[1] "ofn"       "-oTUCS-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/UCS-TP/15096025/UCS-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/UCS-TP/15107627/transformed.cor.cli.txt"

nPatients in clinical file=57, in cluster file=56, common to both=56
[1] 61 56
[1] "AMP PEAK  1(1Q22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         42                          14 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         42                          14 
[1] "AMP PEAK  2(2P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(2P14) MUTATED AMP PEAK  2(2P14) WILD-TYPE 
                         28                          28 
  AMP PEAK  2(2P14) MUTATED AMP PEAK  2(2P14) WILD-TYPE 
                         28                          28 
[1] "AMP PEAK  3(2Q13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(2Q13) MUTATED AMP PEAK  3(2Q13) WILD-TYPE 
                         29                          27 
  AMP PEAK  3(2Q13) MUTATED AMP PEAK  3(2Q13) WILD-TYPE 
                         29                          27 
[1] "AMP PEAK  4(3P25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(3P25.1) MUTATED AMP PEAK  4(3P25.1) WILD-TYPE 
                           20                            36 
  AMP PEAK  4(3P25.1) MUTATED AMP PEAK  4(3P25.1) WILD-TYPE 
                           20                            36 
[1] "AMP PEAK  5(3Q26.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3Q26.2) MUTATED AMP PEAK  5(3Q26.2) WILD-TYPE 
                           37                            19 
  AMP PEAK  5(3Q26.2) MUTATED AMP PEAK  5(3Q26.2) WILD-TYPE 
                           37                            19 
[1] "AMP PEAK  6(4P16.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           25                            31 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           25                            31 
[1] "AMP PEAK  7(5P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P13.2) MUTATED AMP PEAK  7(5P13.2) WILD-TYPE 
                           26                            30 
  AMP PEAK  7(5P13.2) MUTATED AMP PEAK  7(5P13.2) WILD-TYPE 
                           26                            30 
[1] "AMP PEAK  8(6P24.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P24.2) MUTATED AMP PEAK  8(6P24.2) WILD-TYPE 
                           37                            19 
  AMP PEAK  8(6P24.2) MUTATED AMP PEAK  8(6P24.2) WILD-TYPE 
                           37                            19 
[1] "AMP PEAK  9(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(8P11.21) MUTATED AMP PEAK  9(8P11.21) WILD-TYPE 
                            33                             23 
  AMP PEAK  9(8P11.21) MUTATED AMP PEAK  9(8P11.21) WILD-TYPE 
                            33                             23 
[1] "AMP PEAK 10(8Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(8Q11.23) MUTATED AMP PEAK 10(8Q11.23) WILD-TYPE 
                            38                             18 
  AMP PEAK 10(8Q11.23) MUTATED AMP PEAK 10(8Q11.23) WILD-TYPE 
                            38                             18 
[1] "AMP PEAK 11(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            42                             14 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            42                             14 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            40                             16 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            40                             16 
[1] "AMP PEAK 13(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(10Q22.2) MUTATED AMP PEAK 13(10Q22.2) WILD-TYPE 
                            26                             30 
  AMP PEAK 13(10Q22.2) MUTATED AMP PEAK 13(10Q22.2) WILD-TYPE 
                            26                             30 
[1] "AMP PEAK 14(11Q13.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(11Q13.1) MUTATED AMP PEAK 14(11Q13.1) WILD-TYPE 
                            19                             37 
  AMP PEAK 14(11Q13.1) MUTATED AMP PEAK 14(11Q13.1) WILD-TYPE 
                            19                             37 
[1] "AMP PEAK 15(12Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(12Q12) MUTATED AMP PEAK 15(12Q12) WILD-TYPE 
                          22                           34 
  AMP PEAK 15(12Q12) MUTATED AMP PEAK 15(12Q12) WILD-TYPE 
                          22                           34 
[1] "AMP PEAK 16(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          17                           39 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          17                           39 
[1] "AMP PEAK 17(13Q31.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                            25                             31 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                            25                             31 
[1] "AMP PEAK 18(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                            20                             36 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                            20                             36 
[1] "AMP PEAK 19(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          27                           29 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          27                           29 
[1] "AMP PEAK 20(17Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            32                             24 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            32                             24 
[1] "AMP PEAK 21(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            19                             37 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            19                             37 
[1] "AMP PEAK 22(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                          45                           11 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                          45                           11 
[1] "AMP PEAK 23(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                             48                               8 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                             48                               8 
[1] "AMP PEAK 24(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                             48                               8 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                             48                               8 
[1] "AMP PEAK 25(XP11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(XP11.21) MUTATED AMP PEAK 25(XP11.21) WILD-TYPE 
                            28                             28 
  AMP PEAK 25(XP11.21) MUTATED AMP PEAK 25(XP11.21) WILD-TYPE 
                            28                             28 
[1] "DEL PEAK  1(1P36.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            19                             37 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            19                             37 
[1] "DEL PEAK  2(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           11                            45 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           11                            45 
[1] "DEL PEAK  3(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(3P14.2) MUTATED DEL PEAK  3(3P14.2) WILD-TYPE 
                           37                            19 
  DEL PEAK  3(3P14.2) MUTATED DEL PEAK  3(3P14.2) WILD-TYPE 
                           37                            19 
[1] "DEL PEAK  4(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                            22                             34 
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                            22                             34 
[1] "DEL PEAK  5(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                           37                            19 
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                           37                            19 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           37                            19 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           37                            19 
[1] "DEL PEAK  7(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5Q12.1) MUTATED DEL PEAK  7(5Q12.1) WILD-TYPE 
                           26                            30 
  DEL PEAK  7(5Q12.1) MUTATED DEL PEAK  7(5Q12.1) WILD-TYPE 
                           26                            30 
[1] "DEL PEAK  8(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                         10                          46 
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                         10                          46 
[1] "DEL PEAK  9(7Q11.22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(7Q11.22) MUTATED DEL PEAK  9(7Q11.22) WILD-TYPE 
                            12                             44 
  DEL PEAK  9(7Q11.22) MUTATED DEL PEAK  9(7Q11.22) WILD-TYPE 
                            12                             44 
[1] "DEL PEAK 10(7Q36.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(7Q36.2) MUTATED DEL PEAK 10(7Q36.2) WILD-TYPE 
                           20                            36 
  DEL PEAK 10(7Q36.2) MUTATED DEL PEAK 10(7Q36.2) WILD-TYPE 
                           20                            36 
[1] "DEL PEAK 11(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                           33                            23 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                           33                            23 
[1] "DEL PEAK 12(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         34                          22 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         34                          22 
[1] "DEL PEAK 13(9Q21.13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(9Q21.13) MUTATED DEL PEAK 13(9Q21.13) WILD-TYPE 
                            39                             17 
  DEL PEAK 13(9Q21.13) MUTATED DEL PEAK 13(9Q21.13) WILD-TYPE 
                            39                             17 
[1] "DEL PEAK 14(9Q33.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9Q33.3) MUTATED DEL PEAK 14(9Q33.3) WILD-TYPE 
                           39                            17 
  DEL PEAK 14(9Q33.3) MUTATED DEL PEAK 14(9Q33.3) WILD-TYPE 
                           39                            17 
[1] "DEL PEAK 15(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             20                              36 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             20                              36 
[1] "DEL PEAK 16(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(11P15.5) MUTATED DEL PEAK 16(11P15.5) WILD-TYPE 
                            25                             31 
  DEL PEAK 16(11P15.5) MUTATED DEL PEAK 16(11P15.5) WILD-TYPE 
                            25                             31 
[1] "DEL PEAK 17(11Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            26                             30 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            26                             30 
[1] "DEL PEAK 18(11Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(11Q23.2) MUTATED DEL PEAK 18(11Q23.2) WILD-TYPE 
                            26                             30 
  DEL PEAK 18(11Q23.2) MUTATED DEL PEAK 18(11Q23.2) WILD-TYPE 
                            26                             30 
[1] "DEL PEAK 19(12Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(12Q23.1) MUTATED DEL PEAK 19(12Q23.1) WILD-TYPE 
                            20                             36 
  DEL PEAK 19(12Q23.1) MUTATED DEL PEAK 19(12Q23.1) WILD-TYPE 
                            20                             36 
[1] "DEL PEAK 20(12Q24.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12Q24.31) MUTATED DEL PEAK 20(12Q24.31) WILD-TYPE 
                             20                              36 
  DEL PEAK 20(12Q24.31) MUTATED DEL PEAK 20(12Q24.31) WILD-TYPE 
                             20                              36 
[1] "DEL PEAK 21(13Q12.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             30                              26 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             30                              26 
[1] "DEL PEAK 22(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                            32                             24 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                            32                             24 
[1] "DEL PEAK 23(14Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(14Q21.1) MUTATED DEL PEAK 23(14Q21.1) WILD-TYPE 
                            28                             28 
  DEL PEAK 23(14Q21.1) MUTATED DEL PEAK 23(14Q21.1) WILD-TYPE 
                            28                             28 
[1] "DEL PEAK 24(15Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(15Q11.2) MUTATED DEL PEAK 24(15Q11.2) WILD-TYPE 
                            41                             15 
  DEL PEAK 24(15Q11.2) MUTATED DEL PEAK 24(15Q11.2) WILD-TYPE 
                            41                             15 
[1] "DEL PEAK 25(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(15Q15.1) MUTATED DEL PEAK 25(15Q15.1) WILD-TYPE 
                            43                             13 
  DEL PEAK 25(15Q15.1) MUTATED DEL PEAK 25(15Q15.1) WILD-TYPE 
                            43                             13 
[1] "DEL PEAK 26(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                            33                             23 
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                            33                             23 
[1] "DEL PEAK 27(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            39                             17 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            39                             17 
[1] "DEL PEAK 28(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(17P13.1) MUTATED DEL PEAK 28(17P13.1) WILD-TYPE 
                            42                             14 
  DEL PEAK 28(17P13.1) MUTATED DEL PEAK 28(17P13.1) WILD-TYPE 
                            42                             14 
[1] "DEL PEAK 29(17Q21.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(17Q21.32) MUTATED DEL PEAK 29(17Q21.32) WILD-TYPE 
                             19                              37 
  DEL PEAK 29(17Q21.32) MUTATED DEL PEAK 29(17Q21.32) WILD-TYPE 
                             19                              37 
[1] "DEL PEAK 30(18Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(18Q22.2) MUTATED DEL PEAK 30(18Q22.2) WILD-TYPE 
                            26                             30 
  DEL PEAK 30(18Q22.2) MUTATED DEL PEAK 30(18Q22.2) WILD-TYPE 
                            26                             30 
[1] "DEL PEAK 31(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            47                              9 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            47                              9 
[1] "DEL PEAK 32(19Q13.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                             17                              39 
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                             17                              39 
[1] "DEL PEAK 33(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                             9                             47 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                             9                             47 
[1] "DEL PEAK 34(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             40                              16 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             40                              16 
[1] "DEL PEAK 35(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XP21.1) MUTATED DEL PEAK 35(XP21.1) WILD-TYPE 
                           18                            38 
  DEL PEAK 35(XP21.1) MUTATED DEL PEAK 35(XP21.1) WILD-TYPE 
                           18                            38 
[1] "DEL PEAK 36(XQ25) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(XQ25) MUTATED DEL PEAK 36(XQ25) WILD-TYPE 
                         23                          33 
  DEL PEAK 36(XQ25) MUTATED DEL PEAK 36(XQ25) WILD-TYPE 
                         23                          33 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "NEOPLASM_DISEASESTAGE"                 
 [6] "PATHOLOGY_T_STAGE"                     
 [7] "PATHOLOGY_N_STAGE"                     
 [8] "PATHOLOGY_M_STAGE"                     
 [9] "DCC_UPLOAD_DATE"                       
[10] "GENDER"                                
[11] "RADIATION_THERAPY"                     
[12] "RADIATIONS_RADIATION_REGIMENINDICATION"
[13] "RACE"                                  
[14] "ETHNICITY"                             
[15] "BATCH_NUMBER"                          

Input Data has 15 rows and 56 columns.

[1] "Batch" "15"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=30,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'NEOPLASM_DISEASESTAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "NEOPLASM_DISEASESTAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGY_T_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_T_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 7:'PATHOLOGY_N_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_N_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'PATHOLOGY_M_STAGE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PATHOLOGY_M_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 9:'DCC_UPLOAD_DATE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 10:'GENDER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "GENDER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 11:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 12:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 13:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "42"                  
freq.contrast "42"               "1"                   
both >= 3     "FALSE"            "FALSE"               
Variable 15:'BATCH_NUMBER':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "BATCH_NUMBER is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "****** SUMMARY ***** "
Output Data has 56 columns, 1 survival variables, and 2 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "RACE"          
YEARS_TO_BIRTH, nv=30, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q22) MUTATION ANALYSIS
D1V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  1(1Q22) MUTATED   17 24
  AMP PEAK  1(1Q22) WILD-TYPE  4 10
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         41                          14 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                         24                          10 
$`AMP PEAK  1(1Q22) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RS 
       52.31         4.67        59.38         4.87        34.62        29.95 
TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       81.70        50.17        67.13        14.70        11.87        17.42 
TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y8 TCGA-N7-A59B 
       19.63         9.57        17.16        39.75        12.43        13.38 
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S 
       13.74        27.25        26.70        25.68        20.09        12.20 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       21.93        67.17        54.97        35.80        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4WX 
      140.35         3.75        17.79         6.67         5.49        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        2.66         5.49        14.53        31.20        19.30 

$`AMP PEAK  1(1Q22) WILD-TYPE`
TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI 
       18.08        22.52         3.68        25.35         0.26        26.63 
TCGA-N8-A4PQ TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       18.81        80.78        27.55        88.11        10.42        23.47 
TCGA-ND-A4WC TCGA-NF-A4WU 
       25.18         9.80 

  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                       2.66                        0.26 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                     140.35                       88.11 
  AMP PEAK  1(1Q22) MUTATED AMP PEAK  1(1Q22) WILD-TYPE 
                     19.300                      22.995 
[1] "2.7 - 140.3 (19.3)" "0.3 - 88.1 (23.0)" 
[1] "hr=" "1.2"
D1V2, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q22) MUTATED       1                         7    33
  AMP PEAK  1(1Q22) WILD-TYPE     2                         2    10
D1V3, multiclass
                           clus
vv                          AMP PEAK  1(1Q22) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            33
                           clus
vv                          AMP PEAK  1(1Q22) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           2
  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(2) Variable = AMP PEAK  2(2P14) MUTATION ANALYSIS
D2V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  2(2P14) MUTATED    9 19
  AMP PEAK  2(2P14) WILD-TYPE 12 15
  AMP PEAK  2(2P14) MUTATED AMP PEAK  2(2P14) WILD-TYPE 
                         28                          27 
  AMP PEAK  2(2P14) MUTATED AMP PEAK  2(2P14) WILD-TYPE 
                         19                          15 
$`AMP PEAK  2(2P14) MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC 
       18.08        29.95        50.17        14.70        11.87        19.63 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PP 
        0.26        12.43        13.38        13.74        25.68        20.09 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QV 
       18.81        12.20        67.17        54.97        35.80       140.35 
TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       80.78         3.75        17.79         6.67        10.42        23.47 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU 
        9.80        14.86         5.49        14.53 

$`AMP PEAK  2(2P14) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31         4.67        59.38         4.87        34.62        22.52 
TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       81.70        67.13        17.42         3.68         9.57        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N9-A4PZ 
       39.75        25.35        26.63        27.25        26.70        21.93 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QX TCGA-NA-A5I1 TCGA-ND-A4WC TCGA-ND-A4WF 
       19.86        15.81        27.55        88.11        25.18         5.49 
TCGA-NF-A4X2 TCGA-NG-A4VW TCGA-QM-A5NM 
        2.66        31.20        19.30 

  AMP PEAK  2(2P14) MUTATED AMP PEAK  2(2P14) WILD-TYPE 
                       0.26                        2.66 
  AMP PEAK  2(2P14) MUTATED AMP PEAK  2(2P14) WILD-TYPE 
                     140.35                       88.11 
  AMP PEAK  2(2P14) MUTATED AMP PEAK  2(2P14) WILD-TYPE 
                     16.325                      25.180 
[1] "0.3 - 140.3 (16.3)" "2.7 - 88.1 (25.2)" 
[1] "hr=" "1.5"
D2V2, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(2P14) MUTATED       1                         7    19
  AMP PEAK  2(2P14) WILD-TYPE     2                         2    24
D2V3, multiclass
                           clus
vv                          AMP PEAK  2(2P14) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            19
                           clus
vv                          AMP PEAK  2(2P14) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              24
[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(2Q13) MUTATION ANALYSIS
D3V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  3(2Q13) MUTATED   11 18
  AMP PEAK  3(2Q13) WILD-TYPE 10 16
  AMP PEAK  3(2Q13) MUTATED AMP PEAK  3(2Q13) WILD-TYPE 
                         29                          26 
  AMP PEAK  3(2Q13) MUTATED AMP PEAK  3(2Q13) WILD-TYPE 
                         18                          16 
$`AMP PEAK  3(2Q13) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59F TCGA-N6-A4VC 
       52.31        18.08        29.95        50.17        11.87        19.63 
TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PM 
       39.75         0.26        12.43        13.38        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q4 
       26.70        25.68        20.09        12.20        21.93        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 
       19.86       140.35        80.78         3.75        17.79         6.67 
TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU 
       23.47         9.80        14.86         5.49        14.53 

$`AMP PEAK  3(2Q13) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RT 
        4.67        59.38         4.87        34.62        22.52        81.70 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       67.13        14.70        17.42         3.68         9.57        17.16 
TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 
       25.35        26.63        18.81        67.17        54.97        15.81 
TCGA-NA-A4QX TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4X2 
       27.55        88.11        10.42        25.18         5.49         2.66 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.20        19.30 

  AMP PEAK  3(2Q13) MUTATED AMP PEAK  3(2Q13) WILD-TYPE 
                       0.26                        2.66 
  AMP PEAK  3(2Q13) MUTATED AMP PEAK  3(2Q13) WILD-TYPE 
                     140.35                       88.11 
  AMP PEAK  3(2Q13) MUTATED AMP PEAK  3(2Q13) WILD-TYPE 
                      19.63                       20.91 
[1] "0.3 - 140.3 (19.6)" "2.7 - 88.1 (20.9)" 
[1] "hr=" "1.1"
D3V2, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(2Q13) MUTATED       1                         6    21
  AMP PEAK  3(2Q13) WILD-TYPE     2                         3    22
D3V3, multiclass
                           clus
vv                          AMP PEAK  3(2Q13) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         6
  WHITE                                            21
                           clus
vv                          AMP PEAK  3(2Q13) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              22
[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(3P25.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(3P25.1) MUTATED    8 11
  AMP PEAK  4(3P25.1) WILD-TYPE 13 23
  AMP PEAK  4(3P25.1) MUTATED AMP PEAK  4(3P25.1) WILD-TYPE 
                           19                            36 
  AMP PEAK  4(3P25.1) MUTATED AMP PEAK  4(3P25.1) WILD-TYPE 
                           11                            23 
$`AMP PEAK  4(3P25.1) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4VG TCGA-N7-A4Y5 
       52.31        50.17        67.13        11.87        39.75         0.26 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       26.70        25.68        18.81        54.97        15.81       140.35 
TCGA-NA-A4QX TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4X2 TCGA-NG-A4VU 
       27.55        88.11        10.42        23.47         2.66        14.53 
TCGA-NG-A4VW 
       31.20 

$`AMP PEAK  4(3P25.1) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
        4.67        59.38        18.08         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD 
       29.95        81.70        14.70        17.42        19.63         3.68 
TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
        9.57        17.16        25.35        12.43        13.38        26.63 
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       13.74        27.25        20.09        12.20        21.93        67.17 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 
       35.80        19.86        80.78         3.75        17.79         6.67 
TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-QM-A5NM 
       25.18         5.49         9.80        14.86         5.49        19.30 

  AMP PEAK  4(3P25.1) MUTATED AMP PEAK  4(3P25.1) WILD-TYPE 
                         0.26                          3.68 
  AMP PEAK  4(3P25.1) MUTATED AMP PEAK  4(3P25.1) WILD-TYPE 
                       140.35                         81.70 
  AMP PEAK  4(3P25.1) MUTATED AMP PEAK  4(3P25.1) WILD-TYPE 
                       26.700                        17.935 
[1] "0.3 - 140.3 (26.7)" "3.7 - 81.7 (17.9)" 
[1] "hr=" "1.7"
D4V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(3P25.1) MUTATED       2                         4    14
  AMP PEAK  4(3P25.1) WILD-TYPE     1                         5    29
D4V3, multiclass
                           clus
vv                          AMP PEAK  4(3P25.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              14
                           clus
vv                          AMP PEAK  4(3P25.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                29
[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(3Q26.2) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  5(3Q26.2) MUTATED   13 23
  AMP PEAK  5(3Q26.2) WILD-TYPE  8 11
  AMP PEAK  5(3Q26.2) MUTATED AMP PEAK  5(3Q26.2) WILD-TYPE 
                           36                            19 
  AMP PEAK  5(3Q26.2) MUTATED AMP PEAK  5(3Q26.2) WILD-TYPE 
                           23                            11 
$`AMP PEAK  5(3Q26.2) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RT 
       52.31         4.67        18.08        34.62        22.52        81.70 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N7-A4Y5 TCGA-N7-A4Y8 
       14.70        11.87        19.63         9.57         0.26        12.43 
TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ 
       13.38        13.74        26.70        25.68        20.09        18.81 
TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 
       12.20        21.93        67.17        54.97        35.80        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WA 
      140.35        80.78        27.55        17.79         6.67        23.47 
TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        14.86         2.66        14.53        31.20        19.30 

$`AMP PEAK  5(3Q26.2) WILD-TYPE`
TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4V9 
       59.38         4.87        29.95        50.17        67.13        17.42 
TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PM 
        3.68        17.16        39.75        25.35        26.63        27.25 
TCGA-N9-A4Q7 TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-NF-A4WU 
       19.86         3.75        88.11        10.42        25.18         9.80 
TCGA-NF-A5CP 
        5.49 

  AMP PEAK  5(3Q26.2) MUTATED AMP PEAK  5(3Q26.2) WILD-TYPE 
                         0.26                          3.68 
  AMP PEAK  5(3Q26.2) MUTATED AMP PEAK  5(3Q26.2) WILD-TYPE 
                       140.35                         88.11 
  AMP PEAK  5(3Q26.2) MUTATED AMP PEAK  5(3Q26.2) WILD-TYPE 
                       19.055                        25.180 
[1] "0.3 - 140.3 (19.1)" "3.7 - 88.1 (25.2)" 
[1] "hr=" "1.2"
D5V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3Q26.2) MUTATED       2                         7    27
  AMP PEAK  5(3Q26.2) WILD-TYPE     1                         2    16
D5V3, multiclass
                           clus
vv                          AMP PEAK  5(3Q26.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              27
                           clus
vv                          AMP PEAK  5(3Q26.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                16
[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(4P16.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(4P16.3) MUTATED   10 15
  AMP PEAK  6(4P16.3) WILD-TYPE 11 19
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           25                            30 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                           15                            19 
$`AMP PEAK  6(4P16.3) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
       52.31        22.52        29.95        81.70        50.17        67.13 
TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A59B TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PQ 
        9.57        17.16        13.38        27.25        26.70        18.81 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX 
       21.93        67.17        35.80        15.81       140.35        27.55 
TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-NF-A4WX 
        3.75         6.67        88.11        10.42        25.18        14.86 
TCGA-NG-A4VU 
       14.53 

$`AMP PEAK  6(4P16.3) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A59E 
        4.67        59.38        18.08         4.87        34.62        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VG TCGA-N7-A4Y0 
       11.87        17.42        19.63         3.68        39.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PP 
        0.26        12.43        26.63        13.74        25.68        20.09 
TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-ND-A4WA 
       12.20        54.97        19.86        80.78        17.79        23.47 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49         9.80         2.66         5.49        31.20        19.30 

  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                         3.75                          0.26 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                       140.35                         80.78 
  AMP PEAK  6(4P16.3) MUTATED AMP PEAK  6(4P16.3) WILD-TYPE 
                       25.180                        17.935 
[1] "3.8 - 140.3 (25.2)" "0.3 - 80.8 (17.9)" 
[1] "hr=" "1.6"
D6V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(4P16.3) MUTATED       1                         6    17
  AMP PEAK  6(4P16.3) WILD-TYPE     2                         3    26
D6V3, multiclass
                           clus
vv                          AMP PEAK  6(4P16.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              17
                           clus
vv                          AMP PEAK  6(4P16.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                26
[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(5P13.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  7(5P13.2) MUTATED    8 17
  AMP PEAK  7(5P13.2) WILD-TYPE 13 17
  AMP PEAK  7(5P13.2) MUTATED AMP PEAK  7(5P13.2) WILD-TYPE 
                           25                            30 
  AMP PEAK  7(5P13.2) MUTATED AMP PEAK  7(5P13.2) WILD-TYPE 
                           17                            17 
$`AMP PEAK  7(5P13.2) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E 
       52.31         4.87        34.62        81.70        50.17        14.70 
TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N8-A4PN TCGA-N8-A4PO 
        9.57        17.16        39.75         0.26        26.70        25.68 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX 
       20.09        18.81        21.93        15.81        80.78        27.55 
TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU 
       17.79        88.11        10.42        14.86         5.49        14.53 
TCGA-NG-A4VW 
       31.20 

$`AMP PEAK  7(5P13.2) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RV 
        4.67        59.38        18.08        22.52        29.95        67.13 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-N7-A4Y8 
       11.87        17.42        19.63         3.68        25.35        12.43 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A56S TCGA-N9-A4Q1 
       13.38        26.63        13.74        27.25        12.20        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QY TCGA-NA-A4R1 
       54.97        35.80        19.86       140.35         3.75         6.67 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-QM-A5NM 
       23.47        25.18         5.49         9.80         2.66        19.30 

  AMP PEAK  7(5P13.2) MUTATED AMP PEAK  7(5P13.2) WILD-TYPE 
                         0.26                          2.66 
  AMP PEAK  7(5P13.2) MUTATED AMP PEAK  7(5P13.2) WILD-TYPE 
                        88.11                        140.35 
  AMP PEAK  7(5P13.2) MUTATED AMP PEAK  7(5P13.2) WILD-TYPE 
                       20.090                        19.465 
[1] "0.3 - 88.1 (20.1)"  "2.7 - 140.3 (19.5)"
[1] "hr=" "1"  
D7V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5P13.2) MUTATED       1                         2    22
  AMP PEAK  7(5P13.2) WILD-TYPE     2                         7    21
D7V3, multiclass
                           clus
vv                          AMP PEAK  7(5P13.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              22
                           clus
vv                          AMP PEAK  7(5P13.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                21
[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(6P24.2) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  8(6P24.2) MUTATED   15 21
  AMP PEAK  8(6P24.2) WILD-TYPE  6 13
  AMP PEAK  8(6P24.2) MUTATED AMP PEAK  8(6P24.2) WILD-TYPE 
                           36                            19 
  AMP PEAK  8(6P24.2) MUTATED AMP PEAK  8(6P24.2) WILD-TYPE 
                           21                            13 
$`AMP PEAK  8(6P24.2) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RT 
       52.31        59.38        18.08         4.87        34.62        81.70 
TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VE 
       50.17        67.13        14.70        11.87        19.63         9.57 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN 
       17.16        39.75        25.35        13.74        27.25        26.70 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       25.68        20.09        21.93        67.17        54.97        35.80 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 
       19.86        15.81       140.35        80.78        27.55        17.79 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU 
       10.42        23.47         5.49        14.86         2.66        14.53 

$`AMP PEAK  8(6P24.2) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N6-A4V9 TCGA-N6-A4VD TCGA-N7-A4Y5 
        4.67        22.52        29.95        17.42         3.68         0.26 
TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PQ TCGA-N8-A56S TCGA-NA-A4QY 
       12.43        13.38        26.63        18.81        12.20         3.75 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VW 
        6.67        88.11        25.18         9.80         5.49        31.20 
TCGA-QM-A5NM 
       19.30 

  AMP PEAK  8(6P24.2) MUTATED AMP PEAK  8(6P24.2) WILD-TYPE 
                         2.66                          0.26 
  AMP PEAK  8(6P24.2) MUTATED AMP PEAK  8(6P24.2) WILD-TYPE 
                       140.35                         88.11 
  AMP PEAK  8(6P24.2) MUTATED AMP PEAK  8(6P24.2) WILD-TYPE 
                        22.70                         13.38 
[1] "2.7 - 140.3 (22.7)" "0.3 - 88.1 (13.4)" 
[1] "hr=" "1.8"
D8V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P24.2) MUTATED       2                         7    27
  AMP PEAK  8(6P24.2) WILD-TYPE     1                         2    16
D8V3, multiclass
                           clus
vv                          AMP PEAK  8(6P24.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              27
                           clus
vv                          AMP PEAK  8(6P24.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                16
[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(8P11.21) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(8P11.21) MUTATED   12 20
  AMP PEAK  9(8P11.21) WILD-TYPE  9 14
  AMP PEAK  9(8P11.21) MUTATED AMP PEAK  9(8P11.21) WILD-TYPE 
                            32                             23 
  AMP PEAK  9(8P11.21) MUTATED AMP PEAK  9(8P11.21) WILD-TYPE 
                            20                             14 
$`AMP PEAK  9(8P11.21) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RT 
       52.31         4.67        59.38         4.87        34.62        81.70 
TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       50.17        14.70        11.87         9.57        17.16        39.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM 
       25.35         0.26        12.43        13.38        26.63        27.25 
TCGA-N8-A4PO TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QY 
       25.68        67.17        54.97        15.81        80.78         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU 
       17.79         6.67        88.11        14.86         2.66        14.53 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.20        19.30 

$`AMP PEAK  9(8P11.21) WILD-TYPE`
TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VC 
       18.08        22.52        29.95        67.13        17.42        19.63 
TCGA-N6-A4VD TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S 
        3.68        13.74        26.70        20.09        18.81        12.20 
TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-ND-A4W6 
       21.93        35.80        19.86       140.35        27.55        10.42 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A5CP 
       23.47        25.18         5.49         9.80         5.49 

  AMP PEAK  9(8P11.21) MUTATED AMP PEAK  9(8P11.21) WILD-TYPE 
                          0.26                           3.68 
  AMP PEAK  9(8P11.21) MUTATED AMP PEAK  9(8P11.21) WILD-TYPE 
                         88.11                         140.35 
  AMP PEAK  9(8P11.21) MUTATED AMP PEAK  9(8P11.21) WILD-TYPE 
                        18.545                         19.860 
[1] "0.3 - 88.1 (18.5)"  "3.7 - 140.3 (19.9)"
[1] "hr=" "1.1"
D9V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(8P11.21) MUTATED       1                         4    27
  AMP PEAK  9(8P11.21) WILD-TYPE     2                         5    16
D9V3, multiclass
                           clus
vv                          AMP PEAK  9(8P11.21) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               27
                           clus
vv                          AMP PEAK  9(8P11.21) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 16
[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 10(8Q11.23) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 10(8Q11.23) MUTATED   14 23
  AMP PEAK 10(8Q11.23) WILD-TYPE  7 11
  AMP PEAK 10(8Q11.23) MUTATED AMP PEAK 10(8Q11.23) WILD-TYPE 
                            37                             18 
  AMP PEAK 10(8Q11.23) MUTATED AMP PEAK 10(8Q11.23) WILD-TYPE 
                            23                             11 
$`AMP PEAK 10(8Q11.23) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RU 
       52.31         4.67        59.38         4.87        34.62        50.17 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       67.13        14.70        11.87         9.57        17.16        39.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM 
       25.35         0.26        12.43        13.38        26.63        27.25 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q8 
       25.68        20.09        18.81        21.93        35.80        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 
      140.35        80.78        27.55         3.75        17.79        88.11 
TCGA-ND-A4W6 TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
       10.42        14.86         2.66         5.49        14.53        31.20 
TCGA-QM-A5NM 
       19.30 

$`AMP PEAK 10(8Q11.23) WILD-TYPE`
TCGA-N5-A4RJ TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N6-A4V9 TCGA-N6-A4VC 
       18.08        22.52        29.95        81.70        17.42        19.63 
TCGA-N6-A4VD TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 
        3.68        13.74        26.70        12.20        67.17        54.97 
TCGA-N9-A4Q7 TCGA-NA-A4R1 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU 
       19.86         6.67        23.47        25.18         5.49         9.80 

  AMP PEAK 10(8Q11.23) MUTATED AMP PEAK 10(8Q11.23) WILD-TYPE 
                          0.26                           3.68 
  AMP PEAK 10(8Q11.23) MUTATED AMP PEAK 10(8Q11.23) WILD-TYPE 
                        140.35                          81.70 
  AMP PEAK 10(8Q11.23) MUTATED AMP PEAK 10(8Q11.23) WILD-TYPE 
                        19.300                         19.745 
[1] "0.3 - 140.3 (19.3)" "3.7 - 81.7 (19.7)" 
[1] "hr=" "1.1"
D10V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(8Q11.23) MUTATED       1                         5    31
  AMP PEAK 10(8Q11.23) WILD-TYPE     2                         4    12
D10V3, multiclass
                           clus
vv                          AMP PEAK 10(8Q11.23) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               31
                           clus
vv                          AMP PEAK 10(8Q11.23) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  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 11(8Q24.21) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(8Q24.21) MUTATED   15 26
  AMP PEAK 11(8Q24.21) WILD-TYPE  6  8
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            41                             14 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                            26                              8 
$`AMP PEAK 11(8Q24.21) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
        4.67        59.38         4.87        81.70        50.17        67.13 
TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       14.70        17.42        19.63         9.57        17.16        39.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM 
       25.35         0.26        12.43        13.38        26.63        27.25 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q4 
       25.68        20.09        18.81        12.20        21.93        35.80 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 
       19.86        15.81        80.78        27.55         3.75        17.79 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX 
        6.67        88.11        10.42        23.47         5.49        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        2.66         5.49        14.53        31.20        19.30 

$`AMP PEAK 11(8Q24.21) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A59F 
       52.31        18.08        34.62        22.52        29.95        11.87 
TCGA-N6-A4VD TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-NA-A4QV 
        3.68        13.74        26.70        67.17        54.97       140.35 
TCGA-ND-A4WC TCGA-NF-A4WU 
       25.18         9.80 

  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                          0.26                           3.68 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                         88.11                         140.35 
  AMP PEAK 11(8Q24.21) MUTATED AMP PEAK 11(8Q24.21) WILD-TYPE 
                         18.81                          25.94 
[1] "0.3 - 88.1 (18.8)"  "3.7 - 140.3 (25.9)"
[1] "hr=" "1.5"
D11V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(8Q24.21) MUTATED       2                         5    34
  AMP PEAK 11(8Q24.21) WILD-TYPE     1                         4     9
D11V3, multiclass
                           clus
vv                          AMP PEAK 11(8Q24.21) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               34
                           clus
vv                          AMP PEAK 11(8Q24.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  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(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(8Q24.21) MUTATED   13 26
  AMP PEAK 12(8Q24.21) WILD-TYPE  8  8
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            39                             16 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            26                              8 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
        4.67        59.38         4.87        81.70        50.17        67.13 
TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       14.70        17.42        19.63         3.68         9.57        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
       39.75        25.35         0.26        12.43        13.38        26.63 
TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q4 
       27.25        25.68        20.09        18.81        21.93        35.80 
TCGA-N9-A4Q8 TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
       15.81        27.55         3.75        17.79         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       10.42        23.47         5.49        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
       14.53        31.20        19.30 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A59F 
       52.31        18.08        34.62        22.52        29.95        11.87 
TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 
       13.74        26.70        12.20        67.17        54.97        19.86 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-ND-A4WC TCGA-NF-A4WU 
      140.35        80.78        25.18         9.80 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          0.26                           9.80 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         88.11                         140.35 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         17.79                          25.94 
[1] "0.3 - 88.1 (17.8)"  "9.8 - 140.3 (25.9)"
[1] "hr=" "2"  
D12V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q24.21) MUTATED       2                         4    33
  AMP PEAK 12(8Q24.21) WILD-TYPE     1                         5    10
D12V3, multiclass
                           clus
vv                          AMP PEAK 12(8Q24.21) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               33
                           clus
vv                          AMP PEAK 12(8Q24.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              5
  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 = AMP PEAK 13(10Q22.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(10Q22.2) MUTATED    9 16
  AMP PEAK 13(10Q22.2) WILD-TYPE 12 18
  AMP PEAK 13(10Q22.2) MUTATED AMP PEAK 13(10Q22.2) WILD-TYPE 
                            25                             30 
  AMP PEAK 13(10Q22.2) MUTATED AMP PEAK 13(10Q22.2) WILD-TYPE 
                            16                             18 
$`AMP PEAK 13(10Q22.2) MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VE 
       18.08        34.62        67.13        14.70        11.87         9.57 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       39.75        25.35         0.26        13.38        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-NA-A4QV 
       26.70        25.68        18.81        21.93        67.17       140.35 
TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NG-A4VU 
       80.78        17.79        88.11        23.47         5.49        14.53 
TCGA-NG-A4VW 
       31.20 

$`AMP PEAK 13(10Q22.2) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS 
       52.31         4.67        59.38         4.87        22.52        29.95 
TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VF 
       81.70        50.17        17.42        19.63         3.68        17.16 
TCGA-N7-A4Y8 TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       12.43        27.25        20.09        12.20        54.97        35.80 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-ND-A4W6 
       19.86        15.81        27.55         3.75         6.67        10.42 
TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-QM-A5NM 
       25.18         9.80        14.86         2.66         5.49        19.30 

  AMP PEAK 13(10Q22.2) MUTATED AMP PEAK 13(10Q22.2) WILD-TYPE 
                          0.26                           2.66 
  AMP PEAK 13(10Q22.2) MUTATED AMP PEAK 13(10Q22.2) WILD-TYPE 
                        140.35                          81.70 
  AMP PEAK 13(10Q22.2) MUTATED AMP PEAK 13(10Q22.2) WILD-TYPE 
                         23.47                          18.36 
[1] "0.3 - 140.3 (23.5)" "2.7 - 81.7 (18.4)" 
[1] "hr=" "1.3"
D13V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(10Q22.2) MUTATED       2                         4    20
  AMP PEAK 13(10Q22.2) WILD-TYPE     1                         5    23
D13V3, multiclass
                           clus
vv                          AMP PEAK 13(10Q22.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               20
                           clus
vv                          AMP PEAK 13(10Q22.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 23
[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 = AMP PEAK 14(11Q13.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(11Q13.1) MUTATED    9 10
  AMP PEAK 14(11Q13.1) WILD-TYPE 12 24
  AMP PEAK 14(11Q13.1) MUTATED AMP PEAK 14(11Q13.1) WILD-TYPE 
                            19                             36 
  AMP PEAK 14(11Q13.1) MUTATED AMP PEAK 14(11Q13.1) WILD-TYPE 
                            10                             24 
$`AMP PEAK 14(11Q13.1) MUTATED`
TCGA-N5-A4RM TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4VE TCGA-N8-A4PN 
        4.87        81.70        50.17        67.13         9.57        26.70 
TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       20.09        12.20        54.97        35.80        19.86        15.81 
TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 
       80.78        17.79        88.11         5.49        14.86         2.66 
TCGA-NG-A4VU 
       14.53 

$`AMP PEAK 14(11Q13.1) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31         4.67        59.38        18.08        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD 
       29.95        14.70        11.87        17.42        19.63         3.68 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B 
       17.16        39.75        25.35         0.26        12.43        13.38 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ 
       26.63        13.74        27.25        25.68        18.81        21.93 
TCGA-N9-A4Q1 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-ND-A4W6 
       67.17       140.35        27.55         3.75         6.67        10.42 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
       23.47        25.18         9.80         5.49        31.20        19.30 

  AMP PEAK 14(11Q13.1) MUTATED AMP PEAK 14(11Q13.1) WILD-TYPE 
                          2.66                           0.26 
  AMP PEAK 14(11Q13.1) MUTATED AMP PEAK 14(11Q13.1) WILD-TYPE 
                         88.11                         140.35 
  AMP PEAK 14(11Q13.1) MUTATED AMP PEAK 14(11Q13.1) WILD-TYPE 
                        19.860                         19.465 
[1] "2.7 - 88.1 (19.9)"  "0.3 - 140.3 (19.5)"
[1] "hr=" "1.5"
D14V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(11Q13.1) MUTATED       0                         2    16
  AMP PEAK 14(11Q13.1) WILD-TYPE     3                         7    27
D14V3, multiclass
                           clus
vv                          AMP PEAK 14(11Q13.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               16
                           clus
vv                          AMP PEAK 14(11Q13.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 27
[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 = AMP PEAK 15(12Q12) MUTATION ANALYSIS
D15V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 15(12Q12) MUTATED   10 12
  AMP PEAK 15(12Q12) WILD-TYPE 11 22
  AMP PEAK 15(12Q12) MUTATED AMP PEAK 15(12Q12) WILD-TYPE 
                          22                           33 
  AMP PEAK 15(12Q12) MUTATED AMP PEAK 15(12Q12) WILD-TYPE 
                          12                           22 
$`AMP PEAK 15(12Q12) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E 
        4.67         4.87        22.52        81.70        50.17        14.70 
TCGA-N6-A4V9 TCGA-N6-A4VE TCGA-N7-A4Y8 TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO 
       17.42         9.57        12.43        27.25        26.70        25.68 
TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       20.09        12.20        67.17        54.97        35.80        19.86 
TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NF-A4WX 
       80.78        17.79         6.67        14.86 

$`AMP PEAK 15(12Q12) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RV 
       52.31        59.38        18.08        34.62        29.95        67.13 
TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       11.87        19.63         3.68        17.16        39.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PQ TCGA-N9-A4PZ 
        0.26        13.38        26.63        13.74        18.81        21.93 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4W6 
       15.81       140.35        27.55         3.75        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP 
       23.47        25.18         5.49         9.80         2.66         5.49 
TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
       14.53        31.20        19.30 

  AMP PEAK 15(12Q12) MUTATED AMP PEAK 15(12Q12) WILD-TYPE 
                        4.67                         0.26 
  AMP PEAK 15(12Q12) MUTATED AMP PEAK 15(12Q12) WILD-TYPE 
                       81.70                       140.35 
  AMP PEAK 15(12Q12) MUTATED AMP PEAK 15(12Q12) WILD-TYPE 
                      19.975                       19.300 
[1] "4.7 - 81.7 (20.0)"  "0.3 - 140.3 (19.3)"
[1] "hr=" "1.3"
D15V2, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(12Q12) MUTATED       0                         6    15
  AMP PEAK 15(12Q12) WILD-TYPE     3                         3    28
D15V3, multiclass
                           clus
vv                          AMP PEAK 15(12Q12) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             15
                           clus
vv                          AMP PEAK 15(12Q12) WILD-TYPE
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               28
[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 = AMP PEAK 16(12Q15) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 16(12Q15) MUTATED    7 10
  AMP PEAK 16(12Q15) WILD-TYPE 14 24
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          17                           38 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                          10                           24 
$`AMP PEAK 16(12Q15) MUTATED`
TCGA-N5-A4RM TCGA-N5-A4RT TCGA-N5-A59E TCGA-N6-A4VE TCGA-N6-A4VG TCGA-N7-A4Y5 
        4.87        81.70        14.70         9.57        39.75         0.26 
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q4 
       13.74        27.25        20.09        12.20        67.17        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WX 
       19.86       140.35        10.42         5.49        14.86 

$`AMP PEAK 16(12Q15) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31         4.67        59.38        18.08        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       29.95        50.17        67.13        11.87        17.42        19.63 
TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
        3.68        17.16        25.35        12.43        13.38        26.63 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q8 
       26.70        25.68        18.81        21.93        54.97        15.81 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
       80.78        27.55         3.75        17.79         6.67        88.11 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       23.47        25.18         9.80         2.66         5.49        14.53 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.20        19.30 

  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                        0.26                         2.66 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                      140.35                        88.11 
  AMP PEAK 16(12Q15) MUTATED AMP PEAK 16(12Q15) WILD-TYPE 
                       14.86                        20.78 
[1] "0.3 - 140.3 (14.9)" "2.7 - 88.1 (20.8)" 
[1] "hr=" "1"  
D16V2, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(12Q15) MUTATED       0                         5    11
  AMP PEAK 16(12Q15) WILD-TYPE     3                         4    32
D16V3, multiclass
                           clus
vv                          AMP PEAK 16(12Q15) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             11
                           clus
vv                          AMP PEAK 16(12Q15) WILD-TYPE
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               32
[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 = AMP PEAK 17(13Q31.3) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(13Q31.3) MUTATED   11 14
  AMP PEAK 17(13Q31.3) WILD-TYPE 10 20
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                            25                             30 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                            14                             20 
$`AMP PEAK 17(13Q31.3) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RV TCGA-N5-A59E 
        4.67        59.38        34.62        22.52        67.13        14.70 
TCGA-N5-A59F TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN 
       11.87         0.26        12.43        13.74        27.25        26.70 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       54.97        35.80        15.81       140.35        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WX TCGA-NF-A4X2 
        3.75        17.79        10.42        23.47        14.86         2.66 
TCGA-NG-A4VU 
       14.53 

$`AMP PEAK 17(13Q31.3) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU 
       52.31        18.08         4.87        29.95        81.70        50.17 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       17.42        19.63         3.68         9.57        17.16        39.75 
TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ 
       25.35        13.38        26.63        25.68        20.09        18.81 
TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q7 TCGA-NA-A4R1 TCGA-NA-A5I1 
       12.20        21.93        67.17        19.86         6.67        88.11 
TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
       25.18         5.49         9.80         5.49        31.20        19.30 

  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                          0.26                           3.68 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                        140.35                          88.11 
  AMP PEAK 17(13Q31.3) MUTATED AMP PEAK 17(13Q31.3) WILD-TYPE 
                        17.790                         19.745 
[1] "0.3 - 140.3 (17.8)" "3.7 - 88.1 (19.7)" 
[1] "hr=" "1.2"
D17V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(13Q31.3) MUTATED       1                         5    18
  AMP PEAK 17(13Q31.3) WILD-TYPE     2                         4    25
D17V3, multiclass
                           clus
vv                          AMP PEAK 17(13Q31.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               18
                           clus
vv                          AMP PEAK 17(13Q31.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 25
[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 = AMP PEAK 18(16P11.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 18(16P11.2) MUTATED    6 13
  AMP PEAK 18(16P11.2) WILD-TYPE 15 21
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                            19                             36 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                            13                             21 
$`AMP PEAK 18(16P11.2) MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RU TCGA-N5-A59E TCGA-N6-A4VC 
       18.08         4.87        34.62        50.17        14.70        19.63 
TCGA-N6-A4VG TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-NA-A4QW TCGA-NA-A4QX 
       39.75        26.70        12.20        67.17        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NG-A4VU 
        3.75        17.79         6.67         5.49        14.86        14.53 
TCGA-QM-A5NM 
       19.30 

$`AMP PEAK 18(16P11.2) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT 
       52.31         4.67        59.38        22.52        29.95        81.70 
TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       67.13        11.87        17.42         3.68         9.57        17.16 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       25.35         0.26        12.43        13.38        26.63        13.74 
TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q3 
       27.25        25.68        20.09        18.81        21.93        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A5I1 TCGA-ND-A4W6 
       35.80        19.86        15.81       140.35        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW 
       23.47        25.18         9.80         2.66         5.49        31.20 

  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                          3.75                           0.26 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                         80.78                         140.35 
  AMP PEAK 18(16P11.2) MUTATED AMP PEAK 18(16P11.2) WILD-TYPE 
                         18.08                          21.01 
[1] "3.8 - 80.8 (18.1)"  "0.3 - 140.3 (21.0)"
[1] "hr=" "1.3"
D18V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(16P11.2) MUTATED       1                         2    16
  AMP PEAK 18(16P11.2) WILD-TYPE     2                         7    27
D18V3, multiclass
                           clus
vv                          AMP PEAK 18(16P11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               16
                           clus
vv                          AMP PEAK 18(16P11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 27
[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 = AMP PEAK 19(17Q12) MUTATION ANALYSIS
D19V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 19(17Q12) MUTATED   11 16
  AMP PEAK 19(17Q12) WILD-TYPE 10 18
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          27                           28 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                          16                           18 
$`AMP PEAK 19(17Q12) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
       52.31         4.67        18.08        81.70        50.17        67.13 
TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI 
       19.63         9.57        17.16         0.26        13.38        26.63 
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4Q4 
       13.74        27.25        26.70        20.09        18.81        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       19.86        80.78         3.75         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX 
       23.47         9.80        14.86 

$`AMP PEAK 19(17Q12) WILD-TYPE`
TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A59E 
       59.38         4.87        34.62        22.52        29.95        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VD TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y8 
       11.87        17.42         3.68        39.75        25.35        12.43 
TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 
       25.68        12.20        21.93        67.17        54.97        15.81 
TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4X2 
      140.35        27.55        17.79        25.18         5.49         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        14.53        31.20        19.30 

  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                        0.26                         2.66 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                       88.11                       140.35 
  AMP PEAK 19(17Q12) MUTATED AMP PEAK 19(17Q12) WILD-TYPE 
                      19.630                       20.615 
[1] "0.3 - 88.1 (19.6)"  "2.7 - 140.3 (20.6)"
[1] "hr=" "1.1"
D19V2, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q12) MUTATED       1                         4    21
  AMP PEAK 19(17Q12) WILD-TYPE     2                         5    22
D19V3, multiclass
                           clus
vv                          AMP PEAK 19(17Q12) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          4
  WHITE                                             21
                           clus
vv                          AMP PEAK 19(17Q12) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               22
[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 = AMP PEAK 20(17Q25.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(17Q25.1) MUTATED   15 17
  AMP PEAK 20(17Q25.1) WILD-TYPE  6 17
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            32                             23 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                            17                             17 
$`AMP PEAK 20(17Q25.1) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RU 
        4.67        18.08         4.87        34.62        29.95        50.17 
TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 
       67.13        17.42         9.57        17.16        39.75         0.26 
TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ 
       12.43        13.38        27.25        26.70        25.68        18.81 
TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW 
       21.93        67.17        35.80        19.86        15.81        80.78 
TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX 
        3.75         6.67        10.42        23.47         9.80        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VU 
        2.66        14.53 

$`AMP PEAK 20(17Q25.1) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A59E TCGA-N5-A59F 
       52.31        59.38        22.52        81.70        14.70        11.87 
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PP 
       19.63         3.68        25.35        26.63        13.74        20.09 
TCGA-N8-A56S TCGA-N9-A4Q3 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A5I1 
       12.20        54.97       140.35        27.55        17.79        88.11 
TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
       25.18         5.49         5.49        31.20        19.30 

  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                          0.26                           3.68 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                         80.78                         140.35 
  AMP PEAK 20(17Q25.1) MUTATED AMP PEAK 20(17Q25.1) WILD-TYPE 
                         17.75                          22.52 
[1] "0.3 - 80.8 (17.8)"  "3.7 - 140.3 (22.5)"
[1] "hr=" "1"  
D20V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(17Q25.1) MUTATED       1                         6    24
  AMP PEAK 20(17Q25.1) WILD-TYPE     2                         3    19
D20V3, multiclass
                           clus
vv                          AMP PEAK 20(17Q25.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               24
                           clus
vv                          AMP PEAK 20(17Q25.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 19
[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 = AMP PEAK 21(19P13.2) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 21(19P13.2) MUTATED    9 10
  AMP PEAK 21(19P13.2) WILD-TYPE 12 24
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            19                             36 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                            10                             24 
$`AMP PEAK 21(19P13.2) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RV TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VG TCGA-N7-A4Y5 
       52.31        67.13        19.63         9.57        39.75         0.26 
TCGA-N7-A59B TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       13.38        25.68        20.09        21.93        54.97        35.80 
TCGA-N9-A4Q8 TCGA-NA-A4QY TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       15.81         3.75        14.86         2.66         5.49        14.53 
TCGA-QM-A5NM 
       19.30 

$`AMP PEAK 21(19P13.2) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
        4.67        59.38        18.08         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       29.95        81.70        50.17        14.70        11.87        17.42 
TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PL 
        3.68        17.16        25.35        12.43        26.63        13.74 
TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q7 
       27.25        26.70        18.81        12.20        67.17        19.86 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
      140.35        80.78        27.55        17.79         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NG-A4VW 
       10.42        23.47        25.18         5.49         9.80        31.20 

  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                          0.26                           3.68 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         67.13                         140.35 
  AMP PEAK 21(19P13.2) MUTATED AMP PEAK 21(19P13.2) WILD-TYPE 
                         19.30                          21.19 
[1] "0.3 - 67.1 (19.3)"  "3.7 - 140.3 (21.2)"
[1] "hr=" "1"  
D21V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(19P13.2) MUTATED       0                         2    16
  AMP PEAK 21(19P13.2) WILD-TYPE     3                         7    27
D21V3, multiclass
                           clus
vv                          AMP PEAK 21(19P13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               16
                           clus
vv                          AMP PEAK 21(19P13.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 27
[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 = AMP PEAK 22(19Q12) MUTATION ANALYSIS
D22V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 22(19Q12) MUTATED   18 26
  AMP PEAK 22(19Q12) WILD-TYPE  3  8
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                          44                           11 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                          26                            8 
$`AMP PEAK 22(19Q12) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS 
       52.31        18.08         4.87        34.62        22.52        29.95 
TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE 
       81.70        67.13        14.70        17.42        19.63         9.57 
TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PM 
       39.75         0.26        12.43        13.38        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       26.70        25.68        20.09        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       67.17        54.97        35.80        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.55         3.75        17.79         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       23.47         5.49         9.80        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-QM-A5NM 
       14.53        19.30 

$`AMP PEAK 22(19Q12) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RU TCGA-N5-A59F TCGA-N6-A4VD TCGA-N6-A4VF 
        4.67        59.38        50.17        11.87         3.68        17.16 
TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N9-A4Q7 TCGA-ND-A4WC TCGA-NG-A4VW 
       25.35        26.63        19.86        25.18        31.20 

  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                        0.26                         3.68 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                      140.35                        59.38 
  AMP PEAK 22(19Q12) MUTATED AMP PEAK 22(19Q12) WILD-TYPE 
                      19.055                       25.180 
[1] "0.3 - 140.3 (19.1)" "3.7 - 59.4 (25.2)" 
[1] "hr=" "1.3"
D22V2, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(19Q12) MUTATED       2                         7    35
  AMP PEAK 22(19Q12) WILD-TYPE     1                         2     8
D22V3, multiclass
                           clus
vv                          AMP PEAK 22(19Q12) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          7
  WHITE                                             35
                           clus
vv                          AMP PEAK 22(19Q12) WILD-TYPE
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  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(23) Variable = AMP PEAK 23(20Q11.21) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 23(20Q11.21) MUTATED   18 30
  AMP PEAK 23(20Q11.21) WILD-TYPE  3  4
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                             48                               7 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                             30                               4 
$`AMP PEAK 23(20Q11.21) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
       52.31         4.67        59.38        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       22.52        29.95        81.70        50.17        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       11.87        17.42         9.57        17.16        39.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM 
        0.26        12.43        13.38        26.63        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       26.70        25.68        18.81        12.20        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       54.97        35.80        19.86        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.55         3.75        17.79         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
       23.47         5.49        14.86         5.49        14.53        19.30 

$`AMP PEAK 23(20Q11.21) WILD-TYPE`
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N8-A4PP TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4X2 
       19.63         3.68        20.09        25.18         9.80         2.66 
TCGA-NG-A4VW 
       31.20 

  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                           0.26                            2.66 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                         140.35                           31.20 
  AMP PEAK 23(20Q11.21) MUTATED AMP PEAK 23(20Q11.21) WILD-TYPE 
                          19.58                           19.63 
[1] "0.3 - 140.3 (19.6)" "2.7 - 31.2 (19.6)" 
[1] "hr=" "1.4"
D23V2, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(20Q11.21) MUTATED       1                         9    37
  AMP PEAK 23(20Q11.21) WILD-TYPE     2                         0     6
D23V3, multiclass
                           clus
vv                          AMP PEAK 23(20Q11.21) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                                37
                           clus
vv                          AMP PEAK 23(20Q11.21) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                   6
[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 = AMP PEAK 24(20Q11.21) MUTATION ANALYSIS
D24V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 24(20Q11.21) MUTATED   17 31
  AMP PEAK 24(20Q11.21) WILD-TYPE  4  3
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                             48                               7 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                             31                               3 
$`AMP PEAK 24(20Q11.21) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
       52.31         4.67        59.38        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       22.52        29.95        81.70        50.17        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       11.87        17.42         9.57        17.16        39.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM 
        0.26        12.43        13.38        26.63        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       26.70        25.68        20.09        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       67.17        35.80        19.86        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.55         3.75        17.79         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
       23.47         5.49        14.86         5.49        14.53        19.30 

$`AMP PEAK 24(20Q11.21) WILD-TYPE`
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N9-A4Q3 TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4X2 
       19.63         3.68        54.97        25.18         9.80         2.66 
TCGA-NG-A4VW 
       31.20 

  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                           0.26                            2.66 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                         140.35                           54.97 
  AMP PEAK 24(20Q11.21) MUTATED AMP PEAK 24(20Q11.21) WILD-TYPE 
                          19.58                           19.63 
[1] "0.3 - 140.3 (19.6)" "2.7 - 55.0 (19.6)" 
[1] "hr=" "1.2"
D24V2, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(20Q11.21) MUTATED       1                         9    37
  AMP PEAK 24(20Q11.21) WILD-TYPE     2                         0     6
D24V3, multiclass
                           clus
vv                          AMP PEAK 24(20Q11.21) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                                37
                           clus
vv                          AMP PEAK 24(20Q11.21) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                   6
[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 = AMP PEAK 25(XP11.21) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 25(XP11.21) MUTATED    9 18
  AMP PEAK 25(XP11.21) WILD-TYPE 12 16
  AMP PEAK 25(XP11.21) MUTATED AMP PEAK 25(XP11.21) WILD-TYPE 
                            27                             28 
  AMP PEAK 25(XP11.21) MUTATED AMP PEAK 25(XP11.21) WILD-TYPE 
                            18                             16 
$`AMP PEAK 25(XP11.21) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS 
       52.31        18.08         4.87        34.62        22.52        29.95 
TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N7-A4Y0 
       81.70        50.17        67.13        14.70        11.87        25.35 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
        0.26        13.38        26.63        21.93        67.17        54.97 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-NF-A4WX 
       15.81       140.35        80.78        17.79        10.42        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-NG-A4VW 
        2.66        14.53        31.20 

$`AMP PEAK 25(XP11.21) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE 
        4.67        59.38        17.42        19.63         3.68         9.57 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y8 TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN 
       17.16        39.75        12.43        13.74        27.25        26.70 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       25.68        20.09        18.81        12.20        35.80        19.86 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WC 
       27.55         3.75         6.67        88.11        23.47        25.18 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A5CP TCGA-QM-A5NM 
        5.49         9.80         5.49        19.30 

  AMP PEAK 25(XP11.21) MUTATED AMP PEAK 25(XP11.21) WILD-TYPE 
                          0.26                           3.68 
  AMP PEAK 25(XP11.21) MUTATED AMP PEAK 25(XP11.21) WILD-TYPE 
                        140.35                          88.11 
  AMP PEAK 25(XP11.21) MUTATED AMP PEAK 25(XP11.21) WILD-TYPE 
                        22.520                         19.055 
[1] "0.3 - 140.3 (22.5)" "3.7 - 88.1 (19.1)" 
[1] "hr=" "1.2"
D25V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(XP11.21) MUTATED       1                         5    21
  AMP PEAK 25(XP11.21) WILD-TYPE     2                         4    22
D25V3, multiclass
                           clus
vv                          AMP PEAK 25(XP11.21) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               21
                           clus
vv                          AMP PEAK 25(XP11.21) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 22
[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  1(1P36.21) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.21) MUTATED    7 11
  DEL PEAK  1(1P36.21) WILD-TYPE 14 23
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            18                             37 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                            11                             23 
$`DEL PEAK  1(1P36.21) MUTATED`
TCGA-N5-A4RD TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE 
        4.67        14.70        17.42        19.63         3.68         9.57 
TCGA-N6-A4VG TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       39.75        25.68        20.09        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A5I1 TCGA-ND-A4WF TCGA-QM-A5NM 
       67.17        54.97        35.80        88.11         5.49        19.30 

$`DEL PEAK  1(1P36.21) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31        59.38        18.08         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4VF 
       29.95        81.70        50.17        67.13        11.87        17.16 
TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       25.35         0.26        12.43        13.38        26.63        13.74 
TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       27.25        26.70        19.86        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WA 
       27.55         3.75        17.79         6.67        10.42        23.47 
TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       25.18         9.80        14.86         2.66         5.49        14.53 
TCGA-NG-A4VW 
       31.20 

  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                          3.68                           0.26 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                         88.11                         140.35 
  DEL PEAK  1(1P36.21) MUTATED DEL PEAK  1(1P36.21) WILD-TYPE 
                        19.465                         19.860 
[1] "3.7 - 88.1 (19.5)"  "0.3 - 140.3 (19.9)"
[1] "hr=" "1"  
D26V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.21) MUTATED       1                         3    15
  DEL PEAK  1(1P36.21) WILD-TYPE     2                         6    28
D26V3, multiclass
                           clus
vv                          DEL PEAK  1(1P36.21) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               15
                           clus
vv                          DEL PEAK  1(1P36.21) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 28
[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  2(2Q22.1) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  2(2Q22.1) MUTATED    3  8
  DEL PEAK  2(2Q22.1) WILD-TYPE 18 26
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                           11                            44 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                            8                            26 
$`DEL PEAK  2(2Q22.1) MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N9-A4Q7 
       18.08         4.87         0.26        12.43        26.63        19.86 
TCGA-NA-A4QW TCGA-NA-A4QY TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4X2 
       80.78         3.75        23.47         5.49         2.66 

$`DEL PEAK  2(2Q22.1) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS 
       52.31         4.67        59.38        34.62        22.52        29.95 
TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       81.70        50.17        67.13        14.70        11.87        17.42 
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       19.63         3.68         9.57        17.16        39.75        25.35 
TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP 
       13.38        13.74        27.25        26.70        25.68        20.09 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       18.81        12.20        21.93        67.17        54.97        35.80 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 
       15.81       140.35        27.55        17.79         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU 
       10.42        25.18         9.80        14.86         5.49        14.53 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.20        19.30 

  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                         0.26                          3.68 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                        80.78                        140.35 
  DEL PEAK  2(2Q22.1) MUTATED DEL PEAK  2(2Q22.1) WILD-TYPE 
                        12.43                         21.01 
[1] "0.3 - 80.8 (12.4)"  "3.7 - 140.3 (21.0)"
[1] "hr=" "2.1"
D27V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(2Q22.1) MUTATED       1                         1     9
  DEL PEAK  2(2Q22.1) WILD-TYPE     2                         8    34
D27V3, multiclass
                           clus
vv                          DEL PEAK  2(2Q22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               9
                           clus
vv                          DEL PEAK  2(2Q22.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                34
[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  3(3P14.2) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(3P14.2) MUTATED   15 22
  DEL PEAK  3(3P14.2) WILD-TYPE  6 12
  DEL PEAK  3(3P14.2) MUTATED DEL PEAK  3(3P14.2) WILD-TYPE 
                           37                            18 
  DEL PEAK  3(3P14.2) MUTATED DEL PEAK  3(3P14.2) WILD-TYPE 
                           22                            12 
$`DEL PEAK  3(3P14.2) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS 
       52.31         4.67        59.38         4.87        22.52        29.95 
TCGA-N5-A4RT TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE 
       81.70        14.70        11.87        17.42        19.63         9.57 
TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       39.75         0.26        12.43        13.38        26.63        13.74 
TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       27.25        25.68        20.09        12.20        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       54.97        35.80        19.86       140.35        27.55         3.75 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
        5.49         9.80        14.86         2.66         5.49        14.53 
TCGA-QM-A5NM 
       19.30 

$`DEL PEAK  3(3P14.2) WILD-TYPE`
TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4VD TCGA-N6-A4VF 
       18.08        34.62        50.17        67.13         3.68        17.16 
TCGA-N7-A4Y0 TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4R0 
       25.35        26.70        18.81        15.81        80.78        17.79 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NG-A4VW 
        6.67        88.11        10.42        23.47        25.18        31.20 

  DEL PEAK  3(3P14.2) MUTATED DEL PEAK  3(3P14.2) WILD-TYPE 
                         0.26                          3.68 
  DEL PEAK  3(3P14.2) MUTATED DEL PEAK  3(3P14.2) WILD-TYPE 
                       140.35                         88.11 
  DEL PEAK  3(3P14.2) MUTATED DEL PEAK  3(3P14.2) WILD-TYPE 
                       19.300                        24.325 
[1] "0.3 - 140.3 (19.3)" "3.7 - 88.1 (24.3)" 
[1] "hr=" "1.1"
D28V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(3P14.2) MUTATED       0                         7    29
  DEL PEAK  3(3P14.2) WILD-TYPE     3                         2    14
D28V3, multiclass
                           clus
vv                          DEL PEAK  3(3P14.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              29
                           clus
vv                          DEL PEAK  3(3P14.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             2
  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  4(3Q13.31) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  4(3Q13.31) MUTATED    8 14
  DEL PEAK  4(3Q13.31) WILD-TYPE 13 20
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                            22                             33 
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                            14                             20 
$`DEL PEAK  4(3Q13.31) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU 
        4.67        59.38         4.87        22.52        81.70        50.17 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM 
       14.70        11.87        12.43        26.63        13.74        27.25 
TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-ND-A4WF 
       25.68        12.20        19.86        80.78         3.75         5.49 
TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
        9.80         5.49        14.53        19.30 

$`DEL PEAK  4(3Q13.31) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N6-A4V9 
       52.31        18.08        34.62        29.95        67.13        17.42 
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       19.63         3.68         9.57        17.16        39.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PN TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4PZ 
        0.26        13.38        26.70        20.09        18.81        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX 
       67.17        54.97        35.80        15.81       140.35        27.55 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC 
       17.79         6.67        88.11        10.42        23.47        25.18 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VW 
       14.86         2.66        31.20 

  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                          3.75                           0.26 
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                         81.70                         140.35 
  DEL PEAK  4(3Q13.31) MUTATED DEL PEAK  4(3Q13.31) WILD-TYPE 
                        14.615                         21.930 
[1] "3.8 - 81.7 (14.6)"  "0.3 - 140.3 (21.9)"
[1] "hr=" "1.4"
D29V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(3Q13.31) MUTATED       0                         4    18
  DEL PEAK  4(3Q13.31) WILD-TYPE     3                         5    25
D29V3, multiclass
                           clus
vv                          DEL PEAK  4(3Q13.31) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               18
                           clus
vv                          DEL PEAK  4(3Q13.31) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 25
[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  5(4Q22.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(4Q22.1) MUTATED   13 23
  DEL PEAK  5(4Q22.1) WILD-TYPE  8 11
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                           36                            19 
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                           23                            11 
$`DEL PEAK  5(4Q22.1) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
       52.31         4.67        59.38        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       22.52        50.17        67.13        11.87        17.42        19.63 
TCGA-N6-A4VE TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PL TCGA-N8-A4PO 
        9.57        39.75         0.26        12.43        13.74        25.68 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 
       20.09        18.81        12.20        21.93        67.17        35.80 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4W6 
      140.35        80.78        27.55         3.75        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-QM-A5NM 
       23.47         5.49        14.86         2.66        14.53        19.30 

$`DEL PEAK  5(4Q22.1) WILD-TYPE`
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A59E TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y0 
       29.95        81.70        14.70         3.68        17.16        25.35 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N9-A4Q3 TCGA-N9-A4Q7 
       13.38        26.63        27.25        26.70        54.97        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A5CP 
       15.81        17.79         6.67        25.18         9.80         5.49 
TCGA-NG-A4VW 
       31.20 

  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                         0.26                          3.68 
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                       140.35                         81.70 
  DEL PEAK  5(4Q22.1) MUTATED DEL PEAK  5(4Q22.1) WILD-TYPE 
                       19.465                        19.860 
[1] "0.3 - 140.3 (19.5)" "3.7 - 81.7 (19.9)" 
[1] "hr=" "1"  
D30V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(4Q22.1) MUTATED       2                         7    27
  DEL PEAK  5(4Q22.1) WILD-TYPE     1                         2    16
D30V3, multiclass
                           clus
vv                          DEL PEAK  5(4Q22.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              27
                           clus
vv                          DEL PEAK  5(4Q22.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                16
[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  6(4Q34.3) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(4Q34.3) MUTATED   11 25
  DEL PEAK  6(4Q34.3) WILD-TYPE 10  9
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           36                            19 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           25                             9 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       52.31         4.67        59.38        18.08         4.87        22.52 
TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC 
       81.70        50.17        14.70        11.87        17.42        19.63 
TCGA-N6-A4VE TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PP 
        9.57         0.26        12.43        13.74        25.68        20.09 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       18.81        12.20        21.93        67.17        54.97        35.80 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 
      140.35        80.78        27.55         3.75         6.67        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NG-A4VU TCGA-QM-A5NM 
       10.42        23.47         5.49        14.86        14.53        19.30 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N6-A4VG 
       34.62        29.95        67.13         3.68        17.16        39.75 
TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N9-A4Q7 
       25.35        13.38        26.63        27.25        26.70        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4R0 TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP 
       15.81        17.79        25.18         9.80         2.66         5.49 
TCGA-NG-A4VW 
       31.20 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         0.26                          2.66 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       140.35                         67.13 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                       19.055                        25.180 
[1] "0.3 - 140.3 (19.1)" "2.7 - 67.1 (25.2)" 
[1] "hr=" "1.4"
D31V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q34.3) MUTATED       2                         8    26
  DEL PEAK  6(4Q34.3) WILD-TYPE     1                         1    17
D31V3, multiclass
                           clus
vv                          DEL PEAK  6(4Q34.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              26
                           clus
vv                          DEL PEAK  6(4Q34.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                17
[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  7(5Q12.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(5Q12.1) MUTATED   11 15
  DEL PEAK  7(5Q12.1) WILD-TYPE 10 19
  DEL PEAK  7(5Q12.1) MUTATED DEL PEAK  7(5Q12.1) WILD-TYPE 
                           26                            29 
  DEL PEAK  7(5Q12.1) MUTATED DEL PEAK  7(5Q12.1) WILD-TYPE 
                           15                            19 
$`DEL PEAK  7(5Q12.1) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E TCGA-N6-A4VC 
       52.31        34.62        81.70        50.17        14.70        19.63 
TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PM 
       39.75         0.26        12.43        13.38        13.74        27.25 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4R0 
       25.68        18.81        67.17        35.80        15.81        17.79 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX 
        6.67        88.11        23.47         5.49         9.80        14.86 
TCGA-NF-A4X2 TCGA-NG-A4VU 
        2.66        14.53 

$`DEL PEAK  7(5Q12.1) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS 
        4.67        59.38        18.08         4.87        22.52        29.95 
TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       67.13        11.87        17.42         3.68         9.57        17.16 
TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PN TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ 
       25.35        26.63        26.70        20.09        12.20        21.93 
TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
       54.97        19.86       140.35        80.78        27.55         3.75 
TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
       10.42        25.18         5.49        31.20        19.30 

  DEL PEAK  7(5Q12.1) MUTATED DEL PEAK  7(5Q12.1) WILD-TYPE 
                         0.26                          3.68 
  DEL PEAK  7(5Q12.1) MUTATED DEL PEAK  7(5Q12.1) WILD-TYPE 
                        88.11                        140.35 
  DEL PEAK  7(5Q12.1) MUTATED DEL PEAK  7(5Q12.1) WILD-TYPE 
                        18.30                         20.09 
[1] "0.3 - 88.1 (18.3)"  "3.7 - 140.3 (20.1)"
[1] "hr=" "1.2"
D32V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(5Q12.1) MUTATED       1                         4    20
  DEL PEAK  7(5Q12.1) WILD-TYPE     2                         5    23
D32V3, multiclass
                           clus
vv                          DEL PEAK  7(5Q12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              20
                           clus
vv                          DEL PEAK  7(5Q12.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                23
[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  8(6Q26) MUTATION ANALYSIS
D33V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  8(6Q26) MUTATED    3  6
  DEL PEAK  8(6Q26) WILD-TYPE 18 28
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                          9                          46 
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                          6                          28 
$`DEL PEAK  8(6Q26) MUTATED`
TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A59F TCGA-N6-A4VG TCGA-N8-A4PL 
        4.87        22.52        81.70        11.87        39.75        13.74 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-NA-A4QY 
       20.09        18.81         3.75 

$`DEL PEAK  8(6Q26) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RS 
       52.31         4.67        59.38        18.08        34.62        29.95 
TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD 
       50.17        67.13        14.70        17.42        19.63         3.68 
TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B 
        9.57        17.16        25.35         0.26        12.43        13.38 
TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4PZ 
       26.63        27.25        26.70        25.68        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV 
       67.17        54.97        35.80        19.86        15.81       140.35 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       80.78        27.55        17.79         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 
       23.47        25.18         5.49         9.80        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        14.53        31.20        19.30 

  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                       3.75                        0.26 
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                      81.70                      140.35 
  DEL PEAK  8(6Q26) MUTATED DEL PEAK  8(6Q26) WILD-TYPE 
                     18.810                      19.745 
[1] "3.8 - 81.7 (18.8)"  "0.3 - 140.3 (19.7)"
[1] "hr=" "1.3"
D33V2, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(6Q26) MUTATED       1                         2     7
  DEL PEAK  8(6Q26) WILD-TYPE     2                         7    36
D33V3, multiclass
                           clus
vv                          DEL PEAK  8(6Q26) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                             7
                           clus
vv                          DEL PEAK  8(6Q26) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              36
[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  9(7Q11.22) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  9(7Q11.22) MUTATED    4  8
  DEL PEAK  9(7Q11.22) WILD-TYPE 17 26
  DEL PEAK  9(7Q11.22) MUTATED DEL PEAK  9(7Q11.22) WILD-TYPE 
                            12                             43 
  DEL PEAK  9(7Q11.22) MUTATED DEL PEAK  9(7Q11.22) WILD-TYPE 
                             8                             26 
$`DEL PEAK  9(7Q11.22) MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RU TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N7-A4Y5 
       18.08        50.17        11.87        19.63         9.57         0.26 
TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q8 TCGA-ND-A4W6 TCGA-NF-A4WU 
       27.25        26.70        18.81        15.81        10.42         9.80 

$`DEL PEAK  9(7Q11.22) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31         4.67        59.38         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VD 
       29.95        81.70        67.13        14.70        17.42         3.68 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
       17.16        39.75        25.35        12.43        13.38        26.63 
TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       13.74        25.68        20.09        12.20        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       54.97        35.80        19.86       140.35        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WC 
        3.75        17.79         6.67        88.11        23.47        25.18 
TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        5.49        14.86         2.66         5.49        14.53        31.20 
TCGA-QM-A5NM 
       19.30 

  DEL PEAK  9(7Q11.22) MUTATED DEL PEAK  9(7Q11.22) WILD-TYPE 
                          0.26                           2.66 
  DEL PEAK  9(7Q11.22) MUTATED DEL PEAK  9(7Q11.22) WILD-TYPE 
                         50.17                         140.35 
  DEL PEAK  9(7Q11.22) MUTATED DEL PEAK  9(7Q11.22) WILD-TYPE 
                        16.945                         21.930 
[1] "0.3 - 50.2 (16.9)"  "2.7 - 140.3 (21.9)"
[1] "hr=" "1.7"
D34V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(7Q11.22) MUTATED       0                         2    10
  DEL PEAK  9(7Q11.22) WILD-TYPE     3                         7    33
D34V3, multiclass
                           clus
vv                          DEL PEAK  9(7Q11.22) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               10
                           clus
vv                          DEL PEAK  9(7Q11.22) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              7
  WHITE                                                 33
[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 10(7Q36.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(7Q36.2) MUTATED    9 11
  DEL PEAK 10(7Q36.2) WILD-TYPE 12 23
  DEL PEAK 10(7Q36.2) MUTATED DEL PEAK 10(7Q36.2) WILD-TYPE 
                           20                            35 
  DEL PEAK 10(7Q36.2) MUTATED DEL PEAK 10(7Q36.2) WILD-TYPE 
                           11                            23 
$`DEL PEAK 10(7Q36.2) MUTATED`
TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC 
       81.70        50.17        67.13        14.70        11.87        19.63 
TCGA-N6-A4VE TCGA-N7-A4Y5 TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ 
        9.57         0.26        27.25        26.70        25.68        18.81 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A5I1 TCGA-ND-A4W6 
       67.17        54.97        15.81        80.78        88.11        10.42 
TCGA-NF-A4WU TCGA-NG-A4VU 
        9.80        14.53 

$`DEL PEAK 10(7Q36.2) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
       52.31         4.67        59.38        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N6-A4V9 TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N6-A4VG 
       22.52        29.95        17.42         3.68        17.16        39.75 
TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PP 
       25.35        12.43        13.38        26.63        13.74        20.09 
TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QX 
       12.20        21.93        35.80        19.86       140.35        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF 
        3.75        17.79         6.67        23.47        25.18         5.49 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
       14.86         2.66         5.49        31.20        19.30 

  DEL PEAK 10(7Q36.2) MUTATED DEL PEAK 10(7Q36.2) WILD-TYPE 
                         0.26                          2.66 
  DEL PEAK 10(7Q36.2) MUTATED DEL PEAK 10(7Q36.2) WILD-TYPE 
                        88.11                        140.35 
  DEL PEAK 10(7Q36.2) MUTATED DEL PEAK 10(7Q36.2) WILD-TYPE 
                       22.655                        19.300 
[1] "0.3 - 88.1 (22.7)"  "2.7 - 140.3 (19.3)"
[1] "hr=" "1.6"
D35V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(7Q36.2) MUTATED       0                         4    16
  DEL PEAK 10(7Q36.2) WILD-TYPE     3                         5    27
D35V3, multiclass
                           clus
vv                          DEL PEAK 10(7Q36.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              16
                           clus
vv                          DEL PEAK 10(7Q36.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                27
[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 11(8P23.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(8P23.2) MUTATED   12 20
  DEL PEAK 11(8P23.2) WILD-TYPE  9 14
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                           32                            23 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                           20                            14 
$`DEL PEAK 11(8P23.2) MUTATED`
TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E 
       18.08        34.62        22.52        81.70        50.17        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VG TCGA-N7-A4Y5 
       11.87        17.42        19.63         9.57        39.75         0.26 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       26.70        25.68        20.09        18.81        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       35.80        19.86        15.81       140.35        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
        3.75        17.79        88.11        10.42        23.47         5.49 
TCGA-NF-A5CP TCGA-NG-A4VU 
        5.49        14.53 

$`DEL PEAK 11(8P23.2) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RV 
       52.31         4.67        59.38         4.87        29.95        67.13 
TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
        3.68        17.16        25.35        12.43        13.38        26.63 
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A56S TCGA-N9-A4PZ TCGA-NA-A4R1 TCGA-ND-A4WC 
       13.74        27.25        12.20        21.93         6.67        25.18 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VW TCGA-QM-A5NM 
        9.80        14.86         2.66        31.20        19.30 

  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                         0.26                          2.66 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                       140.35                         67.13 
  DEL PEAK 11(8P23.2) MUTATED DEL PEAK 11(8P23.2) WILD-TYPE 
                       19.975                        17.160 
[1] "0.3 - 140.3 (20.0)" "2.7 - 67.1 (17.2)" 
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(8P23.2) MUTATED       2                         8    23
  DEL PEAK 11(8P23.2) WILD-TYPE     1                         1    20
D36V3, multiclass
                           clus
vv                          DEL PEAK 11(8P23.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              23
                           clus
vv                          DEL PEAK 11(8P23.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                20
[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 12(9P23) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 12(9P23) MUTATED   14 19
  DEL PEAK 12(9P23) WILD-TYPE  7 15
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         33                          22 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                         19                          15 
$`DEL PEAK 12(9P23) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N5-A59E 
       52.31        18.08         4.87        29.95        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 
       11.87        17.42         9.57        17.16        39.75         0.26 
TCGA-N7-A4Y8 TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A56S TCGA-N9-A4Q1 
       12.43        27.25        26.70        25.68        12.20        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       54.97        35.80        19.86        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-ND-A4WA TCGA-NF-A4WX TCGA-NF-A4X2 
       27.55         3.75        17.79        23.47        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
        5.49        14.53        19.30 

$`DEL PEAK 12(9P23) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU 
        4.67        59.38        34.62        22.52        81.70        50.17 
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL 
       19.63         3.68        25.35        13.38        26.63        13.74 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       20.09        18.81        21.93         6.67        88.11        10.42 
TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NG-A4VW 
       25.18         5.49         9.80        31.20 

  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                       0.26                        3.68 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                     140.35                       88.11 
  DEL PEAK 12(9P23) MUTATED DEL PEAK 12(9P23) WILD-TYPE 
                      18.08                       21.01 
[1] "0.3 - 140.3 (18.1)" "3.7 - 88.1 (21.0)" 
[1] "hr=" "1.2"
D37V2, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(9P23) MUTATED       2                         6    25
  DEL PEAK 12(9P23) WILD-TYPE     1                         3    18
D37V3, multiclass
                           clus
vv                          DEL PEAK 12(9P23) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         6
  WHITE                                            25
                           clus
vv                          DEL PEAK 12(9P23) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              18
[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(38) Variable = DEL PEAK 13(9Q21.13) MUTATION ANALYSIS
D38V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 13(9Q21.13) MUTATED   17 21
  DEL PEAK 13(9Q21.13) WILD-TYPE  4 13
  DEL PEAK 13(9Q21.13) MUTATED DEL PEAK 13(9Q21.13) WILD-TYPE 
                            38                             17 
  DEL PEAK 13(9Q21.13) MUTATED DEL PEAK 13(9Q21.13) WILD-TYPE 
                            21                             13 
$`DEL PEAK 13(9Q21.13) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N5-A59E 
       52.31        59.38        34.62        81.70        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       11.87        17.42        19.63         9.57        17.16        39.75 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO 
        0.26        12.43        13.38        27.25        26.70        25.68 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       20.09        18.81        12.20        21.93        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       35.80        19.86        15.81       140.35        27.55         3.75 
TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A5CP 
        6.67        10.42        23.47         5.49        14.86         5.49 
TCGA-NG-A4VU TCGA-QM-A5NM 
       14.53        19.30 

$`DEL PEAK 13(9Q21.13) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
        4.67        18.08         4.87        22.52        29.95        50.17 
TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-NA-A4QW TCGA-NA-A4R0 
        3.68        25.35        26.63        13.74        80.78        17.79 
TCGA-NA-A5I1 TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NG-A4VW 
       88.11        25.18         9.80         2.66        31.20 

  DEL PEAK 13(9Q21.13) MUTATED DEL PEAK 13(9Q21.13) WILD-TYPE 
                          0.26                           2.66 
  DEL PEAK 13(9Q21.13) MUTATED DEL PEAK 13(9Q21.13) WILD-TYPE 
                        140.35                          88.11 
  DEL PEAK 13(9Q21.13) MUTATED DEL PEAK 13(9Q21.13) WILD-TYPE 
                        19.465                         22.520 
[1] "0.3 - 140.3 (19.5)" "2.7 - 88.1 (22.5)" 
[1] "hr=" "1.4"
D38V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(9Q21.13) MUTATED       2                         8    28
  DEL PEAK 13(9Q21.13) WILD-TYPE     1                         1    15
D38V3, multiclass
                           clus
vv                          DEL PEAK 13(9Q21.13) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               28
                           clus
vv                          DEL PEAK 13(9Q21.13) WILD-TYPE
  ASIAN                                                  1
  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(39) Variable = DEL PEAK 14(9Q33.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(9Q33.3) MUTATED   18 20
  DEL PEAK 14(9Q33.3) WILD-TYPE  3 14
  DEL PEAK 14(9Q33.3) MUTATED DEL PEAK 14(9Q33.3) WILD-TYPE 
                           38                            17 
  DEL PEAK 14(9Q33.3) MUTATED DEL PEAK 14(9Q33.3) WILD-TYPE 
                           20                            14 
$`DEL PEAK 14(9Q33.3) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N5-A59E 
       52.31        18.08        34.62        81.70        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 
       11.87        17.42        19.63        17.16        39.75         0.26 
TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP 
       12.43        13.38        27.25        26.70        25.68        20.09 
TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       18.81        12.20        67.17        54.97        35.80        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 
       15.81       140.35        80.78        27.55         3.75        17.79 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       10.42        23.47         5.49        14.86         2.66         5.49 
TCGA-NG-A4VU TCGA-QM-A5NM 
       14.53        19.30 

$`DEL PEAK 14(9Q33.3) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RU 
        4.67        59.38         4.87        22.52        29.95        50.17 
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N7-A4Y0 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N9-A4PZ 
        3.68         9.57        25.35        26.63        13.74        21.93 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NG-A4VW 
        6.67        88.11        25.18         9.80        31.20 

  DEL PEAK 14(9Q33.3) MUTATED DEL PEAK 14(9Q33.3) WILD-TYPE 
                         0.26                          3.68 
  DEL PEAK 14(9Q33.3) MUTATED DEL PEAK 14(9Q33.3) WILD-TYPE 
                       140.35                         88.11 
  DEL PEAK 14(9Q33.3) MUTATED DEL PEAK 14(9Q33.3) WILD-TYPE 
                       19.055                        22.520 
[1] "0.3 - 140.3 (19.1)" "3.7 - 88.1 (22.5)" 
[1] "hr=" "1.6"
D39V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9Q33.3) MUTATED       2                         7    29
  DEL PEAK 14(9Q33.3) WILD-TYPE     1                         2    14
D39V3, multiclass
                           clus
vv                          DEL PEAK 14(9Q33.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              29
                           clus
vv                          DEL PEAK 14(9Q33.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  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(40) Variable = DEL PEAK 15(10Q23.31) MUTATION ANALYSIS
D40V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 15(10Q23.31) MUTATED    6 14
  DEL PEAK 15(10Q23.31) WILD-TYPE 15 20
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             20                              35 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             14                              20 
$`DEL PEAK 15(10Q23.31) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT 
       52.31         4.67        18.08         4.87        22.52        81.70 
TCGA-N6-A4V9 TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PM 
       17.42         9.57        17.16        12.43        26.63        27.25 
TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX 
       21.93        35.80        19.86        15.81       140.35        27.55 
TCGA-NA-A4R0 TCGA-NA-A4R1 
       17.79         6.67 

$`DEL PEAK 15(10Q23.31) WILD-TYPE`
TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       59.38        34.62        29.95        50.17        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 
       11.87        19.63         3.68        39.75        25.35         0.26 
TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ 
       13.38        13.74        26.70        25.68        20.09        18.81 
TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A5I1 
       12.20        67.17        54.97        80.78         3.75        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX 
       10.42        23.47        25.18         5.49         9.80        14.86 
TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        2.66         5.49        14.53        31.20        19.30 

  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                           4.67                            0.26 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                         140.35                           88.11 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                          18.97                           19.63 
[1] "4.7 - 140.3 (19.0)" "0.3 - 88.1 (19.6)" 
[1] "hr=" "1.2"
D40V2, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(10Q23.31) MUTATED       0                         5    15
  DEL PEAK 15(10Q23.31) WILD-TYPE     3                         4    28
D40V3, multiclass
                           clus
vv                          DEL PEAK 15(10Q23.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                15
                           clus
vv                          DEL PEAK 15(10Q23.31) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               4
  WHITE                                                  28
[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(41) Variable = DEL PEAK 16(11P15.5) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(11P15.5) MUTATED    8 16
  DEL PEAK 16(11P15.5) WILD-TYPE 13 18
  DEL PEAK 16(11P15.5) MUTATED DEL PEAK 16(11P15.5) WILD-TYPE 
                            24                             31 
  DEL PEAK 16(11P15.5) MUTATED DEL PEAK 16(11P15.5) WILD-TYPE 
                            16                             18 
$`DEL PEAK 16(11P15.5) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RM TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       52.31         4.67         4.87        14.70        11.87        17.42 
TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PL 
       19.63        39.75         0.26        12.43        26.63        13.74 
TCGA-N8-A4PM TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-NA-A4QW TCGA-NA-A4R0 TCGA-NA-A4R1 
       27.25        21.93        35.80        80.78        17.79         6.67 
TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU 
       23.47         9.80        14.86         2.66         5.49        14.53 

$`DEL PEAK 16(11P15.5) WILD-TYPE`
TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT 
       59.38        18.08        34.62        22.52        29.95        81.70 
TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 
       50.17        67.13         3.68         9.57        17.16        25.35 
TCGA-N7-A59B TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S 
       13.38        26.70        25.68        20.09        18.81        12.20 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX 
       67.17        54.97        19.86        15.81       140.35        27.55 
TCGA-NA-A4QY TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NG-A4VW 
        3.75        88.11        10.42        25.18         5.49        31.20 
TCGA-QM-A5NM 
       19.30 

  DEL PEAK 16(11P15.5) MUTATED DEL PEAK 16(11P15.5) WILD-TYPE 
                          0.26                           3.68 
  DEL PEAK 16(11P15.5) MUTATED DEL PEAK 16(11P15.5) WILD-TYPE 
                         80.78                         140.35 
  DEL PEAK 16(11P15.5) MUTATED DEL PEAK 16(11P15.5) WILD-TYPE 
                         14.78                          25.18 
[1] "0.3 - 80.8 (14.8)"  "3.7 - 140.3 (25.2)"
[1] "hr=" "1.9"
D41V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(11P15.5) MUTATED       2                         3    19
  DEL PEAK 16(11P15.5) WILD-TYPE     1                         6    24
D41V3, multiclass
                           clus
vv                          DEL PEAK 16(11P15.5) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               19
                           clus
vv                          DEL PEAK 16(11P15.5) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 24
[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(42) Variable = DEL PEAK 17(11Q14.1) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(11Q14.1) MUTATED   10 16
  DEL PEAK 17(11Q14.1) WILD-TYPE 11 18
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            26                             29 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                            16                             18 
$`DEL PEAK 17(11Q14.1) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31         4.67        59.38         4.87        34.62        22.52 
TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VG 
       67.13        14.70        11.87        17.42        19.63        39.75 
TCGA-N7-A4Y5 TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q8 
        0.26        13.74        25.68        18.81        21.93        15.81 
TCGA-NA-A4QV TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
      140.35        17.79        88.11        10.42        23.47         5.49 
TCGA-NF-A4WX TCGA-QM-A5NM 
       14.86        19.30 

$`DEL PEAK 17(11Q14.1) WILD-TYPE`
TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N6-A4VD TCGA-N6-A4VE 
       18.08        29.95        81.70        50.17         3.68         9.57 
TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM 
       17.16        25.35        12.43        13.38        26.63        27.25 
TCGA-N8-A4PN TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 
       26.70        20.09        12.20        67.17        54.97        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-ND-A4WC 
       19.86        80.78        27.55         3.75         6.67        25.18 
TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        9.80         2.66         5.49        14.53        31.20 

  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                          0.26                           2.66 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                        140.35                          81.70 
  DEL PEAK 17(11Q14.1) MUTATED DEL PEAK 17(11Q14.1) WILD-TYPE 
                        19.055                         20.090 
[1] "0.3 - 140.3 (19.1)" "2.7 - 81.7 (20.1)" 
[1] "hr=" "1"  
D42V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(11Q14.1) MUTATED       1                         5    19
  DEL PEAK 17(11Q14.1) WILD-TYPE     2                         4    24
D42V3, multiclass
                           clus
vv                          DEL PEAK 17(11Q14.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               19
                           clus
vv                          DEL PEAK 17(11Q14.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 24
[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(43) Variable = DEL PEAK 18(11Q23.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(11Q23.2) MUTATED    9 17
  DEL PEAK 18(11Q23.2) WILD-TYPE 12 17
  DEL PEAK 18(11Q23.2) MUTATED DEL PEAK 18(11Q23.2) WILD-TYPE 
                            26                             29 
  DEL PEAK 18(11Q23.2) MUTATED DEL PEAK 18(11Q23.2) WILD-TYPE 
                            17                             17 
$`DEL PEAK 18(11Q23.2) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RV 
       52.31         4.67        59.38         4.87        22.52        67.13 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 
       14.70        11.87        17.42        19.63        39.75         0.26 
TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N9-A4PZ TCGA-NA-A4QV TCGA-NA-A4R0 
       13.74        25.68        20.09        21.93       140.35        17.79 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WX 
        6.67        88.11        10.42        23.47         5.49        14.86 
TCGA-NF-A4X2 TCGA-QM-A5NM 
        2.66        19.30 

$`DEL PEAK 18(11Q23.2) WILD-TYPE`
TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N6-A4VD 
       18.08        34.62        29.95        81.70        50.17         3.68 
TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
        9.57        17.16        25.35        12.43        13.38        26.63 
TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       27.25        26.70        18.81        12.20        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY 
       35.80        19.86        15.81        80.78        27.55         3.75 
TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
       25.18         9.80         5.49        14.53        31.20 

  DEL PEAK 18(11Q23.2) MUTATED DEL PEAK 18(11Q23.2) WILD-TYPE 
                          0.26                           3.68 
  DEL PEAK 18(11Q23.2) MUTATED DEL PEAK 18(11Q23.2) WILD-TYPE 
                        140.35                          81.70 
  DEL PEAK 18(11Q23.2) MUTATED DEL PEAK 18(11Q23.2) WILD-TYPE 
                        18.545                         25.180 
[1] "0.3 - 140.3 (18.5)" "3.7 - 81.7 (25.2)" 
[1] "hr=" "1.2"
D43V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(11Q23.2) MUTATED       1                         6    18
  DEL PEAK 18(11Q23.2) WILD-TYPE     2                         3    25
D43V3, multiclass
                           clus
vv                          DEL PEAK 18(11Q23.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               18
                           clus
vv                          DEL PEAK 18(11Q23.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 25
[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(44) Variable = DEL PEAK 19(12Q23.1) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(12Q23.1) MUTATED    5 14
  DEL PEAK 19(12Q23.1) WILD-TYPE 16 20
  DEL PEAK 19(12Q23.1) MUTATED DEL PEAK 19(12Q23.1) WILD-TYPE 
                            19                             36 
  DEL PEAK 19(12Q23.1) MUTATED DEL PEAK 19(12Q23.1) WILD-TYPE 
                            14                             20 
$`DEL PEAK 19(12Q23.1) MUTATED`
TCGA-N5-A4RM TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VE 
        4.87        29.95        50.17        14.70        11.87         9.57 
TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N9-A4Q3 TCGA-N9-A4Q8 
       12.43        26.63        25.68        20.09        54.97        15.81 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NF-A4WU 
       80.78        27.55         3.75        17.79         6.67         9.80 
TCGA-NF-A4X2 
        2.66 

$`DEL PEAK 19(12Q23.1) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31         4.67        59.38        18.08        34.62        22.52 
TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VF 
       81.70        67.13        17.42        19.63         3.68        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PL TCGA-N8-A4PM 
       39.75        25.35         0.26        13.38        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q4 
       26.70        18.81        12.20        21.93        67.17        35.80 
TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC 
       19.86       140.35        88.11        10.42        23.47        25.18 
TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        14.86         5.49        14.53        31.20        19.30 

  DEL PEAK 19(12Q23.1) MUTATED DEL PEAK 19(12Q23.1) WILD-TYPE 
                          2.66                           0.26 
  DEL PEAK 19(12Q23.1) MUTATED DEL PEAK 19(12Q23.1) WILD-TYPE 
                         80.78                         140.35 
  DEL PEAK 19(12Q23.1) MUTATED DEL PEAK 19(12Q23.1) WILD-TYPE 
                        15.810                         20.895 
[1] "2.7 - 80.8 (15.8)"  "0.3 - 140.3 (20.9)"
[1] "hr=" "1.8"
D44V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(12Q23.1) MUTATED       1                         3    16
  DEL PEAK 19(12Q23.1) WILD-TYPE     2                         6    27
D44V3, multiclass
                           clus
vv                          DEL PEAK 19(12Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               16
                           clus
vv                          DEL PEAK 19(12Q23.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 27
[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(45) Variable = DEL PEAK 20(12Q24.31) MUTATION ANALYSIS
D45V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 20(12Q24.31) MUTATED    4 15
  DEL PEAK 20(12Q24.31) WILD-TYPE 17 19
  DEL PEAK 20(12Q24.31) MUTATED DEL PEAK 20(12Q24.31) WILD-TYPE 
                             19                              36 
  DEL PEAK 20(12Q24.31) MUTATED DEL PEAK 20(12Q24.31) WILD-TYPE 
                             15                              19 
$`DEL PEAK 20(12Q24.31) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A59E TCGA-N5-A59F 
        4.67        18.08        29.95        81.70        14.70        11.87 
TCGA-N7-A4Y8 TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PP TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       12.43        26.63        13.74        20.09        67.17        54.97 
TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 
       15.81        80.78        27.55         3.75        17.79         6.67 
TCGA-NF-A4WU 
        9.80 

$`DEL PEAK 20(12Q24.31) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RU 
       52.31        59.38         4.87        34.62        22.52        50.17 
TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       67.13        17.42        19.63         3.68         9.57        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PM TCGA-N8-A4PN 
       39.75        25.35         0.26        13.38        27.25        26.70 
TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       25.68        18.81        12.20        21.93        35.80        19.86 
TCGA-NA-A4QV TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF 
      140.35        88.11        10.42        23.47        25.18         5.49 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
       14.86         2.66         5.49        14.53        31.20        19.30 

  DEL PEAK 20(12Q24.31) MUTATED DEL PEAK 20(12Q24.31) WILD-TYPE 
                           3.75                            0.26 
  DEL PEAK 20(12Q24.31) MUTATED DEL PEAK 20(12Q24.31) WILD-TYPE 
                          81.70                          140.35 
  DEL PEAK 20(12Q24.31) MUTATED DEL PEAK 20(12Q24.31) WILD-TYPE 
                         17.790                          20.895 
[1] "3.8 - 81.7 (17.8)"  "0.3 - 140.3 (20.9)"
[1] "hr=" "1.6"
D45V2, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12Q24.31) MUTATED       1                         3    16
  DEL PEAK 20(12Q24.31) WILD-TYPE     2                         6    27
D45V3, multiclass
                           clus
vv                          DEL PEAK 20(12Q24.31) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                16
                           clus
vv                          DEL PEAK 20(12Q24.31) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               6
  WHITE                                                  27
[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(46) Variable = DEL PEAK 21(13Q12.11) MUTATION ANALYSIS
D46V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 21(13Q12.11) MUTATED   13 16
  DEL PEAK 21(13Q12.11) WILD-TYPE  8 18
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             29                              26 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                             16                              18 
$`DEL PEAK 21(13Q12.11) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RT 
        4.67        59.38         4.87        34.62        22.52        81.70 
TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       50.17        67.13        11.87         9.57        17.16        39.75 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ 
       13.38        26.63        25.68        20.09        12.20        21.93 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A5I1 
       35.80        19.86       140.35        27.55         3.75        88.11 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-QM-A5NM 
        5.49         9.80         2.66         5.49        19.30 

$`DEL PEAK 21(13Q12.11) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VC 
       52.31        18.08        29.95        14.70        17.42        19.63 
TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N8-A4PL TCGA-N8-A4PM 
        3.68        25.35         0.26        12.43        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QW 
       26.70        18.81        67.17        54.97        15.81        80.78 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WX 
       17.79         6.67        10.42        23.47        25.18        14.86 
TCGA-NG-A4VU TCGA-NG-A4VW 
       14.53        31.20 

  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                           2.66                            0.26 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                         140.35                           80.78 
  DEL PEAK 21(13Q12.11) MUTATED DEL PEAK 21(13Q12.11) WILD-TYPE 
                         20.090                          18.445 
[1] "2.7 - 140.3 (20.1)" "0.3 - 80.8 (18.4)" 
[1] "hr=" "1.4"
D46V2, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(13Q12.11) MUTATED       1                         6    23
  DEL PEAK 21(13Q12.11) WILD-TYPE     2                         3    20
D46V3, multiclass
                           clus
vv                          DEL PEAK 21(13Q12.11) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                23
                           clus
vv                          DEL PEAK 21(13Q12.11) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               3
  WHITE                                                  20
[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(47) Variable = DEL PEAK 22(13Q14.2) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(13Q14.2) MUTATED   12 19
  DEL PEAK 22(13Q14.2) WILD-TYPE  9 15
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                            31                             24 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                            19                             15 
$`DEL PEAK 22(13Q14.2) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RT 
        4.67        59.38         4.87        34.62        22.52        81.70 
TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 
       50.17        67.13         9.57        17.16        39.75         0.26 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ 
       13.38        26.63        25.68        20.09        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4R0 
       67.17        19.86        15.81       140.35        27.55        17.79 
TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VW 
        6.67         5.49         9.80         2.66         5.49        31.20 
TCGA-QM-A5NM 
       19.30 

$`DEL PEAK 22(13Q14.2) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       52.31        18.08        29.95        14.70        11.87        17.42 
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N8-A4PL TCGA-N8-A4PM 
       19.63         3.68        25.35        12.43        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PQ TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QW TCGA-NA-A4QY 
       26.70        18.81        54.97        35.80        80.78         3.75 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WX TCGA-NG-A4VU 
       88.11        10.42        23.47        25.18        14.86        14.53 

  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                          0.26                           3.68 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                        140.35                          88.11 
  DEL PEAK 22(13Q14.2) MUTATED DEL PEAK 22(13Q14.2) WILD-TYPE 
                         19.86                          19.22 
[1] "0.3 - 140.3 (19.9)" "3.7 - 88.1 (19.2)" 
[1] "hr=" "1"  
D47V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(13Q14.2) MUTATED       1                         6    25
  DEL PEAK 22(13Q14.2) WILD-TYPE     2                         3    18
D47V3, multiclass
                           clus
vv                          DEL PEAK 22(13Q14.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               25
                           clus
vv                          DEL PEAK 22(13Q14.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 18
[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(48) Variable = DEL PEAK 23(14Q21.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(14Q21.1) MUTATED    8 20
  DEL PEAK 23(14Q21.1) WILD-TYPE 13 14
  DEL PEAK 23(14Q21.1) MUTATED DEL PEAK 23(14Q21.1) WILD-TYPE 
                            28                             27 
  DEL PEAK 23(14Q21.1) MUTATED DEL PEAK 23(14Q21.1) WILD-TYPE 
                            20                             14 
$`DEL PEAK 23(14Q21.1) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT 
       52.31         4.67        18.08         4.87        22.52        81.70 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A59B 
       14.70        11.87        19.63        39.75         0.26        13.38 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S 
       26.63        13.74        25.68        20.09        18.81        12.20 
TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-NA-A5I1 
       67.17        35.80        19.86        27.55        17.79        88.11 
TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-NF-A4WU TCGA-NG-A4VU 
       10.42        23.47         9.80        14.53 

$`DEL PEAK 23(14Q21.1) WILD-TYPE`
TCGA-N5-A4RF TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4V9 
       59.38        34.62        29.95        50.17        67.13        17.42 
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N8-A4PM 
        3.68         9.57        17.16        25.35        12.43        27.25 
TCGA-N8-A4PN TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       26.70        21.93        54.97        15.81       140.35        80.78 
TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 
        3.75         6.67        25.18         5.49        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        31.20        19.30 

  DEL PEAK 23(14Q21.1) MUTATED DEL PEAK 23(14Q21.1) WILD-TYPE 
                          0.26                           2.66 
  DEL PEAK 23(14Q21.1) MUTATED DEL PEAK 23(14Q21.1) WILD-TYPE 
                         88.11                         140.35 
  DEL PEAK 23(14Q21.1) MUTATED DEL PEAK 23(14Q21.1) WILD-TYPE 
                         19.22                          21.93 
[1] "0.3 - 88.1 (19.2)"  "2.7 - 140.3 (21.9)"
[1] "hr=" "1.5"
D48V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(14Q21.1) MUTATED       1                         7    20
  DEL PEAK 23(14Q21.1) WILD-TYPE     2                         2    23
D48V3, multiclass
                           clus
vv                          DEL PEAK 23(14Q21.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               20
                           clus
vv                          DEL PEAK 23(14Q21.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 23
[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(49) Variable = DEL PEAK 24(15Q11.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(15Q11.2) MUTATED   17 24
  DEL PEAK 24(15Q11.2) WILD-TYPE  4 10
  DEL PEAK 24(15Q11.2) MUTATED DEL PEAK 24(15Q11.2) WILD-TYPE 
                            41                             14 
  DEL PEAK 24(15Q11.2) MUTATED DEL PEAK 24(15Q11.2) WILD-TYPE 
                            24                             10 
$`DEL PEAK 24(15Q11.2) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
        4.67        59.38        18.08         4.87        34.62        22.52 
TCGA-N5-A4RT TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG 
       81.70        17.42        19.63         9.57        17.16        39.75 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM 
        0.26        12.43        13.38        26.63        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ 
       26.70        25.68        20.09        18.81        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       67.17        35.80        15.81       140.35        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU 
        3.75         6.67        88.11        23.47         5.49         9.80 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
       14.86         2.66         5.49        14.53        19.30 

$`DEL PEAK 24(15Q11.2) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
       52.31        29.95        50.17        67.13        14.70        11.87 
TCGA-N6-A4VD TCGA-N7-A4Y0 TCGA-N9-A4Q3 TCGA-N9-A4Q7 TCGA-NA-A4R0 TCGA-ND-A4W6 
        3.68        25.35        54.97        19.86        17.79        10.42 
TCGA-ND-A4WC TCGA-NG-A4VW 
       25.18        31.20 

  DEL PEAK 24(15Q11.2) MUTATED DEL PEAK 24(15Q11.2) WILD-TYPE 
                          0.26                           3.68 
  DEL PEAK 24(15Q11.2) MUTATED DEL PEAK 24(15Q11.2) WILD-TYPE 
                        140.35                          67.13 
  DEL PEAK 24(15Q11.2) MUTATED DEL PEAK 24(15Q11.2) WILD-TYPE 
                        18.810                         25.265 
[1] "0.3 - 140.3 (18.8)" "3.7 - 67.1 (25.3)" 
[1] "hr=" "1"  
D49V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(15Q11.2) MUTATED       1                         6    33
  DEL PEAK 24(15Q11.2) WILD-TYPE     2                         3    10
D49V3, multiclass
                           clus
vv                          DEL PEAK 24(15Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               33
                           clus
vv                          DEL PEAK 24(15Q11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              3
  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(50) Variable = DEL PEAK 25(15Q15.1) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(15Q15.1) MUTATED   18 24
  DEL PEAK 25(15Q15.1) WILD-TYPE  3 10
  DEL PEAK 25(15Q15.1) MUTATED DEL PEAK 25(15Q15.1) WILD-TYPE 
                            42                             13 
  DEL PEAK 25(15Q15.1) MUTATED DEL PEAK 25(15Q15.1) WILD-TYPE 
                            24                             10 
$`DEL PEAK 25(15Q15.1) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
       52.31         4.67        59.38        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E TCGA-N6-A4V9 TCGA-N6-A4VE 
       22.52        81.70        50.17        14.70        17.42         9.57 
TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
       17.16        39.75         0.26        12.43        13.38        26.63 
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ 
       13.74        27.25        26.70        25.68        20.09        18.81 
TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       67.17        35.80        19.86        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WF 
       27.55         3.75         6.67        88.11        23.47         5.49 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
        9.80        14.86         2.66         5.49        14.53        19.30 

$`DEL PEAK 25(15Q15.1) WILD-TYPE`
TCGA-N5-A4RS TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N7-A4Y0 
       29.95        67.13        11.87        19.63         3.68        25.35 
TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q3 TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-ND-A4WC 
       12.20        21.93        54.97        17.79        10.42        25.18 
TCGA-NG-A4VW 
       31.20 

  DEL PEAK 25(15Q15.1) MUTATED DEL PEAK 25(15Q15.1) WILD-TYPE 
                          0.26                           3.68 
  DEL PEAK 25(15Q15.1) MUTATED DEL PEAK 25(15Q15.1) WILD-TYPE 
                        140.35                          67.13 
  DEL PEAK 25(15Q15.1) MUTATED DEL PEAK 25(15Q15.1) WILD-TYPE 
                        19.055                         21.930 
[1] "0.3 - 140.3 (19.1)" "3.7 - 67.1 (21.9)" 
[1] "hr=" "1.4"
D50V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(15Q15.1) MUTATED       2                         7    33
  DEL PEAK 25(15Q15.1) WILD-TYPE     1                         2    10
D50V3, multiclass
                           clus
vv                          DEL PEAK 25(15Q15.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               33
                           clus
vv                          DEL PEAK 25(15Q15.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  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(51) Variable = DEL PEAK 26(16P13.3) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(16P13.3) MUTATED   13 20
  DEL PEAK 26(16P13.3) WILD-TYPE  8 14
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                            33                             22 
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                            20                             14 
$`DEL PEAK 26(16P13.3) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A4RU 
        4.67        59.38         4.87        34.62        22.52        50.17 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF 
       14.70        11.87        17.42        19.63         9.57        17.16 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM 
        0.26        12.43        13.38        26.63        13.74        27.25 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-N9-A4Q7 
       25.68        20.09        18.81        67.17        35.80        19.86 
TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 
       15.81       140.35        80.78         3.75         6.67        88.11 
TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 
        5.49        14.86         2.66 

$`DEL PEAK 26(16P13.3) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RJ TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N6-A4VD 
       52.31        18.08        29.95        81.70        67.13         3.68 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N8-A4PN TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q3 
       39.75        25.35        26.70        12.20        21.93        54.97 
TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WU 
       27.55        17.79        10.42        23.47        25.18         9.80 
TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW TCGA-QM-A5NM 
        5.49        14.53        31.20        19.30 

  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                          0.26                           3.68 
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                        140.35                          81.70 
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                        17.420                         24.325 
[1] "0.3 - 140.3 (17.4)" "3.7 - 81.7 (24.3)" 
[1] "hr=" "1.1"
D51V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(16P13.3) MUTATED       0                         8    24
  DEL PEAK 26(16P13.3) WILD-TYPE     3                         1    19
D51V3, multiclass
                           clus
vv                          DEL PEAK 26(16P13.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               24
                           clus
vv                          DEL PEAK 26(16P13.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 19
[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(52) Variable = DEL PEAK 27(16Q23.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 27(16Q23.1) MUTATED   12 26
  DEL PEAK 27(16Q23.1) WILD-TYPE  9  8
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            38                             17 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            26                              8 
$`DEL PEAK 27(16Q23.1) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO 
       52.31         4.67        59.38        18.08         4.87        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 
       29.95        81.70        50.17        14.70        11.87        17.42 
TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 
       19.63         9.57        17.16        25.35         0.26        12.43 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO 
       13.38        26.63        13.74        27.25        26.70        25.68 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QY 
       20.09        18.81        19.86        15.81        80.78         3.75 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 
       17.79         6.67        10.42         5.49        14.86         2.66 
TCGA-NF-A5CP TCGA-NG-A4VU 
        5.49        14.53 

$`DEL PEAK 27(16Q23.1) WILD-TYPE`
TCGA-N5-A4RN TCGA-N5-A4RV TCGA-N6-A4VD TCGA-N6-A4VG TCGA-N8-A56S TCGA-N9-A4PZ 
       34.62        67.13         3.68        39.75        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A5I1 
       67.17        54.97        35.80       140.35        27.55        88.11 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NG-A4VW TCGA-QM-A5NM 
       23.47        25.18         9.80        31.20        19.30 

  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                          0.26                           3.68 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                         81.70                         140.35 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                         17.29                          31.20 
[1] "0.3 - 81.7 (17.3)"  "3.7 - 140.3 (31.2)"
[1] "hr=" "2.9"
D52V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(16Q23.1) MUTATED       1                         6    31
  DEL PEAK 27(16Q23.1) WILD-TYPE     2                         3    12
D52V3, multiclass
                           clus
vv                          DEL PEAK 27(16Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               31
                           clus
vv                          DEL PEAK 27(16Q23.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              3
  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(53) Variable = DEL PEAK 28(17P13.1) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(17P13.1) MUTATED   16 26
  DEL PEAK 28(17P13.1) WILD-TYPE  5  8
  DEL PEAK 28(17P13.1) MUTATED DEL PEAK 28(17P13.1) WILD-TYPE 
                            42                             13 
  DEL PEAK 28(17P13.1) MUTATED DEL PEAK 28(17P13.1) WILD-TYPE 
                            26                              8 
$`DEL PEAK 28(17P13.1) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
       52.31         4.67        59.38        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
       22.52        81.70        50.17        67.13        14.70        11.87 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 
       17.42        19.63         9.57        39.75         0.26        12.43 
TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ 
       27.25        26.70        25.68        20.09        12.20        21.93 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX 
       67.17        54.97        35.80       140.35        80.78        27.55 
TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA 
        3.75        17.79         6.67        88.11        10.42        23.47 
TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-QM-A5NM 
        5.49         9.80         2.66         5.49        14.53        19.30 

$`DEL PEAK 28(17P13.1) WILD-TYPE`
TCGA-N5-A4RS TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A59B TCGA-N8-A4PI 
       29.95         3.68        17.16        25.35        13.38        26.63 
TCGA-N8-A4PL TCGA-N8-A4PQ TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-ND-A4WC TCGA-NF-A4WX 
       13.74        18.81        19.86        15.81        25.18        14.86 
TCGA-NG-A4VW 
       31.20 

  DEL PEAK 28(17P13.1) MUTATED DEL PEAK 28(17P13.1) WILD-TYPE 
                          0.26                           3.68 
  DEL PEAK 28(17P13.1) MUTATED DEL PEAK 28(17P13.1) WILD-TYPE 
                        140.35                          31.20 
  DEL PEAK 28(17P13.1) MUTATED DEL PEAK 28(17P13.1) WILD-TYPE 
                         19.86                          18.81 
[1] "0.3 - 140.3 (19.9)" "3.7 - 31.2 (18.8)" 
[1] "hr=" "1.2"
D53V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(17P13.1) MUTATED       1                         8    33
  DEL PEAK 28(17P13.1) WILD-TYPE     2                         1    10
D53V3, multiclass
                           clus
vv                          DEL PEAK 28(17P13.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               33
                           clus
vv                          DEL PEAK 28(17P13.1) WILD-TYPE
  ASIAN                                                  2
  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(54) Variable = DEL PEAK 29(17Q21.32) MUTATION ANALYSIS
D54V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 29(17Q21.32) MUTATED    5 14
  DEL PEAK 29(17Q21.32) WILD-TYPE 16 20
  DEL PEAK 29(17Q21.32) MUTATED DEL PEAK 29(17Q21.32) WILD-TYPE 
                             19                              36 
  DEL PEAK 29(17Q21.32) MUTATED DEL PEAK 29(17Q21.32) WILD-TYPE 
                             14                              20 
$`DEL PEAK 29(17Q21.32) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RO TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VG TCGA-N7-A4Y8 
        4.67        22.52        14.70        11.87        39.75        12.43 
TCGA-N7-A59B TCGA-N8-A4PM TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q8 TCGA-NA-A4QX 
       13.38        27.25        18.81        67.17        15.81        27.55 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WF TCGA-NF-A5CP TCGA-NG-A4VU 
       17.79         6.67        10.42         5.49         5.49        14.53 
TCGA-QM-A5NM 
       19.30 

$`DEL PEAK 29(17Q21.32) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RS 
       52.31        59.38        18.08         4.87        34.62        29.95 
TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD 
       81.70        50.17        67.13        17.42        19.63         3.68 
TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N8-A4PI TCGA-N8-A4PL 
        9.57        17.16        25.35         0.26        26.63        13.74 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q3 
       26.70        25.68        20.09        12.20        21.93        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A5I1 
       35.80        19.86       140.35        80.78         3.75        88.11 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VW 
       23.47        25.18         9.80        14.86         2.66        31.20 

  DEL PEAK 29(17Q21.32) MUTATED DEL PEAK 29(17Q21.32) WILD-TYPE 
                           4.67                            0.26 
  DEL PEAK 29(17Q21.32) MUTATED DEL PEAK 29(17Q21.32) WILD-TYPE 
                          67.17                          140.35 
  DEL PEAK 29(17Q21.32) MUTATED DEL PEAK 29(17Q21.32) WILD-TYPE 
                         14.700                          24.325 
[1] "4.7 - 67.2 (14.7)"  "0.3 - 140.3 (24.3)"
[1] "hr=" "2.2"
D54V2, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(17Q21.32) MUTATED       0                         5    14
  DEL PEAK 29(17Q21.32) WILD-TYPE     3                         4    29
D54V3, multiclass
                           clus
vv                          DEL PEAK 29(17Q21.32) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                14
                           clus
vv                          DEL PEAK 29(17Q21.32) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               4
  WHITE                                                  29
[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(55) Variable = DEL PEAK 30(18Q22.2) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(18Q22.2) MUTATED   10 15
  DEL PEAK 30(18Q22.2) WILD-TYPE 11 19
  DEL PEAK 30(18Q22.2) MUTATED DEL PEAK 30(18Q22.2) WILD-TYPE 
                            25                             30 
  DEL PEAK 30(18Q22.2) MUTATED DEL PEAK 30(18Q22.2) WILD-TYPE 
                            15                             19 
$`DEL PEAK 30(18Q22.2) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO TCGA-N5-A59E 
        4.67        18.08         4.87        34.62        22.52        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N8-A4PL TCGA-N8-A4PN TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       11.87        17.42        13.74        26.70        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 
       35.80        19.86       140.35        80.78        27.55        17.79 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A5CP 
       88.11        10.42        23.47        25.18         9.80         5.49 
TCGA-NG-A4VU 
       14.53 

$`DEL PEAK 30(18Q22.2) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV 
       52.31        59.38        29.95        81.70        50.17        67.13 
TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 
       19.63         3.68         9.57        17.16        39.75        25.35 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PM TCGA-N8-A4PO 
        0.26        12.43        13.38        26.63        27.25        25.68 
TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q8 TCGA-NA-A4QY 
       20.09        18.81        12.20        21.93        15.81         3.75 
TCGA-NA-A4R1 TCGA-ND-A4WF TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VW TCGA-QM-A5NM 
        6.67         5.49        14.86         2.66        31.20        19.30 

  DEL PEAK 30(18Q22.2) MUTATED DEL PEAK 30(18Q22.2) WILD-TYPE 
                          4.67                           0.26 
  DEL PEAK 30(18Q22.2) MUTATED DEL PEAK 30(18Q22.2) WILD-TYPE 
                        140.35                          81.70 
  DEL PEAK 30(18Q22.2) MUTATED DEL PEAK 30(18Q22.2) WILD-TYPE 
                        19.860                         19.465 
[1] "4.7 - 140.3 (19.9)" "0.3 - 81.7 (19.5)" 
[1] "hr=" "1.3"
D55V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(18Q22.2) MUTATED       3                         7    16
  DEL PEAK 30(18Q22.2) WILD-TYPE     0                         2    27
D55V3, multiclass
                           clus
vv                          DEL PEAK 30(18Q22.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               16
                           clus
vv                          DEL PEAK 30(18Q22.2) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 27
[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(56) Variable = DEL PEAK 31(19P13.3) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 31(19P13.3) MUTATED   18 29
  DEL PEAK 31(19P13.3) WILD-TYPE  3  5
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            47                              8 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            29                              5 
$`DEL PEAK 31(19P13.3) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN 
       52.31         4.67        59.38        18.08         4.87        34.62 
TCGA-N5-A4RO TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E 
       22.52        29.95        81.70        50.17        67.13        14.70 
TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VE TCGA-N6-A4VG TCGA-N7-A4Y5 
       11.87        17.42        19.63         9.57        39.75         0.26 
TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN 
       12.43        13.38        26.63        13.74        27.25        26.70 
TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A4PQ TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q1 
       25.68        20.09        18.81        12.20        21.93        67.17 
TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       54.97        35.80        19.86        15.81       140.35        80.78 
TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       27.55         3.75        17.79         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WF TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A5CP 
       23.47         5.49         9.80        14.86         5.49 

$`DEL PEAK 31(19P13.3) WILD-TYPE`
TCGA-N6-A4VD TCGA-N6-A4VF TCGA-N7-A4Y0 TCGA-ND-A4WC TCGA-NF-A4X2 TCGA-NG-A4VU 
        3.68        17.16        25.35        25.18         2.66        14.53 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.20        19.30 

  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                          0.26                           2.66 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                        140.35                          31.20 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                         19.86                          18.23 
[1] "0.3 - 140.3 (19.9)" "2.7 - 31.2 (18.2)" 
[1] "hr=" "1.5"
D56V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(19P13.3) MUTATED       1                         9    36
  DEL PEAK 31(19P13.3) WILD-TYPE     2                         0     7
D56V3, multiclass
                           clus
vv                          DEL PEAK 31(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               36
                           clus
vv                          DEL PEAK 31(19P13.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                  7
[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(57) Variable = DEL PEAK 32(19Q13.33) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 32(19Q13.33) MUTATED    6 11
  DEL PEAK 32(19Q13.33) WILD-TYPE 15 23
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                             17                              38 
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                             11                              23 
$`DEL PEAK 32(19Q13.33) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT TCGA-N5-A4RV TCGA-N6-A4VC 
       52.31         4.87        22.52        81.70        67.13        19.63 
TCGA-N8-A4PN TCGA-N8-A4PP TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q4 TCGA-NA-A4QV 
       26.70        20.09        12.20        67.17        35.80       140.35 
TCGA-NA-A4QW TCGA-NA-A4QX TCGA-NA-A4R0 TCGA-ND-A4WF TCGA-NG-A4VU 
       80.78        27.55        17.79         5.49        14.53 

$`DEL PEAK 32(19Q13.33) WILD-TYPE`
TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RU 
        4.67        59.38        18.08        34.62        29.95        50.17 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       14.70        11.87        17.42         3.68         9.57        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI 
       39.75        25.35         0.26        12.43        13.38        26.63 
TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q3 
       13.74        27.25        25.68        18.81        21.93        54.97 
TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QY TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 
       19.86        15.81         3.75         6.67        88.11        10.42 
TCGA-ND-A4WA TCGA-ND-A4WC TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP 
       23.47        25.18         9.80        14.86         2.66         5.49 
TCGA-NG-A4VW TCGA-QM-A5NM 
       31.20        19.30 

  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                           4.87                            0.26 
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                         140.35                           88.11 
  DEL PEAK 32(19Q13.33) MUTATED DEL PEAK 32(19Q13.33) WILD-TYPE 
                          26.70                           17.75 
[1] "4.9 - 140.3 (26.7)" "0.3 - 88.1 (17.8)" 
[1] "hr=" "1.5"
D57V2, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(19Q13.33) MUTATED       0                         4    13
  DEL PEAK 32(19Q13.33) WILD-TYPE     3                         5    30
D57V3, multiclass
                           clus
vv                          DEL PEAK 32(19Q13.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                13
                           clus
vv                          DEL PEAK 32(19Q13.33) WILD-TYPE
  ASIAN                                                   3
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  30
[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(58) Variable = DEL PEAK 33(20P12.1) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 33(20P12.1) MUTATED    5  4
  DEL PEAK 33(20P12.1) WILD-TYPE 16 30
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                             9                             46 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                             4                             30 
$`DEL PEAK 33(20P12.1) MUTATED`
TCGA-N5-A4RJ TCGA-N6-A4VG TCGA-N8-A4PP TCGA-N8-A56S TCGA-NA-A4QW TCGA-NA-A4R0 
       18.08        39.75        20.09        12.20        80.78        17.79 
TCGA-NF-A4WU TCGA-NF-A4X2 TCGA-QM-A5NM 
        9.80         2.66        19.30 

$`DEL PEAK 33(20P12.1) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31         4.67        59.38         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59E TCGA-N5-A59F 
       29.95        81.70        50.17        67.13        14.70        11.87 
TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N7-A4Y0 
       17.42        19.63         3.68         9.57        17.16        25.35 
TCGA-N7-A4Y5 TCGA-N7-A4Y8 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM 
        0.26        12.43        13.38        26.63        13.74        27.25 
TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ TCGA-N9-A4PZ TCGA-N9-A4Q1 TCGA-N9-A4Q3 
       26.70        25.68        18.81        21.93        67.17        54.97 
TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QX TCGA-NA-A4QY 
       35.80        19.86        15.81       140.35        27.55         3.75 
TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF 
        6.67        88.11        10.42        23.47        25.18         5.49 
TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
       14.86         5.49        14.53        31.20 

  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                          2.66                           0.26 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                         80.78                         140.35 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                        18.080                         20.895 
[1] "2.7 - 80.8 (18.1)"  "0.3 - 140.3 (20.9)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(20P12.1) MUTATED       0                         0     9
  DEL PEAK 33(20P12.1) WILD-TYPE     3                         9    34
D58V3, multiclass
                           clus
vv                          DEL PEAK 33(20P12.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                9
                           clus
vv                          DEL PEAK 33(20P12.1) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                 34
[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(59) Variable = DEL PEAK 34(22Q13.31) MUTATION ANALYSIS
D59V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 34(22Q13.31) MUTATED   15 25
  DEL PEAK 34(22Q13.31) WILD-TYPE  6  9
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             40                              15 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             25                               9 
$`DEL PEAK 34(22Q13.31) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RN TCGA-N5-A4RO 
       52.31         4.67        18.08         4.87        34.62        22.52 
TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N5-A59F TCGA-N6-A4V9 
       29.95        81.70        50.17        67.13        11.87        17.42 
TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y5 TCGA-N7-A4Y8 
        3.68         9.57        17.16        39.75         0.26        12.43 
TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PO TCGA-N8-A4PP 
       13.38        26.63        13.74        27.25        25.68        20.09 
TCGA-N8-A56S TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QV TCGA-NA-A4QX 
       12.20        21.93        35.80        19.86       140.35        27.55 
TCGA-NA-A4R0 TCGA-NA-A4R1 TCGA-NA-A5I1 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF 
       17.79         6.67        88.11        23.47        25.18         5.49 
TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-QM-A5NM 
       14.86         2.66        14.53        19.30 

$`DEL PEAK 34(22Q13.31) WILD-TYPE`
TCGA-N5-A4RF TCGA-N5-A59E TCGA-N6-A4VC TCGA-N7-A4Y0 TCGA-N8-A4PN TCGA-N8-A4PQ 
       59.38        14.70        19.63        25.35        26.70        18.81 
TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QW TCGA-NA-A4QY TCGA-ND-A4W6 
       67.17        54.97        15.81        80.78         3.75        10.42 
TCGA-NF-A4WU TCGA-NF-A5CP TCGA-NG-A4VW 
        9.80         5.49        31.20 

  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                           0.26                            3.75 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                         140.35                           80.78 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                          19.58                           19.63 
[1] "0.3 - 140.3 (19.6)" "3.8 - 80.8 (19.6)" 
[1] "hr=" "1.1"
D59V2, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(22Q13.31) MUTATED       2                         7    30
  DEL PEAK 34(22Q13.31) WILD-TYPE     1                         2    13
D59V3, multiclass
                           clus
vv                          DEL PEAK 34(22Q13.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                30
                           clus
vv                          DEL PEAK 34(22Q13.31) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               2
  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(60) Variable = DEL PEAK 35(XP21.1) MUTATION ANALYSIS
D60V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 35(XP21.1) MUTATED    5 13
  DEL PEAK 35(XP21.1) WILD-TYPE 16 21
  DEL PEAK 35(XP21.1) MUTATED DEL PEAK 35(XP21.1) WILD-TYPE 
                           18                            37 
  DEL PEAK 35(XP21.1) MUTATED DEL PEAK 35(XP21.1) WILD-TYPE 
                           13                            21 
$`DEL PEAK 35(XP21.1) MUTATED`
TCGA-N5-A4RD TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RT TCGA-N5-A4RU TCGA-N6-A4V9 
        4.67        34.62        29.95        81.70        50.17        17.42 
TCGA-N7-A4Y5 TCGA-N7-A59B TCGA-N8-A4PI TCGA-N8-A4PO TCGA-N8-A4PP TCGA-N8-A56S 
        0.26        13.38        26.63        25.68        20.09        12.20 
TCGA-N9-A4PZ TCGA-NA-A4QX TCGA-NA-A4R1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WF 
       21.93        27.55         6.67        10.42        23.47         5.49 

$`DEL PEAK 35(XP21.1) WILD-TYPE`
TCGA-N5-A4RA TCGA-N5-A4RF TCGA-N5-A4RJ TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RV 
       52.31        59.38        18.08         4.87        22.52        67.13 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4VC TCGA-N6-A4VD TCGA-N6-A4VE TCGA-N6-A4VF 
       14.70        11.87        19.63         3.68         9.57        17.16 
TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN 
       39.75        25.35        12.43        13.74        27.25        26.70 
TCGA-N8-A4PQ TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-N9-A4Q8 
       18.81        67.17        54.97        35.80        19.86        15.81 
TCGA-NA-A4QV TCGA-NA-A4QW TCGA-NA-A4QY TCGA-NA-A4R0 TCGA-NA-A5I1 TCGA-ND-A4WC 
      140.35        80.78         3.75        17.79        88.11        25.18 
TCGA-NF-A4WU TCGA-NF-A4WX TCGA-NF-A4X2 TCGA-NF-A5CP TCGA-NG-A4VU TCGA-NG-A4VW 
        9.80        14.86         2.66         5.49        14.53        31.20 
TCGA-QM-A5NM 
       19.30 

  DEL PEAK 35(XP21.1) MUTATED DEL PEAK 35(XP21.1) WILD-TYPE 
                         0.26                          2.66 
  DEL PEAK 35(XP21.1) MUTATED DEL PEAK 35(XP21.1) WILD-TYPE 
                        81.70                        140.35 
  DEL PEAK 35(XP21.1) MUTATED DEL PEAK 35(XP21.1) WILD-TYPE 
                        21.01                         19.30 
[1] "0.3 - 81.7 (21.0)"  "2.7 - 140.3 (19.3)"
[1] "hr=" "1.5"
D60V2, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(XP21.1) MUTATED       1                         3    14
  DEL PEAK 35(XP21.1) WILD-TYPE     2                         6    29
D60V3, multiclass
                           clus
vv                          DEL PEAK 35(XP21.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              14
                           clus
vv                          DEL PEAK 35(XP21.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                29
[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(61) Variable = DEL PEAK 36(XQ25) MUTATION ANALYSIS
D61V1, survival
                             sevent
clus2                          0  1
  DEL PEAK 36(XQ25) MUTATED    8 14
  DEL PEAK 36(XQ25) WILD-TYPE 13 20
  DEL PEAK 36(XQ25) MUTATED DEL PEAK 36(XQ25) WILD-TYPE 
                         22                          33 
  DEL PEAK 36(XQ25) MUTATED DEL PEAK 36(XQ25) WILD-TYPE 
                         14                          20 
$`DEL PEAK 36(XQ25) MUTATED`
TCGA-N5-A4RA TCGA-N5-A4RD TCGA-N5-A4RF TCGA-N5-A4RM TCGA-N5-A4RO TCGA-N5-A4RT 
       52.31         4.67        59.38         4.87        22.52        81.70 
TCGA-N5-A59E TCGA-N5-A59F TCGA-N6-A4V9 TCGA-N6-A4VC TCGA-N7-A4Y5 TCGA-N8-A4PP 
       14.70        11.87        17.42        19.63         0.26        20.09 
TCGA-N8-A56S TCGA-N9-A4Q1 TCGA-N9-A4Q3 TCGA-N9-A4Q8 TCGA-NA-A4QV TCGA-NA-A4QW 
       12.20        67.17        54.97        15.81       140.35        80.78 
TCGA-NA-A4R1 TCGA-NF-A4X2 TCGA-NG-A4VU TCGA-QM-A5NM 
        6.67         2.66        14.53        19.30 

$`DEL PEAK 36(XQ25) WILD-TYPE`
TCGA-N5-A4RJ TCGA-N5-A4RN TCGA-N5-A4RS TCGA-N5-A4RU TCGA-N5-A4RV TCGA-N6-A4VD 
       18.08        34.62        29.95        50.17        67.13         3.68 
TCGA-N6-A4VE TCGA-N6-A4VF TCGA-N6-A4VG TCGA-N7-A4Y0 TCGA-N7-A4Y8 TCGA-N7-A59B 
        9.57        17.16        39.75        25.35        12.43        13.38 
TCGA-N8-A4PI TCGA-N8-A4PL TCGA-N8-A4PM TCGA-N8-A4PN TCGA-N8-A4PO TCGA-N8-A4PQ 
       26.63        13.74        27.25        26.70        25.68        18.81 
TCGA-N9-A4PZ TCGA-N9-A4Q4 TCGA-N9-A4Q7 TCGA-NA-A4QX TCGA-NA-A4QY TCGA-NA-A4R0 
       21.93        35.80        19.86        27.55         3.75        17.79 
TCGA-NA-A5I1 TCGA-ND-A4W6 TCGA-ND-A4WA TCGA-ND-A4WC TCGA-ND-A4WF TCGA-NF-A4WU 
       88.11        10.42        23.47        25.18         5.49         9.80 
TCGA-NF-A4WX TCGA-NF-A5CP TCGA-NG-A4VW 
       14.86         5.49        31.20 

  DEL PEAK 36(XQ25) MUTATED DEL PEAK 36(XQ25) WILD-TYPE 
                       0.26                        3.68 
  DEL PEAK 36(XQ25) MUTATED DEL PEAK 36(XQ25) WILD-TYPE 
                     140.35                       88.11 
  DEL PEAK 36(XQ25) MUTATED DEL PEAK 36(XQ25) WILD-TYPE 
                      18.36                       21.93 
[1] "0.3 - 140.3 (18.4)" "3.7 - 88.1 (21.9)" 
[1] "hr=" "1"  
D61V2, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(XQ25) MUTATED       1                         5    17
  DEL PEAK 36(XQ25) WILD-TYPE     2                         4    26
D61V3, multiclass
                           clus
vv                          DEL PEAK 36(XQ25) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            17
                           clus
vv                          DEL PEAK 36(XQ25) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              26
[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"
