10                          25.91 
[1] "12.7 - 57.2 (31.1)" "0.2 - 211.2 (25.9)"
[1] "hr="     "7.8e+07"
D36V2, continuous
D36V3, binary
                                cls
clus                              0  1
  DEL PEAK 25(19Q13.2) MUTATED    2  1
  DEL PEAK 25(19Q13.2) WILD-TYPE 16 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(19Q13.2) MUTATED      2    1
  DEL PEAK 25(19Q13.2) WILD-TYPE   16   16
        clus
vv       DEL PEAK 25(19Q13.2) MUTATED DEL PEAK 25(19Q13.2) WILD-TYPE
  FEMALE                            2                             16
  MALE                              1                             16
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(19Q13.2) MUTATED       2                         0     1
  DEL PEAK 25(19Q13.2) WILD-TYPE    16                         1    15
D36V4, multiclass
                           clus
vv                          DEL PEAK 25(19Q13.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                1
                           clus
vv                          DEL PEAK 25(19Q13.2) WILD-TYPE
  ASIAN                                                 16
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK 26(22Q13.31) MUTATION ANALYSIS
D37V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 26(22Q13.31) MUTATED    5  0
  DEL PEAK 26(22Q13.31) WILD-TYPE 24  5
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              5                              29 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                              0                               5 
$`DEL PEAK 26(22Q13.31) MUTATED`
TCGA-FA-A6HO TCGA-FA-A7Q1 TCGA-FA-A82F TCGA-FF-8043 TCGA-G8-6325 
        0.20         0.72         0.82        31.73        51.98 

$`DEL PEAK 26(22Q13.31) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A7DS TCGA-FF-8041 
        4.34         4.34        14.99         0.20        13.48        35.54 
TCGA-FF-8042 TCGA-FF-8046 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FF-A7CQ 
       31.10        24.69         4.14        27.35        22.32         9.80 
TCGA-FF-A7CR TCGA-FF-A7CW TCGA-FF-A7CX TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 
       10.29        26.01        12.66         4.57        41.16        47.38 
TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
      211.23        19.56       106.09       196.60       150.51        98.07 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 TCGA-RQ-A68N 
       36.13        42.71        43.86        57.17        25.91 

  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                            0.2                             0.2 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                          51.98                          211.23 
  DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE 
                           0.82                           26.01 
[1] "0.2 - 52.0 (0.8)"   "0.2 - 211.2 (26.0)"
[1] "hr="     "7.6e+07"
D37V2, continuous
D37V3, binary
                                 cls
clus                               0  1
  DEL PEAK 26(22Q13.31) MUTATED    4  1
  DEL PEAK 26(22Q13.31) WILD-TYPE 14 16
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 26(22Q13.31) MUTATED      4    1
  DEL PEAK 26(22Q13.31) WILD-TYPE   14   16
        clus
vv       DEL PEAK 26(22Q13.31) MUTATED DEL PEAK 26(22Q13.31) WILD-TYPE
  FEMALE                             4                              14
  MALE                               1                              16
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(22Q13.31) MUTATED       4                         0     1
  DEL PEAK 26(22Q13.31) WILD-TYPE    14                         1    15
D37V4, multiclass
                           clus
vv                          DEL PEAK 26(22Q13.31) MUTATED
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 1
                           clus
vv                          DEL PEAK 26(22Q13.31) WILD-TYPE
  ASIAN                                                  14
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
