[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/10005821/DLBC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/DLBC-TP/10013676/transformed.cor.cli.txt"

nPatients in clinical file=33, in cluster file=28, common to both=25
[1] "Reduce the number of clustering variables from 26 to 24."
[1] 24 25
[1] "AMP PEAK 1(1Q31.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           9                           16 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           9                           16 
[1] "AMP PEAK 2(2P15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         7                         18 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         7                         18 
[1] "AMP PEAK 3(3Q27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           6                           19 
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           6                           19 
[1] "AMP PEAK 4(8Q24.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            6                            19 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            6                            19 
[1] "AMP PEAK 5(12Q13.12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             4                             21 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             4                             21 
[1] "AMP PEAK 6(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            5                            20 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            5                            20 
[1] "AMP PEAK 7(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           5                           20 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           5                           20 
[1] "DEL PEAK  1(1P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            3                            22 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            3                            22 
[1] "DEL PEAK  2(1P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            6                            19 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            6                            19 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          6                          19 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          6                          19 
[1] "DEL PEAK  4(2Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            5                            20 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            5                            20 
[1] "DEL PEAK  5(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            7                            18 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            7                            18 
[1] "DEL PEAK  6(6Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            5                            20 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            5                            20 
[1] "DEL PEAK  8(8P23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                            3                            22 
  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                            3                            22 
[1] "DEL PEAK  9(8Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                            3                            22 
  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                            3                            22 
[1] "DEL PEAK 10(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            7                            18 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            7                            18 
[1] "DEL PEAK 11(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              4                              21 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              4                              21 
[1] "DEL PEAK 12(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             3                             22 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             3                             22 
[1] "DEL PEAK 13(13Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             4                             21 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             4                             21 
[1] "DEL PEAK 14(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             8                             17 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             8                             17 
[1] "DEL PEAK 15(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             8                             17 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             8                             17 
[1] "DEL PEAK 16(16P13.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              4                              21 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              4                              21 
[1] "DEL PEAK 17(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             5                             20 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             5                             20 
[1] "DEL PEAK 18(17Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             3                             22 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             3                             22 
[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 25 columns.

[1] "Batch" "17"   
[1] "Last Follow UP"
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 
         132          132          456            6            6         1081 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
         946          965          126          832          679          139 
TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 TCGA-G8-6909 
          NA         1581         1441           NA           NA         3227 
TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
        5980         3872         2254          812          751          911 
TCGA-GR-A4D9 
        1408 
Variable 1:'AGE':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=20,	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=1,	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=2,	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=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'BATCH.NUMBER':	nDistinctValues=3,	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 25 columns, 1 survival variables, and 3 non-survival variables.
AGE, nv=19, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(1Q31.1) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 1(1Q31.1) MUTATED    9  0
  AMP PEAK 1(1Q31.1) WILD-TYPE 12  4
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           9                           16 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                           0                            4 
$`AMP PEAK 1(1Q31.1) MUTATED`
TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FF-8047 TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6914 
        4.34         0.20         4.14         4.57        51.98       196.60 
TCGA-GR-7353 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        29.95        46.29 

$`AMP PEAK 1(1Q31.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        4.34        14.99         0.20        35.54        31.10        31.73 
TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6907 
       27.35        22.32        41.16        47.38       211.23        19.56 
TCGA-G8-6909 TCGA-GR-7351 TCGA-GR-A4D4 TCGA-GR-A4D5 
      106.09       127.30        26.70        24.69 

  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                         0.2                          0.2 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                      196.60                       211.23 
  AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE 
                      29.950                       29.225 
[1] "0.2 - 196.6 (29.9)" "0.2 - 211.2 (29.2)"
[1] "hr="   "1e+09"
D1V2, continuous
D1V3, binary
                              cls
clus                            0  1
  AMP PEAK 1(1Q31.1) MUTATED    4  5
  AMP PEAK 1(1Q31.1) WILD-TYPE 10  6
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(1Q31.1) MUTATED      4    5
  AMP PEAK 1(1Q31.1) WILD-TYPE   10    6
        clus
vv       AMP PEAK 1(1Q31.1) MUTATED AMP PEAK 1(1Q31.1) WILD-TYPE
  FEMALE                          4                           10
  MALE                            5                            6
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(1Q31.1) MUTATED       3                         0     6
  AMP PEAK 1(1Q31.1) WILD-TYPE     7                         1     8
D1V4, multiclass
                           clus
vv                          AMP PEAK 1(1Q31.1) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                              6
                           clus
vv                          AMP PEAK 1(1Q31.1) WILD-TYPE
  ASIAN                                                7
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                8
[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(2P15) MUTATION ANALYSIS
D2V1, survival
                            sevent
clus2                         0  1
  AMP PEAK 2(2P15) MUTATED    5  2
  AMP PEAK 2(2P15) WILD-TYPE 16  2
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         7                         18 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                         2                          2 
$`AMP PEAK 2(2P15) MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8061 TCGA-FM-8000 TCGA-G8-6907 
       14.99        35.54        31.73        27.35         4.57        19.56 
TCGA-G8-6909 
      106.09 

$`AMP PEAK 2(2P15) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8047 
        4.34         4.34         0.20         0.20        31.10         4.14 
TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6914 
       22.32        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 
      127.30        74.10        26.70        24.69        29.95        46.29 

  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                      4.57                       0.20 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                    106.09                     211.23 
  AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE 
                    27.350                     30.525 
[1] "4.6 - 106.1 (27.4)" "0.2 - 211.2 (30.5)"
[1] "hr=" "8.2"
D2V2, continuous
D2V3, binary
                            cls
clus                          0  1
  AMP PEAK 2(2P15) MUTATED    4  3
  AMP PEAK 2(2P15) WILD-TYPE 10  8
[1] "tbl2"
                            cls
clus                         [,1] [,2]
  AMP PEAK 2(2P15) MUTATED      4    3
  AMP PEAK 2(2P15) WILD-TYPE   10    8
        clus
vv       AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  FEMALE                        4                         10
  MALE                          3                          8
[1] 2 2
[1] FALSE
                            vv
clus                         ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(2P15) MUTATED       4                         0     3
  AMP PEAK 2(2P15) WILD-TYPE     6                         1    11
D2V4, multiclass
                           clus
vv                          AMP PEAK 2(2P15) MUTATED AMP PEAK 2(2P15) WILD-TYPE
  ASIAN                                            4                          6
  BLACK OR AFRICAN AMERICAN                        0                          1
  WHITE                                            3                         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(3) Variable = AMP PEAK 3(3Q27.3) MUTATION ANALYSIS
D3V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 3(3Q27.3) MUTATED    6  0
  AMP PEAK 3(3Q27.3) WILD-TYPE 15  4
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           6                           19 
  AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE 
                           0                            4 
$`AMP PEAK 3(3Q27.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FF-8042 TCGA-G8-6914 TCGA-GR-A4D4 TCGA-GR-A4D6 
       14.99         0.20        31.10       196.60        26.70        29.95 

$`AMP PEAK 3(3Q27.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 
        4.34         4.34         0.20        35.54        31.73         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         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       127.30        74.10        24.69 
TCGA-GR-A4D9 
       46.29 

  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 
                      28.325                       31.730 
[1] "0.2 - 196.6 (28.3)" "0.2 - 211.2 (31.7)"
[1] "hr="     "2.6e+08"
D3V2, continuous
D3V3, binary
                              cls
clus                            0  1
  AMP PEAK 3(3Q27.3) MUTATED    4  2
  AMP PEAK 3(3Q27.3) WILD-TYPE 10  9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.3) MUTATED      4    2
  AMP PEAK 3(3Q27.3) WILD-TYPE   10    9
        clus
vv       AMP PEAK 3(3Q27.3) MUTATED AMP PEAK 3(3Q27.3) WILD-TYPE
  FEMALE                          4                           10
  MALE                            2                            9
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(3Q27.3) MUTATED       4                         0     2
  AMP PEAK 3(3Q27.3) WILD-TYPE     6                         1    12
D3V4, multiclass
                           clus
vv                          AMP PEAK 3(3Q27.3) MUTATED
  ASIAN                                              4
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                              2
                           clus
vv                          AMP PEAK 3(3Q27.3) WILD-TYPE
  ASIAN                                                6
  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(8Q24.12) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 4(8Q24.12) MUTATED    6  0
  AMP PEAK 4(8Q24.12) WILD-TYPE 15  4
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            6                            19 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                            0                             4 
$`AMP PEAK 4(8Q24.12) MUTATED`
TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8061 TCGA-GR-7353 
        0.20        35.54        31.10        31.73        27.35        74.10 

$`AMP PEAK 4(8Q24.12) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8047 TCGA-FF-8062 
        4.34         4.34        14.99         0.20         4.14        22.32 
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-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 
      106.09       196.60       127.30        26.70        24.69        29.95 
TCGA-GR-A4D9 
       46.29 

  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                          0.2                           0.2 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                        74.10                        211.23 
  AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE 
                       31.415                        26.700 
[1] "0.2 - 74.1 (31.4)"  "0.2 - 211.2 (26.7)"
[1] "hr="     "2.7e+08"
D4V2, continuous
D4V3, binary
                               cls
clus                             0  1
  AMP PEAK 4(8Q24.12) MUTATED    4  2
  AMP PEAK 4(8Q24.12) WILD-TYPE 10  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 4(8Q24.12) MUTATED      4    2
  AMP PEAK 4(8Q24.12) WILD-TYPE   10    9
        clus
vv       AMP PEAK 4(8Q24.12) MUTATED AMP PEAK 4(8Q24.12) WILD-TYPE
  FEMALE                           4                            10
  MALE                             2                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(8Q24.12) MUTATED       5                         0     1
  AMP PEAK 4(8Q24.12) WILD-TYPE     5                         1    13
D4V4, multiclass
                           clus
vv                          AMP PEAK 4(8Q24.12) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               1
                           clus
vv                          AMP PEAK 4(8Q24.12) WILD-TYPE
  ASIAN                                                 5
  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(5) Variable = AMP PEAK 5(12Q13.12) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 5(12Q13.12) MUTATED    4  0
  AMP PEAK 5(12Q13.12) WILD-TYPE 17  4
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             4                             21 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                             0                              4 
$`AMP PEAK 5(12Q13.12) MUTATED`
TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8043 TCGA-GR-A4D5 
       14.99        35.54        31.73        24.69 

$`AMP PEAK 5(12Q13.12) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8047 
        4.34         4.34         0.20         0.20        31.10         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         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       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        29.95        46.29 

  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                         14.99                           0.20 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                         35.54                         211.23 
  AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE 
                         28.21                          29.95 
[1] "15.0 - 35.5 (28.2)" "0.2 - 211.2 (29.9)"
[1] "hr="     "8.8e+07"
D5V2, continuous
D5V3, binary
                                cls
clus                              0  1
  AMP PEAK 5(12Q13.12) MUTATED    3  1
  AMP PEAK 5(12Q13.12) WILD-TYPE 11 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 5(12Q13.12) MUTATED      3    1
  AMP PEAK 5(12Q13.12) WILD-TYPE   11   10
        clus
vv       AMP PEAK 5(12Q13.12) MUTATED AMP PEAK 5(12Q13.12) WILD-TYPE
  FEMALE                            3                             11
  MALE                              1                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(12Q13.12) MUTATED       3                         0     1
  AMP PEAK 5(12Q13.12) WILD-TYPE     7                         1    13
D5V4, multiclass
                           clus
vv                          AMP PEAK 5(12Q13.12) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                1
                           clus
vv                          AMP PEAK 5(12Q13.12) WILD-TYPE
  ASIAN                                                  7
  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(6) Variable = AMP PEAK 6(16P11.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 6(16P11.2) MUTATED    4  1
  AMP PEAK 6(16P11.2) WILD-TYPE 17  3
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            5                            20 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                            1                             3 
$`AMP PEAK 6(16P11.2) MUTATED`
TCGA-FA-A4XK TCGA-FF-8043 TCGA-FM-8000 TCGA-G8-6909 TCGA-GR-A4D4 
       14.99        31.73         4.57       106.09        26.70 

$`AMP PEAK 6(16P11.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34         0.20         0.20        35.54        31.10 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
        4.14        27.35        22.32        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       127.30        74.10        24.69 
TCGA-GR-A4D6 TCGA-GR-A4D9 
       29.95        46.29 

  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                         4.57                          0.20 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                       106.09                        211.23 
  AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE 
                       26.700                        30.525 
[1] "4.6 - 106.1 (26.7)" "0.2 - 211.2 (30.5)"
[1] "hr=" "2.4"
D6V2, continuous
D6V3, binary
                               cls
clus                             0  1
  AMP PEAK 6(16P11.2) MUTATED    3  2
  AMP PEAK 6(16P11.2) WILD-TYPE 11  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(16P11.2) MUTATED      3    2
  AMP PEAK 6(16P11.2) WILD-TYPE   11    9
        clus
vv       AMP PEAK 6(16P11.2) MUTATED AMP PEAK 6(16P11.2) WILD-TYPE
  FEMALE                           3                            11
  MALE                             2                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(16P11.2) MUTATED       2                         0     3
  AMP PEAK 6(16P11.2) WILD-TYPE     8                         1    11
D6V4, multiclass
                           clus
vv                          AMP PEAK 6(16P11.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          AMP PEAK 6(16P11.2) WILD-TYPE
  ASIAN                                                 8
  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(XQ27.3) MUTATION ANALYSIS
D7V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 7(XQ27.3) MUTATED    5  0
  AMP PEAK 7(XQ27.3) WILD-TYPE 16  4
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           5                           20 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                           0                            4 
$`AMP PEAK 7(XQ27.3) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
       14.99         0.20        35.54        31.10        31.73 

$`AMP PEAK 7(XQ27.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HO TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 
        4.34         4.34         0.20         4.14        27.35        22.32 
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-A4D5 
      106.09       196.60       127.30        74.10        26.70        24.69 
TCGA-GR-A4D6 TCGA-GR-A4D9 
       29.95        46.29 

  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                         0.2                          0.2 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                       35.54                       211.23 
  AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE 
                       31.10                        28.65 
[1] "0.2 - 35.5 (31.1)"  "0.2 - 211.2 (28.6)"
[1] "hr="     "8.8e+07"
D7V2, continuous
D7V3, binary
                              cls
clus                            0  1
  AMP PEAK 7(XQ27.3) MUTATED    3  2
  AMP PEAK 7(XQ27.3) WILD-TYPE 11  9
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 7(XQ27.3) MUTATED      3    2
  AMP PEAK 7(XQ27.3) WILD-TYPE   11    9
        clus
vv       AMP PEAK 7(XQ27.3) MUTATED AMP PEAK 7(XQ27.3) WILD-TYPE
  FEMALE                          3                           11
  MALE                            2                            9
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(XQ27.3) MUTATED       5                         0     0
  AMP PEAK 7(XQ27.3) WILD-TYPE     5                         1    14
D7V4, multiclass
                           clus
vv                          AMP PEAK 7(XQ27.3) MUTATED
  ASIAN                                              5
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                              0
                           clus
vv                          AMP PEAK 7(XQ27.3) WILD-TYPE
  ASIAN                                                5
  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(8) Variable = DEL PEAK  1(1P22.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  1(1P22.1) MUTATED    3  0
  DEL PEAK  1(1P22.1) WILD-TYPE 18  4
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            3                            22 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                            0                             4 
$`DEL PEAK  1(1P22.1) MUTATED`
TCGA-FA-A6HO TCGA-G8-6325 TCGA-GR-7353 
        0.20        51.98        74.10 

$`DEL PEAK  1(1P22.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34        14.99         0.20        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
       31.73         4.14        27.35        22.32         4.57        41.16 
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       127.30 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        24.69        29.95        46.29 

  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                        74.10                        211.23 
  DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE 
                        51.98                         28.65 
[1] "0.2 - 74.1 (52.0)"  "0.2 - 211.2 (28.6)"
[1] "hr="     "2.5e+08"
D8V2, continuous
D8V3, binary
                               cls
clus                             0  1
  DEL PEAK  1(1P22.1) MUTATED    1  2
  DEL PEAK  1(1P22.1) WILD-TYPE 13  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  1(1P22.1) MUTATED      1    2
  DEL PEAK  1(1P22.1) WILD-TYPE   13    9
        clus
vv       DEL PEAK  1(1P22.1) MUTATED DEL PEAK  1(1P22.1) WILD-TYPE
  FEMALE                           1                            13
  MALE                             2                             9
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P22.1) MUTATED       1                         0     2
  DEL PEAK  1(1P22.1) WILD-TYPE     9                         1    12
D8V4, multiclass
                           clus
vv                          DEL PEAK  1(1P22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               2
                           clus
vv                          DEL PEAK  1(1P22.1) 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(9) Variable = DEL PEAK  2(1P13.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(1P13.1) MUTATED    5  1
  DEL PEAK  2(1P13.1) WILD-TYPE 16  3
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            6                            19 
  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK  2(1P13.1) MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-G8-6325 TCGA-G8-6909 TCGA-GR-7353 TCGA-GR-A4D6 
        0.20         0.20        51.98       106.09        74.10        29.95 

$`DEL PEAK  2(1P13.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8043 
        4.34         4.34        14.99        35.54        31.10        31.73 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 
        4.14        27.35        22.32         4.57        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       127.30        26.70        24.69 
TCGA-GR-A4D9 
       46.29 

  DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE 
                         0.20                          4.14 
  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 
                       40.965                        27.350 
[1] "0.2 - 106.1 (41.0)" "4.1 - 211.2 (27.4)"
[1] "hr=" "1.4"
D9V2, continuous
D9V3, binary
                               cls
clus                             0  1
  DEL PEAK  2(1P13.1) MUTATED    2  4
  DEL PEAK  2(1P13.1) WILD-TYPE 12  7
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P13.1) MUTATED      2    4
  DEL PEAK  2(1P13.1) WILD-TYPE   12    7
        clus
vv       DEL PEAK  2(1P13.1) MUTATED DEL PEAK  2(1P13.1) WILD-TYPE
  FEMALE                           2                            12
  MALE                             4                             7
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P13.1) MUTATED       3                         0     3
  DEL PEAK  2(1P13.1) WILD-TYPE     7                         1    11
D9V4, multiclass
                           clus
vv                          DEL PEAK  2(1P13.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          DEL PEAK  2(1P13.1) WILD-TYPE
  ASIAN                                                 7
  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(10) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D10V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  3(1Q43) MUTATED    6  0
  DEL PEAK  3(1Q43) WILD-TYPE 15  4
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          6                          19 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          0                           4 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-GR-A4D9 
        0.20         0.20        31.10        31.73         4.14        46.29 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8061 TCGA-FF-8062 
        4.34         4.34        14.99        35.54        27.35        22.32 
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-A4D5 
      106.09       196.60       127.30        74.10        26.70        24.69 
TCGA-GR-A4D6 
       29.95 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       0.20                        4.34 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      46.29                      211.23 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                      17.62                       29.95 
[1] "0.2 - 46.3 (17.6)"  "4.3 - 211.2 (29.9)"
[1] "hr="     "2.3e+08"
D10V2, continuous
D10V3, binary
                             cls
clus                           0  1
  DEL PEAK  3(1Q43) MUTATED    5  1
  DEL PEAK  3(1Q43) WILD-TYPE  9 10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      5    1
  DEL PEAK  3(1Q43) WILD-TYPE    9   10
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                         5                           9
  MALE                           1                          10
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q43) MUTATED       5                         0     1
  DEL PEAK  3(1Q43) WILD-TYPE     5                         1    13
D10V4, multiclass
                           clus
vv                          DEL PEAK  3(1Q43) MUTATED
  ASIAN                                             5
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             1
                           clus
vv                          DEL PEAK  3(1Q43) WILD-TYPE
  ASIAN                                               5
  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(11) Variable = DEL PEAK  4(2Q23.1) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(2Q23.1) MUTATED    4  1
  DEL PEAK  4(2Q23.1) WILD-TYPE 17  3
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            5                            20 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK  4(2Q23.1) MUTATED`
TCGA-FA-A6HO TCGA-FF-8043 TCGA-FF-8047 TCGA-G8-6324 TCGA-GR-7351 
        0.20        31.73         4.14        41.16       127.30 

$`DEL PEAK  4(2Q23.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34        14.99         0.20        35.54        31.10 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       27.35        22.32         4.57        51.98        47.38       211.23 
TCGA-G8-6907 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
       19.56       106.09       196.60        74.10        26.70        24.69 
TCGA-GR-A4D6 TCGA-GR-A4D9 
       29.95        46.29 

  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 
                       127.30                        211.23 
  DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE 
                        31.73                         28.65 
[1] "0.2 - 127.3 (31.7)" "0.2 - 211.2 (28.6)"
[1] "hr=" "1.9"
D11V2, continuous
D11V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q23.1) MUTATED    5  0
  DEL PEAK  4(2Q23.1) WILD-TYPE  9 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q23.1) MUTATED      5    0
  DEL PEAK  4(2Q23.1) WILD-TYPE    9   11
        clus
vv       DEL PEAK  4(2Q23.1) MUTATED DEL PEAK  4(2Q23.1) WILD-TYPE
  FEMALE                           5                             9
  MALE                             0                            11
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q23.1) MUTATED       3                         1     1
  DEL PEAK  4(2Q23.1) WILD-TYPE     7                         0    13
D11V4, multiclass
                           clus
vv                          DEL PEAK  4(2Q23.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               1
                           clus
vv                          DEL PEAK  4(2Q23.1) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                             0
  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(12) Variable = DEL PEAK  5(6Q14.1) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(6Q14.1) MUTATED    6  1
  DEL PEAK  5(6Q14.1) WILD-TYPE 15  3
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            7                            18 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                            1                             3 
$`DEL PEAK  5(6Q14.1) MUTATED`
TCGA-FA-A4XK TCGA-FA-A6HO TCGA-FF-8042 TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-A4D5 
       14.99         0.20        31.10        51.98       211.23        24.69 
TCGA-GR-A4D9 
       46.29 

$`DEL PEAK  5(6Q14.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8043 TCGA-FF-8047 
        4.34         4.34         0.20        35.54        31.73         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 
       27.35        22.32         4.57        41.16        47.38        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
      106.09       196.60       127.30        74.10        26.70        29.95 

  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE 
                        31.10                         28.65 
[1] "0.2 - 211.2 (31.1)" "0.2 - 196.6 (28.6)"
[1] "hr="     "8.5e+08"
D12V2, continuous
D12V3, binary
                               cls
clus                             0  1
  DEL PEAK  5(6Q14.1) MUTATED    4  3
  DEL PEAK  5(6Q14.1) WILD-TYPE 10  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(6Q14.1) MUTATED      4    3
  DEL PEAK  5(6Q14.1) WILD-TYPE   10    8
        clus
vv       DEL PEAK  5(6Q14.1) MUTATED DEL PEAK  5(6Q14.1) WILD-TYPE
  FEMALE                           4                            10
  MALE                             3                             8
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(6Q14.1) MUTATED       3                         0     4
  DEL PEAK  5(6Q14.1) WILD-TYPE     7                         1    10
D12V4, multiclass
                           clus
vv                          DEL PEAK  5(6Q14.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               4
                           clus
vv                          DEL PEAK  5(6Q14.1) WILD-TYPE
  ASIAN                                                 7
  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(13) Variable = DEL PEAK  6(6Q23.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(6Q23.3) MUTATED    3  2
  DEL PEAK  6(6Q23.3) WILD-TYPE 18  2
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            5                            20 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                            2                             2 
$`DEL PEAK  6(6Q23.3) MUTATED`
TCGA-G8-6325 TCGA-G8-6906 TCGA-G8-6909 TCGA-GR-A4D5 TCGA-GR-A4D9 
       51.98       211.23       106.09        24.69        46.29 

$`DEL PEAK  6(6Q23.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 
        4.34         4.34        14.99         0.20         0.20        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
       31.10        31.73         4.14        27.35        22.32         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       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D6 
       26.70        29.95 

  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                        24.69                          0.20 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE 
                       51.980                        27.025 
[1] "24.7 - 211.2 (52.0)" "0.2 - 196.6 (27.0)" 
[1] "hr=" "1.4"
D13V2, continuous
D13V3, binary
                               cls
clus                             0  1
  DEL PEAK  6(6Q23.3) MUTATED    2  3
  DEL PEAK  6(6Q23.3) WILD-TYPE 12  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(6Q23.3) MUTATED      2    3
  DEL PEAK  6(6Q23.3) WILD-TYPE   12    8
        clus
vv       DEL PEAK  6(6Q23.3) MUTATED DEL PEAK  6(6Q23.3) WILD-TYPE
  FEMALE                           2                            12
  MALE                             3                             8
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(6Q23.3) MUTATED       0                         0     5
  DEL PEAK  6(6Q23.3) WILD-TYPE    10                         1     9
D13V4, multiclass
                           clus
vv                          DEL PEAK  6(6Q23.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               5
                           clus
vv                          DEL PEAK  6(6Q23.3) WILD-TYPE
  ASIAN                                                10
  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(14) Variable = DEL PEAK  8(8P23.1) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(8P23.1) MUTATED    3  0
  DEL PEAK  8(8P23.1) WILD-TYPE 18  4
  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                            3                            22 
  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                            0                             4 
$`DEL PEAK  8(8P23.1) MUTATED`
TCGA-FA-A6HO TCGA-FF-8047 TCGA-GR-A4D6 
        0.20         4.14        29.95 

$`DEL PEAK  8(8P23.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34        14.99         0.20        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       31.73        27.35        22.32         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       127.30 
TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D9 
       74.10        26.70        24.69        46.29 

  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                        29.95                        211.23 
  DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE 
                        4.140                        31.415 
[1] "0.2 - 29.9 (4.1)"   "0.2 - 211.2 (31.4)"
[1] "hr="     "2.6e+07"
D14V2, continuous
D14V3, binary
                               cls
clus                             0  1
  DEL PEAK  8(8P23.1) MUTATED    3  0
  DEL PEAK  8(8P23.1) WILD-TYPE 11 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(8P23.1) MUTATED      3    0
  DEL PEAK  8(8P23.1) WILD-TYPE   11   11
        clus
vv       DEL PEAK  8(8P23.1) MUTATED DEL PEAK  8(8P23.1) WILD-TYPE
  FEMALE                           3                            11
  MALE                             0                            11
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(8P23.1) MUTATED       3                         0     0
  DEL PEAK  8(8P23.1) WILD-TYPE     7                         1    14
D14V4, multiclass
                           clus
vv                          DEL PEAK  8(8P23.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               0
                           clus
vv                          DEL PEAK  8(8P23.1) WILD-TYPE
  ASIAN                                                 7
  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(15) Variable = DEL PEAK  9(8Q12.1) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(8Q12.1) MUTATED    3  0
  DEL PEAK  9(8Q12.1) WILD-TYPE 18  4
  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                            3                            22 
  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                            0                             4 
$`DEL PEAK  9(8Q12.1) MUTATED`
TCGA-FA-A6HO TCGA-FF-8047 TCGA-GR-7353 
        0.20         4.14        74.10 

$`DEL PEAK  9(8Q12.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34        14.99         0.20        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
       31.73        27.35        22.32         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       127.30 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        24.69        29.95        46.29 

  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                          0.2                           0.2 
  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                        74.10                        211.23 
  DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE 
                        4.140                        30.525 
[1] "0.2 - 74.1 (4.1)"   "0.2 - 211.2 (30.5)"
[1] "hr="     "7.7e+07"
D15V2, continuous
D15V3, binary
                               cls
clus                             0  1
  DEL PEAK  9(8Q12.1) MUTATED    2  1
  DEL PEAK  9(8Q12.1) WILD-TYPE 12 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(8Q12.1) MUTATED      2    1
  DEL PEAK  9(8Q12.1) WILD-TYPE   12   10
        clus
vv       DEL PEAK  9(8Q12.1) MUTATED DEL PEAK  9(8Q12.1) WILD-TYPE
  FEMALE                           2                            12
  MALE                             1                            10
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(8Q12.1) MUTATED       2                         0     1
  DEL PEAK  9(8Q12.1) WILD-TYPE     8                         1    13
D15V4, multiclass
                           clus
vv                          DEL PEAK  9(8Q12.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               1
                           clus
vv                          DEL PEAK  9(8Q12.1) WILD-TYPE
  ASIAN                                                 8
  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(16) Variable = DEL PEAK 10(9P21.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(9P21.3) MUTATED    6  1
  DEL PEAK 10(9P21.3) WILD-TYPE 15  3
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            7                            18 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                            1                             3 
$`DEL PEAK 10(9P21.3) MUTATED`
TCGA-FA-A4XK TCGA-FF-8042 TCGA-FF-8047 TCGA-G8-6325 TCGA-G8-6906 TCGA-GR-A4D6 
       14.99        31.10         4.14        51.98       211.23        29.95 
TCGA-GR-A4D9 
       46.29 

$`DEL PEAK 10(9P21.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8043 
        4.34         4.34         0.20         0.20        35.54        31.73 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6326 TCGA-G8-6907 
       27.35        22.32         4.57        41.16        47.38        19.56 
TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D5 
      106.09       196.60       127.30        74.10        26.70        24.69 

  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                         4.14                          0.20 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                       211.23                        196.60 
  DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE 
                       31.100                        27.025 
[1] "4.1 - 211.2 (31.1)" "0.2 - 196.6 (27.0)"
[1] "hr="     "8.5e+08"
D16V2, continuous
D16V3, binary
                               cls
clus                             0  1
  DEL PEAK 10(9P21.3) MUTATED    4  3
  DEL PEAK 10(9P21.3) WILD-TYPE 10  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(9P21.3) MUTATED      4    3
  DEL PEAK 10(9P21.3) WILD-TYPE   10    8
        clus
vv       DEL PEAK 10(9P21.3) MUTATED DEL PEAK 10(9P21.3) WILD-TYPE
  FEMALE                           4                            10
  MALE                             3                             8
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(9P21.3) MUTATED       4                         0     3
  DEL PEAK 10(9P21.3) WILD-TYPE     6                         1    11
D16V4, multiclass
                           clus
vv                          DEL PEAK 10(9P21.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          DEL PEAK 10(9P21.3) WILD-TYPE
  ASIAN                                                 6
  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(17) Variable = DEL PEAK 11(10Q23.31) MUTATION ANALYSIS
D17V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 11(10Q23.31) MUTATED    3  1
  DEL PEAK 11(10Q23.31) WILD-TYPE 18  3
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              4                              21 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                              1                               3 
$`DEL PEAK 11(10Q23.31) MUTATED`
TCGA-G8-6907 TCGA-GR-7353 TCGA-GR-A4D4 TCGA-GR-A4D6 
       19.56        74.10        26.70        29.95 

$`DEL PEAK 11(10Q23.31) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 
        4.34         4.34        14.99         0.20         0.20        35.54 
TCGA-FF-8042 TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 
       31.10        31.73         4.14        27.35        22.32         4.57 
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-A4D5 TCGA-GR-A4D9 
      127.30        24.69        46.29 

  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                          19.56                            0.20 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                          74.10                          211.23 
  DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE 
                         28.325                          31.100 
[1] "19.6 - 74.1 (28.3)" "0.2 - 211.2 (31.1)"
[1] "hr=" "5.3"
D17V2, continuous
D17V3, binary
                                 cls
clus                               0  1
  DEL PEAK 11(10Q23.31) MUTATED    3  1
  DEL PEAK 11(10Q23.31) WILD-TYPE 11 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 11(10Q23.31) MUTATED      3    1
  DEL PEAK 11(10Q23.31) WILD-TYPE   11   10
        clus
vv       DEL PEAK 11(10Q23.31) MUTATED DEL PEAK 11(10Q23.31) WILD-TYPE
  FEMALE                             3                              11
  MALE                               1                              10
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(10Q23.31) MUTATED       1                         0     3
  DEL PEAK 11(10Q23.31) WILD-TYPE     9                         1    11
D17V4, multiclass
                           clus
vv                          DEL PEAK 11(10Q23.31) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 3
                           clus
vv                          DEL PEAK 11(10Q23.31) WILD-TYPE
  ASIAN                                                   9
  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(18) Variable = DEL PEAK 12(13Q14.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 12(13Q14.2) MUTATED    2  1
  DEL PEAK 12(13Q14.2) WILD-TYPE 19  3
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             3                             22 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                             1                              3 
$`DEL PEAK 12(13Q14.2) MUTATED`
TCGA-FF-8043 TCGA-G8-6907 TCGA-GR-A4D4 
       31.73        19.56        26.70 

$`DEL PEAK 12(13Q14.2) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 
        4.34         4.34        14.99         0.20         0.20        35.54 
TCGA-FF-8042 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 
       31.10         4.14        27.35        22.32         4.57        41.16 
TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 
       51.98        47.38       211.23       106.09       196.60       127.30 
TCGA-GR-7353 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       74.10        24.69        29.95        46.29 

  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                         19.56                           0.20 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                         31.73                         211.23 
  DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE 
                        26.700                         30.525 
[1] "19.6 - 31.7 (26.7)" "0.2 - 211.2 (30.5)"
[1] "hr="     "3.7e+09"
D18V2, continuous
D18V3, binary
                                cls
clus                              0  1
  DEL PEAK 12(13Q14.2) MUTATED    3  0
  DEL PEAK 12(13Q14.2) WILD-TYPE 11 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 12(13Q14.2) MUTATED      3    0
  DEL PEAK 12(13Q14.2) WILD-TYPE   11   11
        clus
vv       DEL PEAK 12(13Q14.2) MUTATED DEL PEAK 12(13Q14.2) WILD-TYPE
  FEMALE                            3                             11
  MALE                              0                             11
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(13Q14.2) MUTATED       1                         0     2
  DEL PEAK 12(13Q14.2) WILD-TYPE     9                         1    12
D18V4, multiclass
                           clus
vv                          DEL PEAK 12(13Q14.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK 12(13Q14.2) 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(19) Variable = DEL PEAK 13(13Q33.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(13Q33.3) MUTATED    4  0
  DEL PEAK 13(13Q33.3) WILD-TYPE 17  4
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             4                             21 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                             0                              4 
$`DEL PEAK 13(13Q33.3) MUTATED`
TCGA-FF-8042 TCGA-FF-8043 TCGA-GR-7351 TCGA-GR-A4D4 
       31.10        31.73       127.30        26.70 

$`DEL PEAK 13(13Q33.3) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 
        4.34         4.34        14.99         0.20         0.20        35.54 
TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 
        4.14        27.35        22.32         4.57        41.16        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        74.10 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       24.69        29.95        46.29 

  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                          26.7                            0.2 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                        127.30                         211.23 
  DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE 
                        31.415                         27.350 
[1] "26.7 - 127.3 (31.4)" "0.2 - 211.2 (27.4)" 
[1] "hr="     "2.6e+08"
D19V2, continuous
D19V3, binary
                                cls
clus                              0  1
  DEL PEAK 13(13Q33.3) MUTATED    4  0
  DEL PEAK 13(13Q33.3) WILD-TYPE 10 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(13Q33.3) MUTATED      4    0
  DEL PEAK 13(13Q33.3) WILD-TYPE   10   11
        clus
vv       DEL PEAK 13(13Q33.3) MUTATED DEL PEAK 13(13Q33.3) WILD-TYPE
  FEMALE                            4                             10
  MALE                              0                             11
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(13Q33.3) MUTATED       2                         0     2
  DEL PEAK 13(13Q33.3) WILD-TYPE     8                         1    12
D19V4, multiclass
                           clus
vv                          DEL PEAK 13(13Q33.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK 13(13Q33.3) WILD-TYPE
  ASIAN                                                  8
  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(20) Variable = DEL PEAK 14(15Q15.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 14(15Q15.1) MUTATED    7  1
  DEL PEAK 14(15Q15.1) WILD-TYPE 14  3
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             8                             17 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                             1                              3 
$`DEL PEAK 14(15Q15.1) 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       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D6 
       26.70        29.95 

$`DEL PEAK 14(15Q15.1) WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8047 
        4.34        14.99         0.20        35.54        31.10         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-A4D5 TCGA-GR-A4D9 
      211.23       106.09       196.60        24.69        46.29 

  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                           0.2                            0.2 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                        127.30                         211.23 
  DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE 
                        28.325                         31.100 
[1] "0.2 - 127.3 (28.3)" "0.2 - 211.2 (31.1)"
[1] "hr=" "1.4"
D20V2, continuous
D20V3, binary
                                cls
clus                             0 1
  DEL PEAK 14(15Q15.1) MUTATED   6 2
  DEL PEAK 14(15Q15.1) WILD-TYPE 8 9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(15Q15.1) MUTATED      6    2
  DEL PEAK 14(15Q15.1) WILD-TYPE    8    9
        clus
vv       DEL PEAK 14(15Q15.1) MUTATED DEL PEAK 14(15Q15.1) WILD-TYPE
  FEMALE                            6                              8
  MALE                              2                              9
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(15Q15.1) MUTATED       3                         0     5
  DEL PEAK 14(15Q15.1) WILD-TYPE     7                         1     9
D20V4, multiclass
                           clus
vv                          DEL PEAK 14(15Q15.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                5
                           clus
vv                          DEL PEAK 14(15Q15.1) WILD-TYPE
  ASIAN                                                  7
  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(21) Variable = DEL PEAK 15(15Q21.1) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(15Q21.1) MUTATED    7  1
  DEL PEAK 15(15Q21.1) WILD-TYPE 14  3
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             8                             17 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                             1                              3 
$`DEL PEAK 15(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       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D6 
       26.70        29.95 

$`DEL PEAK 15(15Q21.1) WILD-TYPE`
TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8047 
        4.34        14.99         0.20        35.54        31.10         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 
       27.35        22.32         4.57        41.16        51.98        47.38 
TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-A4D5 TCGA-GR-A4D9 
      211.23       106.09       196.60        24.69        46.29 

  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                           0.2                            0.2 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                        127.30                         211.23 
  DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE 
                        28.325                         31.100 
[1] "0.2 - 127.3 (28.3)" "0.2 - 211.2 (31.1)"
[1] "hr=" "1.4"
D21V2, continuous
D21V3, binary
                                cls
clus                             0 1
  DEL PEAK 15(15Q21.1) MUTATED   6 2
  DEL PEAK 15(15Q21.1) WILD-TYPE 8 9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(15Q21.1) MUTATED      6    2
  DEL PEAK 15(15Q21.1) WILD-TYPE    8    9
        clus
vv       DEL PEAK 15(15Q21.1) MUTATED DEL PEAK 15(15Q21.1) WILD-TYPE
  FEMALE                            6                              8
  MALE                              2                              9
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(15Q21.1) MUTATED       3                         0     5
  DEL PEAK 15(15Q21.1) WILD-TYPE     7                         1     9
D21V4, multiclass
                           clus
vv                          DEL PEAK 15(15Q21.1) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                5
                           clus
vv                          DEL PEAK 15(15Q21.1) WILD-TYPE
  ASIAN                                                  7
  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(22) Variable = DEL PEAK 16(16P13.13) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 16(16P13.13) MUTATED    4  0
  DEL PEAK 16(16P13.13) WILD-TYPE 17  4
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              4                              21 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                              0                               4 
$`DEL PEAK 16(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 16(16P13.13) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FA-A6HN TCGA-FF-8042 TCGA-FF-8047 
        4.34         4.34        14.99         0.20        31.10         4.14 
TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       27.35        22.32        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       127.30        74.10        26.70 
TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       24.69        29.95        46.29 

  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                            0.2                             0.2 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                          35.54                          211.23 
  DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE 
                          18.15                           29.95 
[1] "0.2 - 35.5 (18.1)"  "0.2 - 211.2 (29.9)"
[1] "hr="     "7.9e+07"
D22V2, continuous
D22V3, binary
                                 cls
clus                               0  1
  DEL PEAK 16(16P13.13) MUTATED    4  0
  DEL PEAK 16(16P13.13) WILD-TYPE 10 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 16(16P13.13) MUTATED      4    0
  DEL PEAK 16(16P13.13) WILD-TYPE   10   11
        clus
vv       DEL PEAK 16(16P13.13) MUTATED DEL PEAK 16(16P13.13) WILD-TYPE
  FEMALE                             4                              10
  MALE                               0                              11
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(16P13.13) MUTATED       3                         0     1
  DEL PEAK 16(16P13.13) WILD-TYPE     7                         1    13
D22V4, multiclass
                           clus
vv                          DEL PEAK 16(16P13.13) MUTATED
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                 1
                           clus
vv                          DEL PEAK 16(16P13.13) WILD-TYPE
  ASIAN                                                   7
  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(23) Variable = DEL PEAK 17(16Q23.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(16Q23.1) MUTATED    5  0
  DEL PEAK 17(16Q23.1) WILD-TYPE 16  4
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             5                             20 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                             0                              4 
$`DEL PEAK 17(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        26.70 

$`DEL PEAK 17(16Q23.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A4XK TCGA-FF-8041 TCGA-FF-8042 TCGA-FF-8061 
        4.34         4.34        14.99        35.54        31.10        27.35 
TCGA-FF-8062 TCGA-FM-8000 TCGA-G8-6324 TCGA-G8-6325 TCGA-G8-6326 TCGA-G8-6906 
       22.32         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-A4D5 
       19.56       106.09       196.60       127.30        74.10        24.69 
TCGA-GR-A4D6 TCGA-GR-A4D9 
       29.95        46.29 

  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                          0.20                           4.34 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                         31.73                         211.23 
  DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE 
                          4.14                          33.32 
[1] "0.2 - 31.7 (4.1)"   "4.3 - 211.2 (33.3)"
[1] "hr="     "7.9e+07"
D23V2, continuous
D23V3, binary
                                cls
clus                              0  1
  DEL PEAK 17(16Q23.1) MUTATED    4  1
  DEL PEAK 17(16Q23.1) WILD-TYPE 10 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(16Q23.1) MUTATED      4    1
  DEL PEAK 17(16Q23.1) WILD-TYPE   10   10
        clus
vv       DEL PEAK 17(16Q23.1) MUTATED DEL PEAK 17(16Q23.1) WILD-TYPE
  FEMALE                            4                             10
  MALE                              1                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(16Q23.1) MUTATED       4                         0     1
  DEL PEAK 17(16Q23.1) WILD-TYPE     6                         1    13
D23V4, multiclass
                           clus
vv                          DEL PEAK 17(16Q23.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                1
                           clus
vv                          DEL PEAK 17(16Q23.1) WILD-TYPE
  ASIAN                                                  6
  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(24) Variable = DEL PEAK 18(17Q24.1) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(17Q24.1) MUTATED    2  1
  DEL PEAK 18(17Q24.1) WILD-TYPE 19  3
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             3                             22 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                             1                              3 
$`DEL PEAK 18(17Q24.1) MUTATED`
TCGA-FA-A4XK TCGA-FM-8000 TCGA-G8-6907 
       14.99         4.57        19.56 

$`DEL PEAK 18(17Q24.1) WILD-TYPE`
TCGA-FA-8693 TCGA-FA-A4BB TCGA-FA-A6HN TCGA-FA-A6HO TCGA-FF-8041 TCGA-FF-8042 
        4.34         4.34         0.20         0.20        35.54        31.10 
TCGA-FF-8043 TCGA-FF-8047 TCGA-FF-8061 TCGA-FF-8062 TCGA-G8-6324 TCGA-G8-6325 
       31.73         4.14        27.35        22.32        41.16        51.98 
TCGA-G8-6326 TCGA-G8-6906 TCGA-G8-6909 TCGA-G8-6914 TCGA-GR-7351 TCGA-GR-7353 
       47.38       211.23       106.09       196.60       127.30        74.10 
TCGA-GR-A4D4 TCGA-GR-A4D5 TCGA-GR-A4D6 TCGA-GR-A4D9 
       26.70        24.69        29.95        46.29 

  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                          4.57                           0.20 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                         19.56                         211.23 
  DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE 
                        14.990                         31.415 
[1] "4.6 - 19.6 (15.0)"  "0.2 - 211.2 (31.4)"
[1] "hr="     "9.7e+09"
D24V2, continuous
D24V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(17Q24.1) MUTATED    2  1
  DEL PEAK 18(17Q24.1) WILD-TYPE 12 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(17Q24.1) MUTATED      2    1
  DEL PEAK 18(17Q24.1) WILD-TYPE   12   10
        clus
vv       DEL PEAK 18(17Q24.1) MUTATED DEL PEAK 18(17Q24.1) WILD-TYPE
  FEMALE                            2                             12
  MALE                              1                             10
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(17Q24.1) MUTATED       1                         0     2
  DEL PEAK 18(17Q24.1) WILD-TYPE     9                         1    12
D24V4, multiclass
                           clus
vv                          DEL PEAK 18(17Q24.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                2
                           clus
vv                          DEL PEAK 18(17Q24.1) 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"
