[1] "ofn"        "-oTSARC-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/SARC-TP/15087563/SARC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/SARC-TP/15098582/transformed.cor.cli.txt"

nPatients in clinical file=250, in cluster file=256, common to both=246
[1]  66 246
[1] "AMP PEAK  1(1P32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           91                           155 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           91                           155 
[1] "AMP PEAK  2(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           99                           147 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           99                           147 
[1] "AMP PEAK  3(1Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                          100                           146 
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                          100                           146 
[1] "AMP PEAK  4(2P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                           60                           186 
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                           60                           186 
[1] "AMP PEAK  5(3P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                           67                           179 
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                           67                           179 
[1] "AMP PEAK  6(4Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         75                         171 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         75                         171 
[1] "AMP PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           114                            132 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           114                            132 
[1] "AMP PEAK  8(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           58                           188 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           58                           188 
[1] "AMP PEAK  9(6Q25.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                           73                           173 
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                           73                           173 
[1] "AMP PEAK 10(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           75                           171 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           75                           171 
[1] "AMP PEAK 11(8P11.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                            78                            168 
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                            78                            168 
[1] "AMP PEAK 12(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            80                            166 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            80                            166 
[1] "AMP PEAK 13(11Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                            35                            211 
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                            35                            211 
[1] "AMP PEAK 14(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                          92                          154 
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                          92                          154 
[1] "AMP PEAK 15(13Q34) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          51                          195 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          51                          195 
[1] "AMP PEAK 16(15Q26.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            81                            165 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            81                            165 
[1] "AMP PEAK 17(17P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                          97                          149 
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                          97                          149 
[1] "AMP PEAK 18(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                            99                            147 
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                            99                            147 
[1] "AMP PEAK 19(17Q24.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                            75                            171 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                            75                            171 
[1] "AMP PEAK 20(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                           101                            145 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                           101                            145 
[1] "AMP PEAK 21(19Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          90                          156 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          90                          156 
[1] "AMP PEAK 22(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             96                             150 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             96                             150 
[1] "AMP PEAK 23(21Q21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                            71                            175 
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                            71                            175 
[1] "AMP PEAK 24(XP21.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                           94                           152 
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                           94                           152 
[1] "AMP PEAK 25(XQ21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           43                           203 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           43                           203 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            64                            182 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            64                            182 
[1] "DEL PEAK  2(1Q44) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         76                         170 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         76                         170 
[1] "DEL PEAK  3(2P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           93                           153 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           93                           153 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          103                           143 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          103                           143 
[1] "DEL PEAK  5(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          105                           141 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          105                           141 
[1] "DEL PEAK  6(3P21.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            64                            182 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            64                            182 
[1] "DEL PEAK  7(3Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            51                            195 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            51                            195 
[1] "DEL PEAK  8(3Q29) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         52                         194 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         52                         194 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           91                           155 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           91                           155 
[1] "DEL PEAK 10(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            33                            213 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            33                            213 
[1] "DEL PEAK 11(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           76                           170 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           76                           170 
[1] "DEL PEAK 12(6Q14.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                           75                           171 
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                           75                           171 
[1] "DEL PEAK 13(7Q36.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           68                           178 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           68                           178 
[1] "DEL PEAK 14(8P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           78                           168 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           78                           168 
[1] "DEL PEAK 15(9P24.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                           96                           150 
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                           96                           150 
[1] "DEL PEAK 16(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          112                           134 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          112                           134 
[1] "DEL PEAK 17(9Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           60                           186 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           60                           186 
[1] "DEL PEAK 18(10P15.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           123                            123 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           123                            123 
[1] "DEL PEAK 19(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            133                             113 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            133                             113 
[1] "DEL PEAK 20(10Q26.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                           128                            118 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                           128                            118 
[1] "DEL PEAK 21(11P15.5) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           104                            142 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           104                            142 
[1] "DEL PEAK 22(11Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(11Q24.2) MUTATED DEL PEAK 22(11Q24.2) WILD-TYPE 
                           118                            128 
  DEL PEAK 22(11Q24.2) MUTATED DEL PEAK 22(11Q24.2) WILD-TYPE 
                           118                            128 
[1] "DEL PEAK 23(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                            84                            162 
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                            84                            162 
[1] "DEL PEAK 24(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(12Q12) MUTATED DEL PEAK 24(12Q12) WILD-TYPE 
                          53                          193 
  DEL PEAK 24(12Q12) MUTATED DEL PEAK 24(12Q12) WILD-TYPE 
                          53                          193 
[1] "DEL PEAK 25(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             68                             178 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             68                             178 
[1] "DEL PEAK 26(13Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           175                             71 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           175                             71 
[1] "DEL PEAK 27(14Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                            77                            169 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                            77                            169 
[1] "DEL PEAK 28(16Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(16Q11.2) MUTATED DEL PEAK 28(16Q11.2) WILD-TYPE 
                           125                            121 
  DEL PEAK 28(16Q11.2) MUTATED DEL PEAK 28(16Q11.2) WILD-TYPE 
                           125                            121 
[1] "DEL PEAK 29(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                           130                            116 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                           130                            116 
[1] "DEL PEAK 30(17P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                           124                            122 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                           124                            122 
[1] "DEL PEAK 31(17Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                            78                            168 
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                            78                            168 
[1] "DEL PEAK 32(17Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(17Q25.3) MUTATED DEL PEAK 32(17Q25.3) WILD-TYPE 
                            61                            185 
  DEL PEAK 32(17Q25.3) MUTATED DEL PEAK 32(17Q25.3) WILD-TYPE 
                            61                            185 
[1] "DEL PEAK 33(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(18Q23) MUTATED DEL PEAK 33(18Q23) WILD-TYPE 
                          82                          164 
  DEL PEAK 33(18Q23) MUTATED DEL PEAK 33(18Q23) WILD-TYPE 
                          82                          164 
[1] "DEL PEAK 34(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            70                            176 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            70                            176 
[1] "DEL PEAK 35(19Q13.43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                            102                             144 
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                            102                             144 
[1] "DEL PEAK 36(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(21Q11.2) MUTATED DEL PEAK 36(21Q11.2) WILD-TYPE 
                            48                            198 
  DEL PEAK 36(21Q11.2) MUTATED DEL PEAK 36(21Q11.2) WILD-TYPE 
                            48                            198 
[1] "DEL PEAK 37(21Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                            65                            181 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                            65                            181 
[1] "DEL PEAK 38(22Q13.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 38(22Q13.32) MUTATED DEL PEAK 38(22Q13.32) WILD-TYPE 
                             79                             167 
  DEL PEAK 38(22Q13.32) MUTATED DEL PEAK 38(22Q13.32) WILD-TYPE 
                             79                             167 
[1] "DEL PEAK 39(XP21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 39(XP21.1) MUTATED DEL PEAK 39(XP21.1) WILD-TYPE 
                           52                           194 
  DEL PEAK 39(XP21.1) MUTATED DEL PEAK 39(XP21.1) WILD-TYPE 
                           52                           194 
[1] "DEL PEAK 40(XQ21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 40(XQ21.1) MUTATED DEL PEAK 40(XQ21.1) WILD-TYPE 
                          111                           135 
  DEL PEAK 40(XQ21.1) MUTATED DEL PEAK 40(XQ21.1) WILD-TYPE 
                          111                           135 
[1] "DEL PEAK 41(XQ22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 41(XQ22.3) MUTATED DEL PEAK 41(XQ22.3) WILD-TYPE 
                          120                           126 
  DEL PEAK 41(XQ22.3) MUTATED DEL PEAK 41(XQ22.3) WILD-TYPE 
                          120                           126 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "DCC_UPLOAD_DATE"                       
 [6] "GENDER"                                
 [7] "RADIATION_THERAPY"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "RACE"                                  
[10] "ETHNICITY"                             
[11] "BATCH_NUMBER"                          

Input Data has 11 rows and 246 columns.

[1] "Batch" "11"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=63,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=78,	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=163,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'DCC_UPLOAD_DATE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "DCC_UPLOAD_DATE excluded in the analysis because there is no case of (both >= 3) in the table below"
              26-3-2015 29-1-2015 31-12-2014
freq.values   "244"     "1"       "1"       
freq.contrast "2"       "245"     "245"     
both >= 3     "FALSE"   "FALSE"   "FALSE"   
Variable 6:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 8:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION excluded in the analysis because there is no case of (both >= 3) in the table below"
              NO      YES    
freq.values   "1"     "245"  
freq.contrast "245"   "1"    
both >= 3     "FALSE" "FALSE"
Variable 9:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'BATCH_NUMBER':	nDistinctValues=17,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[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 246 columns, 1 survival variables, and 4 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
[1] "YEARS_TO_BIRTH" "GENDER"         "RACE"           "ETHNICITY"     
YEARS_TO_BIRTH, nv=63, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P32.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1P32.1) MUTATED    52  39
  AMP PEAK  1(1P32.1) WILD-TYPE 110  43
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           91                           153 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                           39                            43 
$`AMP PEAK  1(1P32.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1L0 
       19.69        44.91        18.64        26.56         0.56        18.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 
        5.26        76.41        66.87         6.28         8.58         9.70 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A48K TCGA-DX-A48L 
       23.08        70.49        42.77        14.99        19.30        24.26 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       26.47        15.95        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF 
       17.79         3.06        23.54        50.50        16.87        21.30 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BO 
        7.04        17.95         9.34        59.87        33.07        35.77 
TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS 
       14.07        27.95        36.69        60.66         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X 
       12.99        86.10        12.07        71.57       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT 
       50.40        60.00        32.15         0.46        20.32        48.30 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
        4.57        15.91        41.33         9.80        80.48        19.53 
TCGA-IF-A3RQ TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
       37.12         1.05        27.29         9.04        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-N1-A6IA 
       11.70        22.03        13.35         8.32         4.34         4.08 
TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SG-A6Z7 
        6.35         5.03        48.59        35.90        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-VT-A80G TCGA-VT-A80J 
        6.58        17.92        19.82         5.06        10.72        26.17 
TCGA-WK-A8XO TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C4 
       11.93        38.27        22.62        26.43        36.82        16.83 
TCGA-X6-A8C6 
       35.08 

$`AMP PEAK  1(1P32.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        88.57        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KW 
       42.84        10.32        31.00        36.03        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       38.24        12.85        36.69        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 
       42.54        74.66        27.81        60.30        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
        9.04       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       17.75         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       34.88        64.18         9.73        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BH TCGA-DX-A6BK 
       72.72        25.08        25.15        11.47        21.63        16.18 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       34.55        66.31        67.20        74.10        64.21        88.31 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       34.49        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BR 
       48.20        14.07        14.43        44.68        38.17       124.37 
TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
       35.54        19.43         8.75         4.67        12.39        40.60 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       49.18         9.21        96.89        22.85       101.98        19.20 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G 
       84.66        50.89        71.31         0.10         0.07         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        0.07         2.07        34.88        12.62        23.97         0.10 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       21.37         3.22         1.38        19.89        25.22        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       22.62        16.41         3.91        71.70        36.39       123.78 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        8.28         0.49        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
        7.46        10.45       120.20        37.55        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       18.08        20.94         9.83         1.84        46.82        18.08 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       30.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        0.72        11.18        27.22         9.93        13.22         0.72 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
        4.80        72.72        41.49        65.46         9.04        57.80 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       29.92        18.08        18.35        25.71        15.95        38.96 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                         0.46                          0.07 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                       106.45                        188.15 
  AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE 
                        19.30                         27.81 
[1] "0.5 - 106.5 (19.3)" "0.1 - 188.2 (27.8)"
[1] "hr=" "2.2"
D1V2, continuous
D1V3, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P32.1) MUTATED   43 48
  AMP PEAK  1(1P32.1) WILD-TYPE 89 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P32.1) MUTATED     43   48
  AMP PEAK  1(1P32.1) WILD-TYPE   89   66
        clus
vv       AMP PEAK  1(1P32.1) MUTATED AMP PEAK  1(1P32.1) WILD-TYPE
  FEMALE                          43                            89
  MALE                            48                            66
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P32.1) MUTATED       0                         8    71
  AMP PEAK  1(1P32.1) WILD-TYPE     6                        10   123
D1V4, multiclass
                           clus
vv                          AMP PEAK  1(1P32.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              71
                           clus
vv                          AMP PEAK  1(1P32.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               123
[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"
D1V5, binary
                               cls
clus                              0   1
  AMP PEAK  1(1P32.1) MUTATED     0  76
  AMP PEAK  1(1P32.1) WILD-TYPE   5 115
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P32.1) MUTATED      0   76
  AMP PEAK  1(1P32.1) WILD-TYPE    5  115
                        clus
vv                       AMP PEAK  1(1P32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          76
                        clus
vv                       AMP PEAK  1(1P32.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           115
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q21.3) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q21.3) MUTATED   67 32
  AMP PEAK  2(1Q21.3) WILD-TYPE 95 50
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           99                           145 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                           32                            50 
$`AMP PEAK  2(1Q21.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 
       19.69        53.49        44.91        42.84        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-DX-A3LT TCGA-DX-A3M2 TCGA-DX-A3U7 
        0.56        12.85        59.24        23.08        34.68        42.77 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N 
       14.99        10.68        28.80        64.18        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV 
       27.22        26.47        15.95        66.31        23.54        50.50 
TCGA-DX-A6YX TCGA-DX-A7EI TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
       16.87        34.49        17.95         9.34        59.87        33.07 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AATS 
       35.77       124.37        27.95        36.69        60.66         1.15 
TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
       86.10        49.18        96.89       106.45        13.28        50.40 
TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A48G 
       19.20        84.66        32.15         0.46        20.32         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 
        2.07        48.30        34.88        15.91        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A6BZ 
       41.33         9.80        80.48        21.37        19.53        19.89 
TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
       25.22        28.21       143.41         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
        1.05        27.29       123.78        10.85         4.08        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DN 
       22.03        13.35         8.32         4.34         4.08        38.63 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       20.94         5.03         9.83        35.90        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QU 
        6.58        17.92        19.82        27.22         5.06         0.72 
TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WB 
       26.17        72.72        38.27        22.62         9.04        18.08 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 
       36.82        25.71        16.83 

$`AMP PEAK  2(1Q21.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY 
       36.30        68.55        88.57        54.74        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ 
       31.00        36.03        14.04        32.71        38.24        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       18.54        54.21        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB 
       17.10        20.05        15.06        17.75         4.54        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48P TCGA-DX-A48U 
       39.35        34.88         9.73        24.26        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        11.47        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YT TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL 
       67.20        74.10        64.21        88.31        21.30        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BT 
        7.04        14.43        44.68        38.17        14.07        35.54 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       19.43         6.58        12.99         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB30 TCGA-DX-AB32 
       40.60        12.07         9.21        71.57        22.85       101.98 
TCGA-DX-AB36 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y 
       60.00        50.89        71.31         0.10         0.07         0.07 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK 
        4.57        12.62         3.22         1.38        37.12        40.08 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
      116.88        13.58        73.28         3.91        71.70        36.39 
TCGA-K1-A6RT TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        9.04         8.28         0.49        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         7.46        10.45       120.20        37.55         6.35 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       81.01        18.08         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       30.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO 
        0.72        11.18         9.93        13.22        10.72        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
        4.80        41.49        65.46        57.80        26.43        29.92 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       18.35        15.95        38.96        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                       143.41                        188.15 
  AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE 
                        22.62                         25.08 
[1] "0.1 - 143.4 (22.6)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.1"
D2V2, continuous
D2V3, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q21.3) MUTATED   60 39
  AMP PEAK  2(1Q21.3) WILD-TYPE 72 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED     60   39
  AMP PEAK  2(1Q21.3) WILD-TYPE   72   75
        clus
vv       AMP PEAK  2(1Q21.3) MUTATED AMP PEAK  2(1Q21.3) WILD-TYPE
  FEMALE                          60                            72
  MALE                            39                            75
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q21.3) MUTATED       2                         8    81
  AMP PEAK  2(1Q21.3) WILD-TYPE     4                        10   113
D2V4, multiclass
                           clus
vv                          AMP PEAK  2(1Q21.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           8
  WHITE                                              81
                           clus
vv                          AMP PEAK  2(1Q21.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            10
  WHITE                                               113
[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"
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q21.3) MUTATED     1  81
  AMP PEAK  2(1Q21.3) WILD-TYPE   4 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q21.3) MUTATED      1   81
  AMP PEAK  2(1Q21.3) WILD-TYPE    4  110
                        clus
vv                       AMP PEAK  2(1Q21.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          81
                        clus
vv                       AMP PEAK  2(1Q21.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           110
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(1Q24.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(1Q24.3) MUTATED   66 33
  AMP PEAK  3(1Q24.3) WILD-TYPE 96 49
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                           99                           145 
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                           33                            49 
$`AMP PEAK  3(1Q24.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-3R-A8YX 
       19.69        53.49        44.91        42.84        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23U 
       14.04        12.85        18.54        59.24        33.53        76.41 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U7 
       60.30         9.70        23.08        34.68        17.75        42.77 
TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       14.99        28.80        64.18        19.30        12.26        27.22 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       26.47        15.95         9.11        17.79        21.63         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EI TCGA-DX-A8BG TCGA-DX-A8BJ 
       34.55        66.31        23.54        34.49        17.95         9.34 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       59.87        33.07        44.68        35.77       124.37        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB35 
       36.69        60.66        86.10        49.18         9.21        19.20 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.46        20.32         0.07         2.07        48.30        34.88 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       15.91        12.62         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 
       21.37        19.53        19.89        37.12        25.22       143.41 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV 
       22.62         1.05        27.29       123.78        10.85         4.08 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DN TCGA-QC-A7B5 
       13.35         8.32         4.34         4.08        38.63         5.03 
TCGA-QQ-A5VC TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
       35.90        10.52        18.94         3.88         6.58        17.92 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XS 
       27.22         5.06         0.72        10.72        11.93        72.72 
TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
       38.27        22.62         9.04        18.08        36.82        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A971 
       16.83        35.08        15.58 

$`AMP PEAK  3(1Q24.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY 
       36.30        68.55        88.57        54.74        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ 
       31.00        36.03        18.64        32.71        38.24        36.69 
TCGA-DX-A1L1 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y 
       54.21        42.54        74.66         5.26        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       27.81         8.58        59.47        54.77         9.04        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U8 TCGA-DX-A3UA 
      108.13        17.10        20.05        15.06         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48P 
       44.45        39.35        34.88         9.73        24.26        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        25.15        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       28.96        16.18        67.20        50.50        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       64.21        88.31        21.30        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH 
      135.48        29.49        48.20        14.07         7.04        14.43 
TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       38.17        14.07        35.54        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       12.99         8.75         4.67        12.39        40.60        12.07 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
       71.57        96.89       106.45        13.28        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
      101.98        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-IE-A4EJ 
        0.10         0.07         0.07         4.57        23.97         3.22 
TCGA-IE-A4EK TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
        1.38        40.08        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT 
        5.92        16.41         3.91        71.70        36.39         9.04 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H 
       11.70        22.03         8.28         0.49        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        15.65         7.46        10.45       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 
        6.35        81.01        18.08        20.94         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       46.82        18.08        48.59        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-AA8C 
       98.27        62.20         0.72        11.18        19.82         9.93 
TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X2-A95T 
       13.22        26.17         4.80        41.49        65.46        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 
       26.43        29.92        18.35        15.95        38.96        17.72 
TCGA-X9-A973 
       36.43 

  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                       143.41                        188.15 
  AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE 
                        21.37                         25.15 
[1] "0.1 - 143.4 (21.4)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.2"
D3V2, continuous
D3V3, binary
                               cls
clus                             0  1
  AMP PEAK  3(1Q24.3) MUTATED   55 45
  AMP PEAK  3(1Q24.3) WILD-TYPE 77 69
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q24.3) MUTATED     55   45
  AMP PEAK  3(1Q24.3) WILD-TYPE   77   69
        clus
vv       AMP PEAK  3(1Q24.3) MUTATED AMP PEAK  3(1Q24.3) WILD-TYPE
  FEMALE                          55                            77
  MALE                            45                            69
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(1Q24.3) MUTATED       2                         5    81
  AMP PEAK  3(1Q24.3) WILD-TYPE     4                        13   113
D3V4, multiclass
                           clus
vv                          AMP PEAK  3(1Q24.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              81
                           clus
vv                          AMP PEAK  3(1Q24.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               113
[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"
D3V5, binary
                               cls
clus                              0   1
  AMP PEAK  3(1Q24.3) MUTATED     2  80
  AMP PEAK  3(1Q24.3) WILD-TYPE   3 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(1Q24.3) MUTATED      2   80
  AMP PEAK  3(1Q24.3) WILD-TYPE    3  111
                        clus
vv                       AMP PEAK  3(1Q24.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          80
                        clus
vv                       AMP PEAK  3(1Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           111
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(2P11.2) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(2P11.2) MUTATED    36  24
  AMP PEAK  4(2P11.2) WILD-TYPE 126  58
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                           60                           184 
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                           24                            58 
$`AMP PEAK  4(2P11.2) MUTATED`
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW 
       25.25        42.84        10.32        26.56        14.04        32.71 
TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3M2 TCGA-DX-A3U7 
       18.54        74.66         6.28        23.08        34.68        42.77 
TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A6YS 
       39.35        64.18        19.30        24.26        66.05        66.31 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A8BG 
       23.54        50.50        74.10        21.30        34.49        17.95 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BZ TCGA-DX-AB2O 
        9.34        59.87        33.07        38.17         6.58        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB37 
       12.07        49.18       106.45        13.28        50.40        84.66 
TCGA-DX-AB3A TCGA-FX-A2QS TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IF-A3RQ 
       32.15         0.46         4.57        15.91         3.22        37.12 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-KF-A41W TCGA-MB-A8JK 
       40.08        13.58         5.92        22.62        11.70         4.34 
TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QQ-A8VB TCGA-SG-A6Z7 TCGA-SI-A71P 
       10.45        37.55        81.01       188.15         3.88        19.82 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS TCGA-X6-A7W8 TCGA-X6-A8C4 TCGA-X6-A8C6 
        0.72        10.72        72.72        26.43        16.83        35.08 

$`AMP PEAK  4(2P11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KX 
       54.74        31.00        36.03        18.64         0.56        38.24 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        36.69        54.21        59.24        33.53        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       17.10        20.05        15.06        17.75         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N 
       10.68        44.45        28.80        34.88         9.73        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       15.95        11.47        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YX 
       21.63        16.18         3.06        34.55        67.20        16.87 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       64.21        88.31        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BM 
       29.49        48.20        14.07         7.04        14.43        44.68 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       35.77        14.07       124.37        27.95        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       60.66        19.43         1.15        12.99         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB30 
       12.39        40.60         9.21        71.57        96.89        22.85 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
      101.98        19.20        60.00        50.89        71.31         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.07        20.32         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
       34.88        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
       80.48        21.37        19.53         1.38        19.89        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF 
       28.21       143.41       116.88        73.28        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       10.85         4.08        22.03        13.35         8.32         8.28 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        19.73        14.99        17.98        15.65         7.46 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX 
        4.08       120.20         6.35        38.63        18.08        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        30.90       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71Q 
        0.72        11.18        18.94         6.58        17.92        27.22 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
        5.06         9.93        13.22        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       41.49        38.27        65.46        22.62         9.04        57.80 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       29.92        18.08        36.82        18.35        25.71        15.95 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       38.96        17.72        15.58        36.43 

  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                         0.46                          0.07 
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                       188.15                        143.41 
  AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE 
                        25.84                         21.83 
[1] "0.5 - 188.2 (25.8)" "0.1 - 143.4 (21.8)"
[1] "hr=" "1.2"
D4V2, continuous
D4V3, binary
                               cls
clus                             0  1
  AMP PEAK  4(2P11.2) MUTATED   36 24
  AMP PEAK  4(2P11.2) WILD-TYPE 96 90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P11.2) MUTATED     36   24
  AMP PEAK  4(2P11.2) WILD-TYPE   96   90
        clus
vv       AMP PEAK  4(2P11.2) MUTATED AMP PEAK  4(2P11.2) WILD-TYPE
  FEMALE                          36                            96
  MALE                            24                            90
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(2P11.2) MUTATED       3                         2    51
  AMP PEAK  4(2P11.2) WILD-TYPE     3                        16   143
D4V4, multiclass
                           clus
vv                          AMP PEAK  4(2P11.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              51
                           clus
vv                          AMP PEAK  4(2P11.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                            16
  WHITE                                               143
[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"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(2P11.2) MUTATED     1  51
  AMP PEAK  4(2P11.2) WILD-TYPE   4 140
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(2P11.2) MUTATED      1   51
  AMP PEAK  4(2P11.2) WILD-TYPE    4  140
                        clus
vv                       AMP PEAK  4(2P11.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          51
                        clus
vv                       AMP PEAK  4(2P11.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           140
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(3P12.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(3P12.1) MUTATED    40  26
  AMP PEAK  5(3P12.1) WILD-TYPE 122  56
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                           66                           178 
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                           26                            56 
$`AMP PEAK  5(3P12.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KW 
       19.69        88.57        42.84        18.64         0.56        32.71 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3U8 
       74.66         6.28         9.04        23.08        42.77         4.54 
TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YZ TCGA-DX-A7EF 
       64.18        26.47        16.18        66.31        74.10        21.30 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
        7.04        17.95        14.43        33.07        44.68        38.17 
TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2E 
       14.07        27.95        35.54        36.69         1.15        12.99 
TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
        4.67        86.10        12.07        96.89       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB37 TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IE-A3OV 
       50.40       101.98        84.66        20.32        48.30        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-K1-A6RU TCGA-KF-A41W 
       19.53         3.22        25.22        40.08        10.85        11.70 
TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V9 
       14.99         6.35        18.08        20.94         5.03        46.82 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS 
        6.58         5.06         0.72        10.72        26.17        72.72 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C6 TCGA-X9-A971 
       22.62         9.04        26.43        36.82        35.08        15.58 

$`AMP PEAK  5(3P12.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KX 
       10.32        31.00        36.03        26.56        14.04        38.24 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        36.69        18.54        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58         9.70        59.47        54.77        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 
       17.10        20.05        34.68        15.06        17.75        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       10.68        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       25.08        25.15        15.95        11.47        66.05        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       28.96         9.11        17.79        21.63         3.06        34.55 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       67.20        23.54        50.50        16.87        64.21        88.31 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       34.49        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BR 
       48.20        14.07         9.34        59.87        35.77       124.37 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2J 
       60.66        19.43         6.58         8.75        12.39        40.60 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
       49.18         9.21        71.57        22.85        19.20        60.00 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       32.15        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         0.07         2.07        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
       12.62        23.97         0.10        41.33         9.80        21.37 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        1.38        19.89        37.12        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
       13.58        73.28         5.92        22.62        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        4.08        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        4.34        19.73        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
        4.08       120.20        37.55        38.63        81.01         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        1.84        18.08        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32        98.27        62.20        10.52         0.72        11.18 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
       18.94         3.88        17.92        19.82        27.22         9.93 
TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       13.22        11.93         4.80        41.49        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       57.80        29.92        18.08        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        38.96        17.72        36.43 

  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                         0.56                          0.07 
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                       106.45                        188.15 
  AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE 
                       21.960                        23.755 
[1] "0.6 - 106.5 (22.0)" "0.1 - 188.2 (23.8)"
[1] "hr=" "1.3"
D5V2, continuous
D5V3, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P12.1) MUTATED    32  35
  AMP PEAK  5(3P12.1) WILD-TYPE 100  79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P12.1) MUTATED     32   35
  AMP PEAK  5(3P12.1) WILD-TYPE  100   79
        clus
vv       AMP PEAK  5(3P12.1) MUTATED AMP PEAK  5(3P12.1) WILD-TYPE
  FEMALE                          32                           100
  MALE                            35                            79
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(3P12.1) MUTATED       1                         6    55
  AMP PEAK  5(3P12.1) WILD-TYPE     5                        12   139
D5V4, multiclass
                           clus
vv                          AMP PEAK  5(3P12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              55
                           clus
vv                          AMP PEAK  5(3P12.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               139
[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"
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(3P12.1) MUTATED     0  57
  AMP PEAK  5(3P12.1) WILD-TYPE   5 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(3P12.1) MUTATED      0   57
  AMP PEAK  5(3P12.1) WILD-TYPE    5  134
                        clus
vv                       AMP PEAK  5(3P12.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          57
                        clus
vv                       AMP PEAK  5(3P12.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           134
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(4Q12) MUTATION ANALYSIS
D6V1, survival
                             sevent
clus2                           0   1
  AMP PEAK  6(4Q12) MUTATED    47  27
  AMP PEAK  6(4Q12) WILD-TYPE 115  55
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         74                         170 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                         27                          55 
$`AMP PEAK  6(4Q12) MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       88.57        44.91        42.84        18.64        26.56         0.56 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A3LY 
       38.24        12.85        18.54        54.21        74.66        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6YR 
       34.68        42.77        19.30        15.95        66.05        34.55 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7ES 
       66.31        23.54        50.50        74.10        64.21        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
        7.04        17.95        14.43         9.34        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2E 
       44.68        35.77        27.95        36.69        60.66        12.99 
TCGA-DX-AB2F TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2W TCGA-HB-A3YV TCGA-HS-A5N9 
        8.75        12.07        49.18       106.45         4.57        41.33 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-K1-A6RU TCGA-K1-A6RV 
        3.22        19.89       143.41        13.58        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MO-A47R 
       11.70        22.03         8.28         4.34        14.99        10.45 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       37.55         6.35        81.01         5.03        18.08        48.59 
TCGA-QQ-A8VB TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QT 
      188.15        11.18        18.94        17.92         5.06        13.22 
TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB 
        0.72        10.72        26.17        72.72        22.62         9.04 
TCGA-X6-A7W8 TCGA-X6-A8C2 
       26.43        25.71 

$`AMP PEAK  6(4Q12) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        53.49        68.55        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ 
       10.32        31.00        36.03        14.04        32.71        36.69 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 
       54.77         9.04        23.08        70.49       108.13        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.15        11.47        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6Z2 
       21.63        16.18         3.06        67.20        16.87        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       21.30        34.49        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT 
       29.49        48.20        38.17        14.07       124.37        35.54 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
       19.43         6.58         1.15         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z 
       86.10         9.21        71.57        96.89        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z 
        0.07         0.07         2.07        48.30        34.88        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97         0.10         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       19.53         1.38        37.12        25.22        40.08        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        73.28         5.92        22.62        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
       13.35         8.32         0.49        19.73        17.98        15.65 
TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX 
        7.46         4.08       120.20        38.63        18.08        20.94 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
        9.83         1.84        46.82        35.90        30.90       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 
       98.27        62.20        10.52         0.72         3.88         6.58 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
       19.82        27.22         9.93        11.93         4.80        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       38.27        65.46        57.80        29.92        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       18.35        15.95        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                       0.56                        0.07 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                     188.15                      135.48 
  AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE 
                     20.960                      24.115 
[1] "0.6 - 188.2 (21.0)" "0.1 - 135.5 (24.1)"
[1] "hr=" "1.2"
D6V2, continuous
D6V3, binary
                             cls
clus                           0  1
  AMP PEAK  6(4Q12) MUTATED   37 38
  AMP PEAK  6(4Q12) WILD-TYPE 95 76
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED     37   38
  AMP PEAK  6(4Q12) WILD-TYPE   95   76
        clus
vv       AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  FEMALE                        37                          95
  MALE                          38                          76
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(4Q12) MUTATED       3                         5    60
  AMP PEAK  6(4Q12) WILD-TYPE     3                        13   134
D6V4, multiclass
                           clus
vv                          AMP PEAK  6(4Q12) MUTATED
  ASIAN                                             3
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                            60
                           clus
vv                          AMP PEAK  6(4Q12) WILD-TYPE
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             134
[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"
D6V5, binary
                             cls
clus                            0   1
  AMP PEAK  6(4Q12) MUTATED     1  60
  AMP PEAK  6(4Q12) WILD-TYPE   4 131
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  6(4Q12) MUTATED      1   60
  AMP PEAK  6(4Q12) WILD-TYPE    4  131
                        clus
vv                       AMP PEAK  6(4Q12) MUTATED AMP PEAK  6(4Q12) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        60                         131
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(5P15.33) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  7(5P15.33) MUTATED   69 44
  AMP PEAK  7(5P15.33) WILD-TYPE 93 38
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                           113                            131 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                            44                             38 
$`AMP PEAK  7(5P15.33) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HY 
       19.69        68.55        88.57        44.91        54.74        10.32 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       18.64        26.56         0.56        14.04        32.71        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23Y 
       36.69        18.54        54.21        59.24        33.53         6.28 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U7 
        8.58         9.70         9.04        17.10        34.68        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48P 
        4.54        14.99        28.80        64.18        24.26        14.96 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BG TCGA-DX-A6BK TCGA-DX-A6YR 
       26.47        15.95        66.05        17.79        16.18        34.55 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI 
       66.31        23.54        16.87        74.10        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL 
       75.32        15.62         7.04        14.43        59.87        33.07 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       38.17        35.77        14.07        27.95        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       60.66        19.43         1.15        12.99         8.75         4.67 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB3A 
       12.07        49.18        96.89       106.45        19.20        32.15 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EI 
        0.46        20.32        48.30        15.91         0.10        19.53 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IW-A3M5 
        3.22        19.89        25.22        40.08        28.21         5.92 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MJ-A68H 
        1.05        71.70        27.29        22.03        13.35        14.99 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
       10.45         4.08         6.35        18.08        20.94         5.03 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ 
       46.82        18.08       188.15        98.27        10.52        11.18 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT 
       18.94         3.88        17.92        19.82        27.22        13.22 
TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
        0.72        72.72        38.27         9.04        57.80        26.43 
TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A971 
       36.82        25.71        16.83        35.08        15.58 

$`AMP PEAK  7(5P15.33) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I0 
       36.30        53.49        25.25        42.84        31.00        36.03 
TCGA-DX-A1KY TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       12.85        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU 
       27.81        60.30        59.47        54.77        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3UA TCGA-DX-A3UB 
      108.13        20.05        15.06        17.75        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       39.35        34.88         9.73        19.30        12.26        27.22 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        25.15        11.47        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6Z0 
        9.11        21.63         3.06        67.20        50.50        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       88.31        48.36       135.48        29.49        48.20        14.07 
TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BR TCGA-DX-A8BZ TCGA-DX-AB2H 
       17.95         9.34        44.68       124.37         6.58        12.39 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB2Z 
       40.60        86.10         9.21        71.57        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C 
       22.85       101.98        60.00        84.66        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
        0.10         0.07         0.07         0.07         2.07        34.88 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
        4.57        12.62        23.97        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       21.37         1.38        37.12       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X 
       73.28        22.62        16.41         3.91        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A5Y9 
        9.04        10.85         4.08        11.70         8.32         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49         4.34        19.73        17.98        15.65         7.46 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N TCGA-QQ-A5V2 
      120.20        37.55        38.63        81.01         9.83         1.84 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q 
       48.59        35.90        30.90       130.32        62.20         0.72 
TCGA-SG-A849 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
        6.58         5.06         9.93        10.72        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A7WB 
        4.80        41.49        65.46        22.62        29.92        18.08 
TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       18.35        15.95        38.96        17.72        36.43 

  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                        188.15                         143.41 
  AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE 
                         20.32                          25.15 
[1] "0.1 - 188.2 (20.3)" "0.1 - 143.4 (25.1)"
[1] "hr=" "1.6"
D7V2, continuous
D7V3, binary
                                cls
clus                              0  1
  AMP PEAK  7(5P15.33) MUTATED   56 58
  AMP PEAK  7(5P15.33) WILD-TYPE 76 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED     56   58
  AMP PEAK  7(5P15.33) WILD-TYPE   76   56
        clus
vv       AMP PEAK  7(5P15.33) MUTATED AMP PEAK  7(5P15.33) WILD-TYPE
  FEMALE                           56                             76
  MALE                             58                             56
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(5P15.33) MUTATED       3                         9    88
  AMP PEAK  7(5P15.33) WILD-TYPE     3                         9   106
D7V4, multiclass
                           clus
vv                          AMP PEAK  7(5P15.33) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               88
                           clus
vv                          AMP PEAK  7(5P15.33) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                106
[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"
D7V5, binary
                                cls
clus                               0   1
  AMP PEAK  7(5P15.33) MUTATED     2  88
  AMP PEAK  7(5P15.33) WILD-TYPE   3 103
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(5P15.33) MUTATED      2   88
  AMP PEAK  7(5P15.33) WILD-TYPE    3  103
                        clus
vv                       AMP PEAK  7(5P15.33) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       AMP PEAK  7(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            103
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(6P21.1) MUTATION ANALYSIS
D8V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  8(6P21.1) MUTATED    31  26
  AMP PEAK  8(6P21.1) WILD-TYPE 131  56
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           57                           187 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                           26                            56 
$`AMP PEAK  8(6P21.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX 
       19.69        88.57        44.91         0.56        32.71        38.24 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LU TCGA-DX-A3M2 TCGA-DX-A3U9 TCGA-DX-A6B8 
       59.24         6.28        70.49        34.68        14.99        15.95 
TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7ET TCGA-DX-A8BL 
       21.63        50.50        74.10        21.30         7.04        33.07 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       38.17        27.95        36.69        60.66        19.43         1.15 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB35 TCGA-FX-A2QS TCGA-HB-A2OT TCGA-HB-A3YV 
       49.18        71.57        19.20         0.46        48.30         4.57 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 TCGA-IS-A3KA 
        0.10        41.33         3.22        19.89       143.41        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A67I 
        5.92         1.05         9.04        10.85        11.70        22.03 
TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V9 TCGA-QQ-A5VC 
        4.34         4.08         6.35        38.63        46.82        35.90 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-WK-A8Y0 TCGA-WP-A9GB 
       18.94         3.88        17.92         5.06        22.62         9.04 
TCGA-X6-A8C2 TCGA-X6-A8C6 TCGA-X9-A971 
       25.71        35.08        15.58 

$`AMP PEAK  8(6P21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        68.55        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64        26.56        14.04 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        36.69        18.54        54.21        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        20.05        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BK 
       66.05        23.44        28.96         9.11        17.79        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX 
        3.06        34.55        66.31        67.20        23.54        16.87 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       64.21        88.31        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BH 
      135.48        29.49        48.20        14.07        17.95        14.43 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
        9.34        59.87        44.68        35.77        14.07       124.37 
TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       35.54         6.58        12.99         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W 
       40.60        86.10        12.07         9.21        96.89       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 
       13.28        50.40        22.85       101.98        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       32.15        50.89        71.31         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07         2.07        34.88        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
       23.97         9.80        80.48        21.37        19.53         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 
       37.12        25.22        40.08        28.21       116.88        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       22.62        16.41         3.91        71.70        36.39        27.29 
TCGA-K1-A42X TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
      123.78         4.08        13.35         8.32         8.28         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        15.65         7.46        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
      120.20        37.55        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB 
        9.83         1.84        18.08        48.59        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32        98.27        62.20        10.52         0.72        11.18 
TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        6.58        19.82        27.22         9.93        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       10.72        26.17        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       36.82        18.35        15.95        16.83        38.96        17.72 
TCGA-X9-A973 
       36.43 

  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                         0.10                          0.07 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                       143.41                        188.15 
  AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE 
                        19.89                         25.08 
[1] "0.1 - 143.4 (19.9)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.9"
D8V2, continuous
D8V3, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED    28  30
  AMP PEAK  8(6P21.1) WILD-TYPE 104  84
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED     28   30
  AMP PEAK  8(6P21.1) WILD-TYPE  104   84
        clus
vv       AMP PEAK  8(6P21.1) MUTATED AMP PEAK  8(6P21.1) WILD-TYPE
  FEMALE                          28                           104
  MALE                            30                            84
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(6P21.1) MUTATED       0                         7    44
  AMP PEAK  8(6P21.1) WILD-TYPE     6                        11   150
D8V4, multiclass
                           clus
vv                          AMP PEAK  8(6P21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              44
                           clus
vv                          AMP PEAK  8(6P21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               150
[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"
D8V5, binary
                               cls
clus                              0   1
  AMP PEAK  8(6P21.1) MUTATED     2  45
  AMP PEAK  8(6P21.1) WILD-TYPE   3 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  8(6P21.1) MUTATED      2   45
  AMP PEAK  8(6P21.1) WILD-TYPE    3  146
                        clus
vv                       AMP PEAK  8(6P21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          45
                        clus
vv                       AMP PEAK  8(6P21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           146
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(6Q25.1) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(6Q25.1) MUTATED    48  24
  AMP PEAK  9(6Q25.1) WILD-TYPE 114  58
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                           72                           172 
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                           24                            58 
$`AMP PEAK  9(6Q25.1) MUTATED`
TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L4 
       44.91         0.56        32.71        38.24        36.69        42.54 
TCGA-DX-A23T TCGA-DX-A23Z TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
        5.26        27.81        59.47        23.08        70.49        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A48N TCGA-DX-A6B8 
       20.05        15.06        17.75        14.99        12.26        15.95 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV 
       21.63        16.18        34.55        66.31        23.54        50.50 
TCGA-DX-A6Z0 TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       64.21        14.07         7.04        59.87        33.07        44.68 
TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F 
       35.77        27.95        36.69        19.43         1.15         8.75 
TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB35 TCGA-HB-A2OT 
        4.67        86.10         9.21        71.57        19.20        48.30 
TCGA-HB-A43Z TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-IW-A3M5 
       15.91         3.22        19.89        37.12       143.41         5.92 
TCGA-JV-A5VF TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 
        1.05         9.04        10.85        22.03        13.35         8.28 
TCGA-MB-A8JK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5VB 
        4.34        37.55         6.35        20.94         5.03        48.59 
TCGA-QQ-A5VC TCGA-SG-A6Z4 TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QU TCGA-WK-A8XS 
       35.90        18.94        19.82        27.22         0.72        72.72 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X9-A971 
       38.27         9.04        26.43        15.95        35.08        15.58 

$`AMP PEAK  9(6Q25.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       26.56        14.04        12.85        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 
       33.53        74.66        76.41        66.87         6.28        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M2 
        8.58         9.70        54.77         9.04       108.13        34.68 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6YQ 
       66.05        23.44        28.96         9.11        17.79         3.06 
TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       67.20        16.87        74.10        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
       17.95        14.43         9.34        38.17        14.07       124.37 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2H TCGA-DX-AB2J 
       35.54        60.66         6.58        12.99        12.39        40.60 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
       12.07        49.18        96.89       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85       101.98        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.31         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         2.07        34.88         4.57        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
        0.10        41.33         9.80        80.48        21.37        19.53 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA 
        1.38        25.22        40.08        28.21       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       73.28        22.62        16.41         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A5YA 
       27.29       123.78         4.08        11.70         8.32         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N 
        4.08       120.20        38.63        81.01        18.08         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
        1.84        46.82        18.08        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 
       98.27        62.20        10.52         0.72        11.18         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G 
        6.58        17.92         5.06         9.93        13.22        10.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 
       26.17        11.93         4.80        41.49        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        38.96        17.72        36.43 

  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                         0.56                          0.07 
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                       143.41                        188.15 
  AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE 
                       20.495                        25.115 
[1] "0.6 - 143.4 (20.5)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.2"
D9V2, continuous
D9V3, binary
                               cls
clus                             0  1
  AMP PEAK  9(6Q25.1) MUTATED   33 40
  AMP PEAK  9(6Q25.1) WILD-TYPE 99 74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6Q25.1) MUTATED     33   40
  AMP PEAK  9(6Q25.1) WILD-TYPE   99   74
        clus
vv       AMP PEAK  9(6Q25.1) MUTATED AMP PEAK  9(6Q25.1) WILD-TYPE
  FEMALE                          33                            99
  MALE                            40                            74
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(6Q25.1) MUTATED       2                         6    57
  AMP PEAK  9(6Q25.1) WILD-TYPE     4                        12   137
D9V4, multiclass
                           clus
vv                          AMP PEAK  9(6Q25.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              57
                           clus
vv                          AMP PEAK  9(6Q25.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               137
[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"
D9V5, binary
                               cls
clus                              0   1
  AMP PEAK  9(6Q25.1) MUTATED     2  55
  AMP PEAK  9(6Q25.1) WILD-TYPE   3 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(6Q25.1) MUTATED      2   55
  AMP PEAK  9(6Q25.1) WILD-TYPE    3  136
                        clus
vv                       AMP PEAK  9(6Q25.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          55
                        clus
vv                       AMP PEAK  9(6Q25.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           136
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(7Q31.2) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(7Q31.2) MUTATED    45  30
  AMP PEAK 10(7Q31.2) WILD-TYPE 117  52
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           75                           169 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                           30                            52 
$`AMP PEAK 10(7Q31.2) MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 
       44.91        42.84        38.24        12.85        36.69        54.21 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UF 
       59.24         6.28        27.81        23.08        20.05        64.18 
TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6BH TCGA-DX-A6YQ TCGA-DX-A6YR 
       24.26        15.95        23.44        21.63         3.06        34.55 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI 
       50.50        16.87        74.10        64.21        21.30        34.49 
TCGA-DX-A7EM TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       48.36        14.43        59.87        35.77       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F 
       35.54        36.69        19.43         6.58         1.15         8.75 
TCGA-DX-AB2H TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 
       12.39         9.21        96.89       106.45        13.28        19.20 
TCGA-DX-AB37 TCGA-FX-A3RE TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 
       84.66         0.07        48.30         4.57        15.91         0.10 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-JV-A5VF TCGA-K1-A6RU 
       19.53         3.22        19.89        13.58         1.05        10.85 
TCGA-MB-A5Y9 TCGA-MO-A47R TCGA-PC-A5DL TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
        8.28        10.45        37.55        20.94         5.03         9.83 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A849 
       18.08        35.90       188.15        98.27        11.18         6.58 
TCGA-SI-A71O TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8Y0 TCGA-X6-A7WC 
       17.92         0.72        26.17        11.93        22.62        36.82 
TCGA-X6-A8C2 TCGA-X6-A8C6 TCGA-X9-A973 
       25.71        35.08        36.43 

$`AMP PEAK 10(7Q31.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       25.25        10.32        31.00        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 
        0.56        14.04        32.71        18.54        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A240 TCGA-DX-A2IZ 
       74.66         5.26        76.41        66.87        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE 
       72.72        25.08        25.15        11.47        66.05        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
        9.11        17.79        16.18        66.31        67.20        23.54 
TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       88.31        75.32        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM 
       14.07         7.04        17.95         9.34        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BV TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2J 
       38.17        14.07        60.66        12.99         4.67        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB30 
       86.10        12.07        49.18        71.57        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
      101.98        60.00        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
        0.10        20.32         0.07         0.07         2.07        34.88 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       12.62        23.97        41.33         9.80        80.48        21.37 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        1.38        37.12        25.22        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        73.28         5.92        22.62        16.41         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
       71.70        36.39        27.29       123.78         9.04         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
       11.70        22.03        13.35         8.32         0.49         4.34 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QQ-A5V2 
      120.20         6.35        38.63        81.01        18.08         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH 
       46.82        48.59        30.90       130.32        62.20        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
        0.72        18.94         3.88        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
        9.93        13.22        10.72         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       38.27        65.46         9.04        57.80        26.43        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 
       18.08        18.35        15.95        16.83        38.96        17.72 
TCGA-X9-A971 
       15.58 

  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                         0.07                          0.07 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                       188.15                        143.41 
  AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE 
                        21.63                         25.08 
[1] "0.1 - 188.2 (21.6)" "0.1 - 143.4 (25.1)"
[1] "hr=" "1.4"
D10V2, continuous
D10V3, binary
                               cls
clus                             0  1
  AMP PEAK 10(7Q31.2) MUTATED   40 35
  AMP PEAK 10(7Q31.2) WILD-TYPE 92 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q31.2) MUTATED     40   35
  AMP PEAK 10(7Q31.2) WILD-TYPE   92   79
        clus
vv       AMP PEAK 10(7Q31.2) MUTATED AMP PEAK 10(7Q31.2) WILD-TYPE
  FEMALE                          40                            92
  MALE                            35                            79
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(7Q31.2) MUTATED       2                         5    58
  AMP PEAK 10(7Q31.2) WILD-TYPE     4                        13   136
D10V4, multiclass
                           clus
vv                          AMP PEAK 10(7Q31.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              58
                           clus
vv                          AMP PEAK 10(7Q31.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               136
[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"
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(7Q31.2) MUTATED     2  59
  AMP PEAK 10(7Q31.2) WILD-TYPE   3 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(7Q31.2) MUTATED      2   59
  AMP PEAK 10(7Q31.2) WILD-TYPE    3  132
                        clus
vv                       AMP PEAK 10(7Q31.2) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          59
                        clus
vv                       AMP PEAK 10(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           132
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(8P11.22) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 11(8P11.22) MUTATED    44  34
  AMP PEAK 11(8P11.22) WILD-TYPE 118  48
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                            78                            166 
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                            34                             48 
$`AMP PEAK 11(8P11.22) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HT TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       19.69        54.74        18.64        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A23R TCGA-DX-A3LS TCGA-DX-A3M1 
       32.71        12.85        36.69        74.66         9.04        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A6B8 TCGA-DX-A6BA 
       34.68         4.54        14.99        64.18        15.95        66.05 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
        3.06        34.55        66.31        23.54        16.87        74.10 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       88.31        21.30        48.36        14.43         9.34        59.87 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AB2P 
       38.17        35.77        27.95        36.69        19.43        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-FX-A3NJ 
       49.18        96.89       106.45        22.85        19.20         0.10 
TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
        4.57        41.33        80.48        19.53         3.22        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE 
       37.12        25.22        40.08        13.58         5.92        16.41 
TCGA-JV-A5VF TCGA-K1-A6RU TCGA-KF-A41W TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
        1.05        10.85        11.70        14.99        17.98        10.45 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A5VA TCGA-QQ-A8VF TCGA-RN-AAAQ 
        4.08        37.55         6.35        18.08        98.27        11.18 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J 
       18.94         6.58         5.06        13.22         0.72        26.17 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X9-A971 
       22.62         9.04        36.82        15.95        35.08        15.58 

$`AMP PEAK 11(8P11.22) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU 
       36.30        53.49        68.55        88.57        44.91        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KX TCGA-DX-A1L0 
       42.84        10.32        31.00        36.03        38.24        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        59.24        33.53        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       59.47        54.77        23.08        70.49       108.13        17.10 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7EL 
       16.18        67.20        50.50        64.21        34.49        75.32 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT 
       17.95        33.07        44.68        14.07       124.37        35.54 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       60.66         6.58         1.15        12.99         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2X 
       12.39        40.60        86.10         9.21        71.57        13.28 
TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       50.40       101.98        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.46         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        2.07        48.30        34.88        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IS-A3K6 TCGA-IS-A3K7 
        0.10         9.80        21.37         1.38        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
      116.88        73.28        22.62         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH 
       27.29       123.78         9.04         4.08        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A850 
        8.32         8.28         0.49         4.34        19.73        15.65 
TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
        7.46       120.20        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
        5.03         9.83         1.84        46.82        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       30.90       188.15       130.32        62.20        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-VT-A80G 
        3.88        17.92        19.82        27.22         9.93        10.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        26.43        29.92        18.08        18.35        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        38.96        17.72        36.43 

  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                        106.45                         188.15 
  AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE 
                         19.48                          26.07 
[1] "0.1 - 106.5 (19.5)" "0.1 - 188.2 (26.1)"
[1] "hr=" "1.8"
D11V2, continuous
D11V3, binary
                                cls
clus                              0  1
  AMP PEAK 11(8P11.22) MUTATED   42 36
  AMP PEAK 11(8P11.22) WILD-TYPE 90 78
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.22) MUTATED     42   36
  AMP PEAK 11(8P11.22) WILD-TYPE   90   78
        clus
vv       AMP PEAK 11(8P11.22) MUTATED AMP PEAK 11(8P11.22) WILD-TYPE
  FEMALE                           42                             90
  MALE                             36                             78
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(8P11.22) MUTATED       4                         7    58
  AMP PEAK 11(8P11.22) WILD-TYPE     2                        11   136
D11V4, multiclass
                           clus
vv                          AMP PEAK 11(8P11.22) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               58
                           clus
vv                          AMP PEAK 11(8P11.22) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                136
[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"
D11V5, binary
                                cls
clus                               0   1
  AMP PEAK 11(8P11.22) MUTATED     2  64
  AMP PEAK 11(8P11.22) WILD-TYPE   3 127
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(8P11.22) MUTATED      2   64
  AMP PEAK 11(8P11.22) WILD-TYPE    3  127
                        clus
vv                       AMP PEAK 11(8P11.22) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           64
                        clus
vv                       AMP PEAK 11(8P11.22) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            127
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(8Q24.21) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 12(8Q24.21) MUTATED    48  31
  AMP PEAK 12(8Q24.21) WILD-TYPE 114  51
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            79                            165 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                            31                             51 
$`AMP PEAK 12(8Q24.21) MUTATED`
TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       53.49        54.74        42.84        18.64        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
       14.04        12.85        36.69        59.24        74.66         6.28 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48N 
       42.77         4.54        14.99        10.68        64.18        12.26 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YU TCGA-DX-A6YV 
       26.47        15.95        66.05         9.11        23.54        50.50 
TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL 
       16.87        88.31        48.36        14.43         9.34        33.07 
TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2O 
       44.68        35.77        14.07        19.43        12.99        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-FX-A2QS 
       12.07        49.18        13.28        22.85        19.20         0.46 
TCGA-FX-A3NJ TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI 
        0.10        15.91         0.10        41.33        80.48        19.53 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A6RV 
       25.22        40.08         5.92         1.05         3.91         4.08 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MO-A47R 
       13.35         8.32         4.34        14.99        17.98        10.45 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VH TCGA-RN-AAAQ 
        4.08        37.55        46.82        48.59        10.52        11.18 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88         6.58        17.92        27.22         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8Y0 TCGA-X6-A7W8 
       13.22         0.72        10.72        26.17        22.62        26.43 
TCGA-X6-A8C3 
       15.95 

$`AMP PEAK 12(8Q24.21) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU 
       36.30        19.69        68.55        88.57        44.91        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       10.32        31.00        36.03        32.71        38.24        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       54.21        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
        9.04        23.08        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       34.68        15.06        17.75        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       34.88         9.73        19.30        24.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        25.15        11.47        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       17.79        21.63        16.18         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       67.20        74.10        64.21        21.30        34.49        75.32 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       17.95        59.87        38.17       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G 
       36.69        60.66         6.58         1.15         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
       12.39        40.60         9.21        71.57        96.89       106.45 
TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       50.40       101.98        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31         0.07        20.32         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA 
       48.30        34.88         4.57        12.62        23.97         9.80 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 
       21.37         3.22         1.38        19.89        37.12        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        13.58        73.28        22.62        16.41 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
       71.70        36.39        27.29       123.78         9.04        10.85 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A850 
       11.70        22.03         8.28         0.49        19.73        15.65 
TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        7.46       120.20         6.35        38.63        81.01        18.08 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       20.94         5.03         9.83         1.84        18.08        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       30.90       188.15       130.32        98.27        62.20         0.72 
TCGA-SI-A71P TCGA-SI-AA8C TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       19.82         9.93        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46         9.04        57.80        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       36.82        18.35        25.71        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         88.31                         188.15 
  AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE 
                         16.87                          27.81 
[1] "0.1 - 88.3 (16.9)"  "0.1 - 188.2 (27.8)"
[1] "hr=" "1.9"
D12V2, continuous
D12V3, binary
                                cls
clus                              0  1
  AMP PEAK 12(8Q24.21) MUTATED   41 39
  AMP PEAK 12(8Q24.21) WILD-TYPE 91 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED     41   39
  AMP PEAK 12(8Q24.21) WILD-TYPE   91   75
        clus
vv       AMP PEAK 12(8Q24.21) MUTATED AMP PEAK 12(8Q24.21) WILD-TYPE
  FEMALE                           41                             91
  MALE                             39                             75
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(8Q24.21) MUTATED       4                         6    60
  AMP PEAK 12(8Q24.21) WILD-TYPE     2                        12   134
D12V4, multiclass
                           clus
vv                          AMP PEAK 12(8Q24.21) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               60
                           clus
vv                          AMP PEAK 12(8Q24.21) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                134
[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"
D12V5, binary
                                cls
clus                               0   1
  AMP PEAK 12(8Q24.21) MUTATED     3  63
  AMP PEAK 12(8Q24.21) WILD-TYPE   2 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(8Q24.21) MUTATED      3   63
  AMP PEAK 12(8Q24.21) WILD-TYPE    2  128
                        clus
vv                       AMP PEAK 12(8Q24.21) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       AMP PEAK 12(8Q24.21) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE

Clustering(13) Variable = AMP PEAK 13(11Q22.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 13(11Q22.2) MUTATED    17  17
  AMP PEAK 13(11Q22.2) WILD-TYPE 145  65
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                            34                            210 
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                            17                             65 
$`AMP PEAK 13(11Q22.2) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23T TCGA-DX-A23Z TCGA-DX-A2J1 
       38.24        54.21        59.24         5.26        27.81        59.47 
TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       23.08        20.05        34.68        19.30        24.26        12.26 
TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF 
       15.95         3.06        50.50        16.87        64.21        21.30 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-AATS TCGA-DX-AB2Q TCGA-DX-AB2W 
       17.95        14.43         9.34         1.15        49.18       106.45 
TCGA-DX-AB2X TCGA-FX-A3TO TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EH TCGA-KF-A41W 
       13.28        20.32        15.91         0.10        21.37        11.70 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A8VH 
       18.08         5.03        18.08        10.52 

$`AMP PEAK 13(11Q22.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY 
       18.64        26.56         0.56        14.04        32.71        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23U 
       36.69        18.54        33.53        42.54        74.66        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J4 
       66.87         6.28        60.30         8.58         9.70        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 
        9.04        70.49       108.13        17.10        15.06        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       42.77         4.54        14.99        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P 
       28.80        34.88        64.18         9.73        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA 
       26.47        72.72        25.08        25.15        11.47        66.05 
TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       23.44        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z2 
       34.55        66.31        67.20        23.54        74.10        88.31 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       34.49        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.20        14.07         7.04        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        35.77        14.07       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        60.66        19.43         6.58        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S 
        4.67        12.39        40.60        86.10        12.07         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       71.57        96.89        50.40        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.10         0.07         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
       34.88         4.57        12.62        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       80.48        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       25.22        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       73.28         5.92        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU 
       71.70        36.39        27.29       123.78         9.04        10.85 
TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        4.08        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN 
       10.45         4.08       120.20        37.55         6.35        38.63 
TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
       81.01        20.94         9.83         1.84        46.82        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
        0.72        11.18        18.94         3.88         6.58        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       19.82        27.22         5.06         9.93        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       10.72        26.17        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       38.27        65.46        22.62         9.04        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       29.92        18.08        36.82        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        15.58        36.43 

  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                        106.45                         188.15 
  AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE 
                        18.690                         25.235 
[1] "0.1 - 106.5 (18.7)" "0.1 - 188.2 (25.2)"
[1] "hr=" "2.1"
D13V2, continuous
D13V3, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q22.2) MUTATED    18  17
  AMP PEAK 13(11Q22.2) WILD-TYPE 114  97
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q22.2) MUTATED     18   17
  AMP PEAK 13(11Q22.2) WILD-TYPE  114   97
        clus
vv       AMP PEAK 13(11Q22.2) MUTATED AMP PEAK 13(11Q22.2) WILD-TYPE
  FEMALE                           18                            114
  MALE                             17                             97
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(11Q22.2) MUTATED       0                         0    26
  AMP PEAK 13(11Q22.2) WILD-TYPE     6                        18   168
D13V4, multiclass
                           clus
vv                          AMP PEAK 13(11Q22.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               26
                           clus
vv                          AMP PEAK 13(11Q22.2) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             18
  WHITE                                                168
[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"
D13V5, binary
                                cls
clus                               0   1
  AMP PEAK 13(11Q22.2) MUTATED     1  24
  AMP PEAK 13(11Q22.2) WILD-TYPE   4 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(11Q22.2) MUTATED      1   24
  AMP PEAK 13(11Q22.2) WILD-TYPE    4  167
                        clus
vv                       AMP PEAK 13(11Q22.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           24
                        clus
vv                       AMP PEAK 13(11Q22.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            167
[1] 2 2
[1] FALSE

Clustering(14) Variable = AMP PEAK 14(12Q15) MUTATION ANALYSIS
D14V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 14(12Q15) MUTATED    53  38
  AMP PEAK 14(12Q15) WILD-TYPE 109  44
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                          91                          153 
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                          38                           44 
$`AMP PEAK 14(12Q15) MUTATED`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.30        19.69        44.91         0.56        14.04        32.71 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        36.69        18.54        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       42.54        74.66         5.26        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
       23.08        70.49       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       15.06        17.75        12.26        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI 
       21.63        34.55        16.87        74.10        64.21        34.49 
TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BX 
       14.07        14.43         9.34        33.07        35.77        19.43 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2S 
        1.15         8.75         4.67        12.39        40.60         9.21 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       96.89       106.45        19.20        60.00        84.66        32.15 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EJ 
        0.46        20.32         4.57         0.10        41.33         3.22 
TCGA-IF-A3RQ TCGA-KF-A41W TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A6FX 
       37.12        11.70        10.45        37.55        38.63        20.94 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ 
       18.08        48.59        35.90        98.27        10.52        11.18 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QU 
        3.88         6.58        17.92        19.82        27.22         0.72 
TCGA-VT-A80G TCGA-WK-A8XO TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C6 
       10.72        11.93        26.43        15.95        16.83        35.08 
TCGA-X9-A973 
       36.43 

$`AMP PEAK 14(12Q15) WILD-TYPE`
TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       53.49        68.55        88.57        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KX 
       10.32        31.00        36.03        18.64        26.56        38.24 
TCGA-DX-A23U TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       76.41        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BK 
       25.15        15.95        11.47        66.05        23.44        16.18 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6Z2 
        3.06        66.31        67.20        23.54        50.50        88.31 
TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       21.30        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20         7.04        17.95        59.87        44.68        38.17 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       14.07       124.37        27.95        35.54        36.69        60.66 
TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T 
        6.58        12.99        86.10        12.07        49.18        71.57 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB3B TCGA-DX-AB3C 
       13.28        50.40        22.85       101.98        50.89        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.10         0.07         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV 
       34.88        15.91        12.62        23.97         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       21.37        19.53         1.38        19.89        25.22        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       28.21       143.41       116.88        13.58        73.28         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
       22.62        16.41         1.05         3.91        71.70        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I 
       27.29       123.78         9.04        10.85         4.08        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35         8.32         8.28         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK 
       14.99        17.98        15.65         7.46         4.08       120.20 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
        6.35        81.01        18.08         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q 
       46.82        30.90       188.15       130.32        62.20         0.72 
TCGA-SG-A6Z4 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XQ 
       18.94         5.06         9.93        13.22        26.17         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
       72.72        41.49        38.27        65.46        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       38.96        17.72        15.58 

  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                        0.10                         0.07 
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                      108.13                       188.15 
  AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE 
                       20.05                        25.08 
[1] "0.1 - 108.1 (20.1)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.7"
D14V2, continuous
D14V3, binary
                              cls
clus                            0  1
  AMP PEAK 14(12Q15) MUTATED   36 56
  AMP PEAK 14(12Q15) WILD-TYPE 96 58
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(12Q15) MUTATED     36   56
  AMP PEAK 14(12Q15) WILD-TYPE   96   58
        clus
vv       AMP PEAK 14(12Q15) MUTATED AMP PEAK 14(12Q15) WILD-TYPE
  FEMALE                         36                           96
  MALE                           56                           58
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(12Q15) MUTATED       3                         1    66
  AMP PEAK 14(12Q15) WILD-TYPE     3                        17   128
D14V4, multiclass
                           clus
vv                          AMP PEAK 14(12Q15) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                             66
                           clus
vv                          AMP PEAK 14(12Q15) WILD-TYPE
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           17
  WHITE                                              128
[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"
D14V5, binary
                              cls
clus                             0   1
  AMP PEAK 14(12Q15) MUTATED     2  64
  AMP PEAK 14(12Q15) WILD-TYPE   3 127
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 14(12Q15) MUTATED      2   64
  AMP PEAK 14(12Q15) WILD-TYPE    3  127
                        clus
vv                       AMP PEAK 14(12Q15) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         64
                        clus
vv                       AMP PEAK 14(12Q15) WILD-TYPE
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          127
[1] 2 2
[1] FALSE

Clustering(15) Variable = AMP PEAK 15(13Q34) MUTATION ANALYSIS
D15V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 15(13Q34) MUTATED    33  18
  AMP PEAK 15(13Q34) WILD-TYPE 129  64
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          51                          193 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                          18                           64 
$`AMP PEAK 15(13Q34) MUTATED`
TCGA-3B-A9HR TCGA-DX-A23R TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 
       88.57        74.66        14.99        24.26        12.26        15.95 
TCGA-DX-A6BB TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A8BG 
       23.44        16.18        34.55        23.54        50.50        17.95 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-AB2F 
       59.87        44.68        38.17        27.95        60.66         8.75 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-HS-A5N9 TCGA-IE-A6BZ 
       86.10        12.07        71.57        50.40        41.33        19.89 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-JV-A5VE TCGA-K1-A6RU TCGA-K1-A6RV 
       40.08       143.41        13.58        16.41        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM 
       11.70        13.35        14.99         4.08        37.55         6.35 
TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5VB TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O 
       18.08         9.83        48.59        11.18        18.94        17.92 
TCGA-SI-AA8B TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A8C2 
        5.06        22.62         9.04        26.43        18.08        25.71 
TCGA-X6-A8C5 TCGA-X9-A971 TCGA-X9-A973 
       38.96        15.58        36.43 

$`AMP PEAK 15(13Q34) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       26.56         0.56        14.04        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.69        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       70.49       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       17.75        42.77         4.54        10.68        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48O 
       28.80        34.88        64.18         9.73        19.30        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       66.05        28.96         9.11        17.79        21.63         3.06 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       66.31        67.20        16.87        74.10        64.21        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       21.30        34.49        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ 
       29.49        48.20        14.07         7.04        14.43         9.34 
TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU 
       33.07        35.77        14.07       124.37        35.54        36.69 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H 
       19.43         6.58         1.15        12.99         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       40.60        49.18         9.21        96.89       106.45        13.28 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.07         0.07         2.07        48.30        34.88         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV 
       15.91        12.62        23.97         0.10         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ 
       21.37        19.53         3.22         1.38        37.12        25.22 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF 
       28.21       116.88        73.28         5.92        22.62         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       22.03         8.32         8.28         0.49         4.34        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN 
       17.98        15.65         7.46        10.45       120.20        38.63 
TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA 
       81.01        20.94         5.03         1.84        46.82        18.08 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         0.72         3.88         6.58        19.82        27.22 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
        9.93        13.22         0.72        10.72        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
        4.80        72.72        41.49        38.27        65.46        57.80 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C6 
       29.92        36.82        18.35        15.95        16.83        35.08 
TCGA-X6-A8C7 
       17.72 

  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                        4.08                         0.07 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                      143.41                       188.15 
  AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE 
                       19.89                        25.08 
[1] "4.1 - 143.4 (19.9)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.2"
D15V2, continuous
D15V3, binary
                              cls
clus                            0  1
  AMP PEAK 15(13Q34) MUTATED   33 18
  AMP PEAK 15(13Q34) WILD-TYPE 99 96
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED     33   18
  AMP PEAK 15(13Q34) WILD-TYPE   99   96
        clus
vv       AMP PEAK 15(13Q34) MUTATED AMP PEAK 15(13Q34) WILD-TYPE
  FEMALE                         33                           99
  MALE                           18                           96
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q34) MUTATED       0                         8    41
  AMP PEAK 15(13Q34) WILD-TYPE     6                        10   153
D15V4, multiclass
                           clus
vv                          AMP PEAK 15(13Q34) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          8
  WHITE                                             41
                           clus
vv                          AMP PEAK 15(13Q34) WILD-TYPE
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              153
[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"
D15V5, binary
                              cls
clus                             0   1
  AMP PEAK 15(13Q34) MUTATED     0  45
  AMP PEAK 15(13Q34) WILD-TYPE   5 146
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 15(13Q34) MUTATED      0   45
  AMP PEAK 15(13Q34) WILD-TYPE    5  146
                        clus
vv                       AMP PEAK 15(13Q34) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         45
                        clus
vv                       AMP PEAK 15(13Q34) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          146
[1] 2 2
[1] FALSE

Clustering(16) Variable = AMP PEAK 16(15Q26.3) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(15Q26.3) MUTATED    50  30
  AMP PEAK 16(15Q26.3) WILD-TYPE 112  52
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            80                            164 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                            30                             52 
$`AMP PEAK 16(15Q26.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I0 
       19.69        68.55        88.57        44.91        42.84        36.03 
TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R 
       26.56        14.04        32.71        38.24        18.54        74.66 
TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UF 
        6.28         8.58        42.77        14.99        39.35        64.18 
TCGA-DX-A48L TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       24.26        66.05         3.06        34.55        66.31        67.20 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BK 
       16.87        74.10        64.21        34.49         7.04        59.87 
TCGA-DX-A8BO TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2P TCGA-DX-AB2Q 
       35.77        19.43         1.15         8.75        12.07        49.18 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-FX-A3RE TCGA-FX-A3TO 
       96.89       106.45        13.28        19.20         0.07        20.32 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ 
       15.91        12.62        19.53         3.22        19.89        25.22 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A6RU 
       40.08       143.41        13.58         3.91        27.29        10.85 
TCGA-LI-A67I TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP 
       22.03         4.34        14.99        37.55        81.01        18.08 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ 
       46.82        18.08        35.90        98.27        10.52        11.18 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         3.88         6.58        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC 
        9.93         0.72        72.72         9.04        26.43        36.82 
TCGA-X6-A8C3 TCGA-X9-A971 
       15.95        15.58 

$`AMP PEAK 16(15Q26.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ 
       36.30        53.49        54.74        25.25        10.32        31.00 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       18.64         0.56        12.85        36.69        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
       60.30         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       70.49       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
       17.75         4.54        10.68        44.45        28.80        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB 
       72.72        25.08        25.15        15.95        11.47        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YU 
       28.96         9.11        17.79        21.63        16.18        23.54 
TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       50.50        88.31        21.30        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BH 
      135.48        29.49        48.20        14.07        17.95        14.43 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
        9.34        33.07        44.68        38.17        14.07       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E 
       27.95        35.54        36.69        60.66         6.58        12.99 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        12.39        40.60        86.10         9.21        71.57 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       50.40        22.85       101.98        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y 
       50.89        71.31         0.46         0.10         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N8 
        2.07        48.30        34.88         4.57        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ 
       41.33         9.80        80.48        21.37         1.38        37.12 
TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
       28.21       116.88        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
        1.05        71.70        36.39       123.78         9.04         4.08 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       11.70        13.35         8.32         8.28         0.49        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
        6.35        38.63        20.94         5.03         9.83         1.84 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q 
       48.59        30.90       188.15       130.32        62.20         0.72 
TCGA-SI-A71O TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       17.92        13.22        10.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        38.27        65.46        22.62        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.08        18.35        25.71        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A973 
       17.72        36.43 

  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                        143.41                         188.15 
  AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE 
                        20.105                         23.755 
[1] "0.1 - 143.4 (20.1)" "0.1 - 188.2 (23.8)"
[1] "hr=" "1.2"
D16V2, continuous
D16V3, binary
                                cls
clus                              0  1
  AMP PEAK 16(15Q26.3) MUTATED   48 33
  AMP PEAK 16(15Q26.3) WILD-TYPE 84 81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED     48   33
  AMP PEAK 16(15Q26.3) WILD-TYPE   84   81
        clus
vv       AMP PEAK 16(15Q26.3) MUTATED AMP PEAK 16(15Q26.3) WILD-TYPE
  FEMALE                           48                             84
  MALE                             33                             81
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(15Q26.3) MUTATED       2                         4    67
  AMP PEAK 16(15Q26.3) WILD-TYPE     4                        14   127
D16V4, multiclass
                           clus
vv                          AMP PEAK 16(15Q26.3) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               67
                           clus
vv                          AMP PEAK 16(15Q26.3) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                127
[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"
D16V5, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.3) MUTATED     3  67
  AMP PEAK 16(15Q26.3) WILD-TYPE   2 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.3) MUTATED      3   67
  AMP PEAK 16(15Q26.3) WILD-TYPE    2  124
                        clus
vv                       AMP PEAK 16(15Q26.3) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           67
                        clus
vv                       AMP PEAK 16(15Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            124
[1] 2 2
[1] FALSE

Clustering(17) Variable = AMP PEAK 17(17P12) MUTATION ANALYSIS
D17V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 17(17P12) MUTATED    61  36
  AMP PEAK 17(17P12) WILD-TYPE 101  46
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                          97                          147 
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                          36                           46 
$`AMP PEAK 17(17P12) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9HY 
       19.69        68.55        88.57        44.91        42.84        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 
       31.00        26.56         0.56        32.71        12.85        54.21 
TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3UC TCGA-DX-A3UE 
       59.24         6.28        34.68        15.06        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R 
       64.18        19.30        24.26        12.26        27.22        26.47 
TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YV 
       15.95        66.05        16.18         3.06        67.20        50.50 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM 
       75.32        48.36        17.95         9.34        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2T 
       38.17        27.95        60.66        86.10        12.07        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 TCGA-FX-A3RE TCGA-FX-A3TO 
       96.89       106.45        13.28        84.66         0.07        20.32 
TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
        0.07        34.88         4.57        12.62        23.97        41.33 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       80.48        21.37         3.22        19.89        25.22        40.08 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
        3.91        71.70         4.08        11.70        22.03        13.35 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 
       10.45         4.08         6.35        81.01        18.08         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-RN-AAAQ TCGA-SG-A6Z4 
        9.83        46.82        18.08        30.90        11.18        18.94 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G 
        6.58        17.92        19.82         5.06         0.72        10.72 
TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC 
       72.72        22.62         9.04        26.43        29.92        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.35        25.71        15.95        16.83        38.96        35.08 
TCGA-X9-A971 
       15.58 

$`AMP PEAK 17(17P12) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9I0 TCGA-3B-A9I1 
       36.30        53.49        54.74        25.25        36.03        18.64 
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        38.24        36.69        18.54        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 
       70.49       108.13        17.10        20.05        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J 
        4.54        14.99        10.68        44.45        28.80         9.73 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB 
       14.96        72.72        25.08        25.15        11.47        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS 
       28.96         9.11        17.79        21.63        34.55        66.31 
TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       23.54        16.87        74.10        64.21        88.31        21.30 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
        7.04        14.43        59.87        35.77        14.07       124.37 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       35.54        36.69        19.43         6.58         1.15        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S 
        8.75         4.67        12.39        40.60        49.18         9.21 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A 
       50.40        22.85       101.98        19.20        60.00        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO 
       50.89        71.31         0.46         0.10         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK 
       48.30        15.91         0.10         9.80        19.53         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42W 
        5.92        22.62        16.41         1.05        36.39        27.29 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
      123.78         9.04        10.85         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A6FX TCGA-QQ-A5V2 TCGA-QQ-A5VB 
      120.20        37.55        38.63        20.94         1.84        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90       188.15       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J 
        0.72         3.88        27.22         9.93        13.22        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X2-A95T 
       11.93         4.80        41.49        38.27        65.46        57.80 
TCGA-X6-A7WB TCGA-X6-A8C7 TCGA-X9-A973 
       18.08        17.72        36.43 

  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                        0.07                         0.07 
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                      106.45                       188.15 
  AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE 
                       22.62                        23.44 
[1] "0.1 - 106.5 (22.6)" "0.1 - 188.2 (23.4)"
[1] "hr=" "1.3"
D17V2, continuous
D17V3, binary
                              cls
clus                            0  1
  AMP PEAK 17(17P12) MUTATED   53 44
  AMP PEAK 17(17P12) WILD-TYPE 79 70
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17P12) MUTATED     53   44
  AMP PEAK 17(17P12) WILD-TYPE   79   70
        clus
vv       AMP PEAK 17(17P12) MUTATED AMP PEAK 17(17P12) WILD-TYPE
  FEMALE                         53                           79
  MALE                           44                           70
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(17P12) MUTATED       3                         6    79
  AMP PEAK 17(17P12) WILD-TYPE     3                        12   115
D17V4, multiclass
                           clus
vv                          AMP PEAK 17(17P12) MUTATED
  ASIAN                                              3
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             79
                           clus
vv                          AMP PEAK 17(17P12) WILD-TYPE
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              115
[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"
D17V5, binary
                              cls
clus                             0   1
  AMP PEAK 17(17P12) MUTATED     1  85
  AMP PEAK 17(17P12) WILD-TYPE   4 106
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 17(17P12) MUTATED      1   85
  AMP PEAK 17(17P12) WILD-TYPE    4  106
                        clus
vv                       AMP PEAK 17(17P12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         85
                        clus
vv                       AMP PEAK 17(17P12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          106
[1] 2 2
[1] FALSE

Clustering(18) Variable = AMP PEAK 18(17P11.2) MUTATION ANALYSIS
D18V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 18(17P11.2) MUTATED   63 36
  AMP PEAK 18(17P11.2) WILD-TYPE 99 46
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                            99                            145 
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                            36                             46 
$`AMP PEAK 18(17P11.2) MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I3 
       88.57        44.91        42.84        10.32        31.00        26.56 
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M2 
        0.56        32.71        12.85        59.24         6.28        34.68 
TCGA-DX-A3U5 TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       15.06        39.35        34.88        64.18        19.30        24.26 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BK TCGA-DX-A6YQ 
       26.47        15.95        66.05        23.44        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EL 
       34.55        67.20        23.54        50.50        74.10        75.32 
TCGA-DX-A7EM TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.36        17.95         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-AB2O TCGA-DX-AB2P 
       38.17        35.77        27.95        60.66        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB37 TCGA-FX-A3RE 
       49.18        96.89       106.45        13.28        84.66         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 
       20.32         0.07        34.88         4.57        12.62        23.97 
TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-JV-A75J 
       41.33        21.37         3.22        19.89        25.22         3.91 
TCGA-K1-A3PN TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
       71.70         4.08        11.70        22.03        13.35         8.32 
TCGA-MB-A8JK TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP 
        4.34        10.45         4.08         6.35        81.01        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VH 
        5.03         9.83        46.82        18.08        48.59        10.52 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QU 
       18.94         6.58        17.92        19.82         5.06         0.72 
TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 
       10.72        72.72        65.46        22.62         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       29.92        36.82        18.35        25.71        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X9-A971 
       38.96        35.08        15.58 

$`AMP PEAK 18(17P11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        53.49        68.55        54.74        25.25 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 
       36.03        18.64        14.04        38.24        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       54.21        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       20.05        17.75        42.77         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       44.45        28.80         9.73        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        25.08        25.15        11.47        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       17.79        21.63        66.31        16.87        64.21        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        34.49        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT 
       14.07         7.04        14.43        14.07       124.37        35.54 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        19.43         6.58         1.15        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z 
        4.67        12.39        40.60         9.21        71.57        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85       101.98        19.20        60.00        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       71.31         0.46         0.10         0.07         2.07        48.30 
TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK 
       15.91         0.10         9.80        80.48        19.53         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA 
       37.12        40.08        28.21       143.41       116.88        13.58 
TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PO 
       73.28         5.92        22.62        16.41         1.05        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-MB-A5Y9 TCGA-MB-A5YA 
       27.29       123.78         9.04        10.85         8.28         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK 
       19.73        14.99        17.98        15.65         7.46       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QC-A6FX TCGA-QQ-A5V2 TCGA-QQ-A5VC TCGA-QQ-A5VD 
       37.55        38.63        20.94         1.84        35.90        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
      188.15       130.32        98.27        62.20         0.72        11.18 
TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO 
        3.88        27.22         9.93        13.22        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C7 
        4.80        41.49        38.27        57.80        18.08        17.72 
TCGA-X9-A973 
       36.43 

  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                        106.45                         188.15 
  AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE 
                         23.44                          23.08 
[1] "0.1 - 106.5 (23.4)" "0.1 - 188.2 (23.1)"
[1] "hr=" "1.2"
D18V2, continuous
D18V3, binary
                                cls
clus                              0  1
  AMP PEAK 18(17P11.2) MUTATED   57 42
  AMP PEAK 18(17P11.2) WILD-TYPE 75 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17P11.2) MUTATED     57   42
  AMP PEAK 18(17P11.2) WILD-TYPE   75   72
        clus
vv       AMP PEAK 18(17P11.2) MUTATED AMP PEAK 18(17P11.2) WILD-TYPE
  FEMALE                           57                             75
  MALE                             42                             72
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(17P11.2) MUTATED       3                         5    83
  AMP PEAK 18(17P11.2) WILD-TYPE     3                        13   111
D18V4, multiclass
                           clus
vv                          AMP PEAK 18(17P11.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               83
                           clus
vv                          AMP PEAK 18(17P11.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                111
[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"
D18V5, binary
                                cls
clus                               0   1
  AMP PEAK 18(17P11.2) MUTATED     2  86
  AMP PEAK 18(17P11.2) WILD-TYPE   3 105
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 18(17P11.2) MUTATED      2   86
  AMP PEAK 18(17P11.2) WILD-TYPE    3  105
                        clus
vv                       AMP PEAK 18(17P11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           86
                        clus
vv                       AMP PEAK 18(17P11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            105
[1] 2 2
[1] FALSE

Clustering(19) Variable = AMP PEAK 19(17Q24.3) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 19(17Q24.3) MUTATED    50  25
  AMP PEAK 19(17Q24.3) WILD-TYPE 112  57
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                            75                            169 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                            25                             57 
$`AMP PEAK 19(17Q24.3) MUTATED`
TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       68.55        54.74        42.84        18.64        26.56         0.56 
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A2J0 TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A48K 
       32.71        59.24         9.70        20.05        10.68        19.30 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
        9.11        16.18        66.31        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A8BG TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       74.10        21.30        17.95        44.68        38.17        35.77 
TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       60.66         1.15        71.57        96.89       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G 
       50.40        84.66        32.15         0.46         0.07         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5N9 
       48.30         4.57        15.91        12.62         0.10        41.33 
TCGA-IE-A6BZ TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A75J TCGA-LI-A67I TCGA-LI-A9QH 
       19.89        13.58        73.28         3.91        22.03        13.35 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5VA 
       10.45         4.08        18.08        20.94         5.03        18.08 
TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 
       35.90       188.15        11.18        18.94         3.88         6.58 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU 
       17.92        19.82        27.22         5.06         9.93         0.72 
TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       10.72        72.72        22.62         9.04        57.80        26.43 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X9-A971 
       25.71        15.95        15.58 

$`AMP PEAK 19(17Q24.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU 
       36.30        19.69        53.49        88.57        44.91        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY 
       10.32        31.00        36.03        14.04        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       36.69        18.54        54.21        33.53        42.54        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        8.58        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
      108.13        17.10        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
        4.54        14.99        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       64.18         9.73        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47        72.72        25.08        25.15        15.95        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YQ 
       66.05        23.44        28.96        17.79        21.63         3.06 
TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL 
       34.55        67.20        64.21        88.31        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BP 
        7.04        14.43         9.34        59.87        33.07        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ 
      124.37        27.95        35.54        36.69        19.43         6.58 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
       12.99         8.75         4.67        12.39        40.60        86.10 
TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       12.07        49.18         9.21        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y 
       60.00        50.89        71.31         0.10        20.32         0.07 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
        2.07        34.88        23.97         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
       19.53         3.22         1.38        37.12        25.22        40.08 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
       28.21       143.41       116.88         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        1.05        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       10.85         4.08        11.70         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-AA9N 
      120.20        37.55         6.35        38.63        81.01         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
        1.84        46.82        48.59        30.90       130.32        98.27 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO 
       62.20        10.52         0.72        13.22        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X6-A7WA TCGA-X6-A7WB 
        4.80        41.49        38.27        65.46        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       36.82        18.35        16.83        38.96        35.08        17.72 
TCGA-X9-A973 
       36.43 

  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                        188.15                         143.41 
  AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE 
                         19.30                          26.17 
[1] "0.1 - 188.2 (19.3)" "0.1 - 143.4 (26.2)"
[1] "hr=" "1.2"
D19V2, continuous
D19V3, binary
                                cls
clus                              0  1
  AMP PEAK 19(17Q24.3) MUTATED   48 27
  AMP PEAK 19(17Q24.3) WILD-TYPE 84 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.3) MUTATED     48   27
  AMP PEAK 19(17Q24.3) WILD-TYPE   84   87
        clus
vv       AMP PEAK 19(17Q24.3) MUTATED AMP PEAK 19(17Q24.3) WILD-TYPE
  FEMALE                           48                             84
  MALE                             27                             87
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q24.3) MUTATED       3                         5    60
  AMP PEAK 19(17Q24.3) WILD-TYPE     3                        13   134
D19V4, multiclass
                           clus
vv                          AMP PEAK 19(17Q24.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               60
                           clus
vv                          AMP PEAK 19(17Q24.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                134
[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"
D19V5, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.3) MUTATED     1  63
  AMP PEAK 19(17Q24.3) WILD-TYPE   4 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.3) MUTATED      1   63
  AMP PEAK 19(17Q24.3) WILD-TYPE    4  128
                        clus
vv                       AMP PEAK 19(17Q24.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       AMP PEAK 19(17Q24.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE

Clustering(20) Variable = AMP PEAK 20(19P13.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 20(19P13.2) MUTATED   66 33
  AMP PEAK 20(19P13.2) WILD-TYPE 96 49
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            99                            145 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            33                             49 
$`AMP PEAK 20(19P13.2) MUTATED`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9I0 
       36.30        19.69        53.49        88.57        44.91        36.03 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64         0.56        14.04        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A23Y 
       36.69        54.21        59.24        33.53        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD 
        9.70       108.13        34.68        42.77        14.99        28.80 
TCGA-DX-A3UF TCGA-DX-A48N TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6YR 
       64.18        12.26        25.15        11.47        66.05        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       66.31        67.20        50.50        74.10        64.21        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7ES TCGA-DX-A7ET 
       21.30        34.49        75.32        48.36        14.07         7.04 
TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT 
       14.43        33.07        44.68        35.77        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2T 
       36.69        19.43        12.99        86.10        49.18        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3RE 
       96.89       106.45        13.28        19.20        32.15         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       20.32         0.07         4.57        41.33         9.80        80.48 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A42X 
       19.53         3.22         1.38         3.91        27.29       123.78 
TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-N1-A6IA TCGA-QC-A6FX 
       13.35         0.49         4.34        14.99         4.08        20.94 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-SG-A849 TCGA-SI-A71O 
       46.82        18.08        35.90       188.15         6.58        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       19.82        27.22         5.06         9.93        13.22         0.72 
TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WB TCGA-X6-A7WC 
       10.72        72.72        38.27         9.04        18.08        36.82 
TCGA-X6-A8C6 TCGA-X9-A971 TCGA-X9-A973 
       35.08        15.58        36.43 

$`AMP PEAK 20(19P13.2) WILD-TYPE`
TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ 
       68.55        54.74        25.25        42.84        10.32        31.00 
TCGA-3B-A9I3 TCGA-DX-A1L0 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       26.56        18.54        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 
       23.08        70.49        17.10        20.05        15.06        17.75 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
        4.54        10.68        44.45        39.35        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        24.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        15.95        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A7EN 
       21.63        16.18         3.06        23.54        16.87        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK 
      135.48        29.49        48.20        17.95         9.34        59.87 
TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS 
       38.17        14.07       124.37        60.66         6.58         1.15 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2S 
        8.75         4.67        12.39        40.60        12.07         9.21 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B 
       50.40        22.85       101.98        60.00        84.66        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
       71.31         0.46         0.10         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EH 
       34.88        15.91        12.62        23.97         0.10        21.37 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
       19.89        37.12        25.22        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
        1.05        71.70        36.39         9.04        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68J 
       11.70        22.03         8.32         8.28        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
       15.65         7.46        10.45       120.20        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        81.01        18.08         5.03         9.83         1.84 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       48.59        30.90       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-VT-A80J TCGA-WK-A8XO 
        0.72        11.18        18.94         3.88        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 
        4.80        41.49        65.46        22.62        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       29.92        18.35        25.71        15.95        16.83        38.96 
TCGA-X6-A8C7 
       17.72 

  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                          0.07                           0.07 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                        188.15                         143.41 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                         28.80                          22.03 
[1] "0.1 - 188.2 (28.8)" "0.1 - 143.4 (22.0)"
[1] "hr=" "1.1"
D20V2, continuous
D20V3, binary
                                cls
clus                              0  1
  AMP PEAK 20(19P13.2) MUTATED   48 53
  AMP PEAK 20(19P13.2) WILD-TYPE 84 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     48   53
  AMP PEAK 20(19P13.2) WILD-TYPE   84   61
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  FEMALE                           48                             84
  MALE                             53                             61
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(19P13.2) MUTATED       2                         9    77
  AMP PEAK 20(19P13.2) WILD-TYPE     4                         9   117
D20V4, multiclass
                           clus
vv                          AMP PEAK 20(19P13.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               77
                           clus
vv                          AMP PEAK 20(19P13.2) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                117
[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"
D20V5, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED     3  79
  AMP PEAK 20(19P13.2) WILD-TYPE   2 112
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED      3   79
  AMP PEAK 20(19P13.2) WILD-TYPE    2  112
                        clus
vv                       AMP PEAK 20(19P13.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           79
                        clus
vv                       AMP PEAK 20(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                            112
[1] 2 2
[1] FALSE

Clustering(21) Variable = AMP PEAK 21(19Q12) MUTATION ANALYSIS
D21V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 21(19Q12) MUTATED    56  33
  AMP PEAK 21(19Q12) WILD-TYPE 106  49
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          89                          155 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                          33                           49 
$`AMP PEAK 21(19Q12) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       19.69        88.57        42.84        14.04        32.71        38.24 
TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LT 
       12.85        54.21        59.24        74.66         6.28        23.08 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N 
       42.77        14.99        39.35        64.18        19.30        12.26 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       26.47        15.95        11.47         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI 
       67.20        23.54        50.50        74.10        64.21        34.49 
TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.36         7.04        17.95        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
       38.17        27.95        35.54        36.69        60.66        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB35 
        1.15        12.99        86.10        96.89        13.28        19.20 
TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N8 
       32.15         0.46        20.32         4.57        12.62         0.10 
TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IS-A3KA 
        9.80        19.53         3.22         1.38        19.89        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
        5.92         1.05         4.08        11.70        22.03        13.35 
TCGA-MB-A8JK TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A5VA TCGA-QQ-A5VB 
        4.34         6.35        18.08        20.94        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-A71P 
       35.90        98.27        10.52        18.94        17.92        19.82 
TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XS 
        5.06         0.72        10.72        26.17        11.93        72.72 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X9-A973 
       38.27         9.04        36.82        15.95        36.43 

$`AMP PEAK 21(19Q12) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX 
       10.32        31.00        36.03        18.64        26.56         0.56 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       36.69        18.54        33.53        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        70.49       108.13        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       34.68        15.06        17.75         4.54        10.68        44.45 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       28.80        34.88         9.73        24.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        25.15        66.05        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YX TCGA-DX-A6Z2 
        9.11        17.79        21.63        16.18        16.87        88.31 
TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        75.32        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
       14.07        14.43         9.34        35.77        14.07       124.37 
TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
        6.58         8.75         4.67        12.39        40.60        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 
       49.18         9.21        71.57       106.45        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
      101.98        60.00        84.66        50.89        71.31         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.07         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IF-A3RQ 
       15.91        23.97        41.33        80.48        21.37        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       25.22        40.08        28.21       143.41       116.88        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       22.62        16.41         3.91        71.70        36.39        27.29 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
      123.78         9.04        10.85         8.32         8.28         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
        4.08       120.20        37.55        38.63        81.01         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
        9.83         1.84        46.82        30.90       188.15       130.32 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71Q 
       62.20         0.72        11.18         3.88         6.58        27.22 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 
        9.93        13.22         4.80        41.49        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        26.43        29.92        18.08        18.35        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       16.83        38.96        35.08        17.72        15.58 

  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                        0.10                         0.07 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                       98.27                       188.15 
  AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE 
                       19.82                        25.22 
[1] "0.1 - 98.3 (19.8)"  "0.1 - 188.2 (25.2)"
[1] "hr=" "1.4"
D21V2, continuous
D21V3, binary
                              cls
clus                            0  1
  AMP PEAK 21(19Q12) MUTATED   44 46
  AMP PEAK 21(19Q12) WILD-TYPE 88 68
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(19Q12) MUTATED     44   46
  AMP PEAK 21(19Q12) WILD-TYPE   88   68
        clus
vv       AMP PEAK 21(19Q12) MUTATED AMP PEAK 21(19Q12) WILD-TYPE
  FEMALE                         44                           88
  MALE                           46                           68
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(19Q12) MUTATED       2                         5    73
  AMP PEAK 21(19Q12) WILD-TYPE     4                        13   121
D21V4, multiclass
                           clus
vv                          AMP PEAK 21(19Q12) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          5
  WHITE                                             73
                           clus
vv                          AMP PEAK 21(19Q12) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              121
[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"
D21V5, binary
                              cls
clus                             0   1
  AMP PEAK 21(19Q12) MUTATED     1  72
  AMP PEAK 21(19Q12) WILD-TYPE   4 119
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 21(19Q12) MUTATED      1   72
  AMP PEAK 21(19Q12) WILD-TYPE    4  119
                        clus
vv                       AMP PEAK 21(19Q12) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         72
                        clus
vv                       AMP PEAK 21(19Q12) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          119
[1] 2 2
[1] FALSE

Clustering(22) Variable = AMP PEAK 22(20Q13.33) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 22(20Q13.33) MUTATED    59  37
  AMP PEAK 22(20Q13.33) WILD-TYPE 103  45
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             96                             148 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                             37                              45 
$`AMP PEAK 22(20Q13.33) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU 
       19.69        88.57        44.91        26.56         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3U5 
       59.24        74.66         6.28         8.58       108.13        15.06 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6B8 
       14.99        10.68        12.26        14.96        25.08        15.95 
TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       23.44         3.06        66.31        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK 
       64.21        21.30        34.49         7.04        14.43        59.87 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BX 
       33.07        44.68        35.77        27.95        36.69        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2V 
        1.15        12.99         8.75        12.07        49.18        96.89 
TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB35 TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G 
      106.45        22.85        19.20         0.10        20.32         0.07 
TCGA-HB-A3YV TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-IS-A3K7 
        4.57        80.48        19.53         3.22        40.08       143.41 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV 
       13.58         5.92        16.41        27.29        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-N1-A6IA 
       11.70        22.03        13.35         8.32         8.28         4.08 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 
       37.55         6.35        20.94         5.03         9.83        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A849 
       18.08        30.90        98.27        10.52        11.18         6.58 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G 
       17.92        19.82        27.22         5.06         0.72        10.72 
TCGA-VT-A80J TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C6 
       26.17        26.43        18.08        36.82        15.95        35.08 

$`AMP PEAK 22(20Q13.33) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        68.55        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       10.32        31.00        36.03        18.64        33.53        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
        5.26        76.41        66.87        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
       59.47        54.77         9.04        23.08        70.49        17.10 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB 
       20.05        34.68        17.75        42.77         4.54        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       24.26        27.22        26.47        72.72        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       66.05        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM 
       34.55        67.20        50.50        88.31        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG 
       15.62       135.48        29.49        48.20        14.07        17.95 
TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV 
        9.34        38.17        14.07       124.37        35.54        60.66 
TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S 
        6.58         4.67        12.39        40.60        86.10         9.21 
TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 
       71.57        13.28        50.40       101.98        60.00        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A76Y 
       32.15        50.89        71.31         0.46         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        2.07        48.30        34.88        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ 
        0.10        41.33         9.80        21.37         1.38        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M6 
       37.12        25.22        28.21       116.88        73.28        22.62 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        71.70        36.39       123.78         9.04 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        0.49         4.34        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        7.46        10.45       120.20        38.63        81.01        18.08 
TCGA-QQ-A5V2 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG 
        1.84        48.59        35.90       188.15       130.32        62.20 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO 
        0.72        18.94         3.88         9.93        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
        4.80        72.72        41.49        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 
        9.04        57.80        29.92        18.35        25.71        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       38.96        17.72        15.58        36.43 

  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                           0.07                            0.07 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                         143.41                          188.15 
  AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE 
                         19.315                          28.010 
[1] "0.1 - 143.4 (19.3)" "0.1 - 188.2 (28.0)"
[1] "hr=" "1.6"
D22V2, continuous
D22V3, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q13.33) MUTATED   42 54
  AMP PEAK 22(20Q13.33) WILD-TYPE 90 60
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED     42   54
  AMP PEAK 22(20Q13.33) WILD-TYPE   90   60
        clus
vv       AMP PEAK 22(20Q13.33) MUTATED AMP PEAK 22(20Q13.33) WILD-TYPE
  FEMALE                            42                              90
  MALE                              54                              60
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20Q13.33) MUTATED       2                         7    74
  AMP PEAK 22(20Q13.33) WILD-TYPE     4                        11   120
D22V4, multiclass
                           clus
vv                          AMP PEAK 22(20Q13.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                                74
                           clus
vv                          AMP PEAK 22(20Q13.33) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                              11
  WHITE                                                 120
[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"
D22V5, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q13.33) MUTATED     2  75
  AMP PEAK 22(20Q13.33) WILD-TYPE   3 116
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q13.33) MUTATED      2   75
  AMP PEAK 22(20Q13.33) WILD-TYPE    3  116
                        clus
vv                       AMP PEAK 22(20Q13.33) MUTATED
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            75
                        clus
vv                       AMP PEAK 22(20Q13.33) WILD-TYPE
  HISPANIC OR LATINO                                   3
  NOT HISPANIC OR LATINO                             116
[1] 2 2
[1] FALSE

Clustering(23) Variable = AMP PEAK 23(21Q21.1) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 23(21Q21.1) MUTATED    42  29
  AMP PEAK 23(21Q21.1) WILD-TYPE 120  53
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                            71                            173 
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                            29                             53 
$`AMP PEAK 23(21Q21.1) MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       44.91        42.84        18.64        32.71        38.24        12.85 
TCGA-DX-A1L1 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A2IZ TCGA-DX-A3LW TCGA-DX-A3M2 
       54.21         5.26        76.41         8.58       108.13        34.68 
TCGA-DX-A3U9 TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6BF 
       14.99        64.18        19.30        15.95        23.44         9.11 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF 
       34.55        66.31        23.54        50.50        74.10        21.30 
TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS 
       48.36         7.04        59.87        33.07        44.68        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2V TCGA-DX-AB2W 
       36.69        60.66         1.15        12.99        96.89       106.45 
TCGA-DX-AB2X TCGA-DX-AB35 TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV 
       13.28        19.20         4.57         0.10        41.33        80.48 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-K1-A6RU TCGA-KF-A41W 
        3.22        19.89        25.22        13.58        10.85        11.70 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL 
       22.03         8.32         0.49        14.99         4.08        37.55 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB 
        6.35        20.94         5.03         9.83        46.82        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-UE-A6QT TCGA-WK-A8XX 
       35.90        98.27         3.88        27.22        13.22        38.27 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X9-A971 
       22.62         9.04        26.43        36.82        15.58 

$`AMP PEAK 23(21Q21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX 
       25.25        10.32        31.00        36.03        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        36.69        18.54        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
       74.66        66.87         6.28        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
       59.47        54.77         9.04        23.08        70.49        17.10 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA 
       20.05        15.06        17.75        42.77         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L 
       44.45        39.35        28.80        34.88         9.73        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       25.15        11.47        66.05        28.96        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       16.18         3.06        67.20        16.87        64.21        88.31 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        75.32        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO 
       14.07        17.95        14.43         9.34        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2F 
       14.07       124.37        35.54        19.43         6.58         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
        9.21        71.57        50.40        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       84.66        32.15        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT 
        0.07        20.32         0.07         0.07         2.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EH 
       34.88        15.91        12.62        23.97         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
       19.53         1.38        37.12        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        73.28         5.92        22.62        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J 
        4.08        13.35         8.28         4.34        19.73        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO 
       15.65         7.46        10.45       120.20        38.63        81.01 
TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       18.08         1.84        18.08        30.90       188.15       130.32 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 
       62.20        10.52         0.72        11.18        18.94         6.58 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       17.92        19.82         5.06         9.93         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY 
       26.17        11.93         4.80        72.72        41.49        65.46 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       57.80        29.92        18.08        18.35        25.71        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       16.83        38.96        35.08        17.72        36.43 

  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                          0.10                           0.07 
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                        108.13                         188.15 
  AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE 
                         23.44                          23.08 
[1] "0.1 - 108.1 (23.4)" "0.1 - 188.2 (23.1)"
[1] "hr=" "1.4"
D23V2, continuous
D23V3, binary
                                cls
clus                               0   1
  AMP PEAK 23(21Q21.1) MUTATED    32  39
  AMP PEAK 23(21Q21.1) WILD-TYPE 100  75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(21Q21.1) MUTATED     32   39
  AMP PEAK 23(21Q21.1) WILD-TYPE  100   75
        clus
vv       AMP PEAK 23(21Q21.1) MUTATED AMP PEAK 23(21Q21.1) WILD-TYPE
  FEMALE                           32                            100
  MALE                             39                             75
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(21Q21.1) MUTATED       1                         7    54
  AMP PEAK 23(21Q21.1) WILD-TYPE     5                        11   140
D23V4, multiclass
                           clus
vv                          AMP PEAK 23(21Q21.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               54
                           clus
vv                          AMP PEAK 23(21Q21.1) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                140
[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"
D23V5, binary
                                cls
clus                               0   1
  AMP PEAK 23(21Q21.1) MUTATED     0  58
  AMP PEAK 23(21Q21.1) WILD-TYPE   5 133
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 23(21Q21.1) MUTATED      0   58
  AMP PEAK 23(21Q21.1) WILD-TYPE    5  133
                        clus
vv                       AMP PEAK 23(21Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           58
                        clus
vv                       AMP PEAK 23(21Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            133
[1] 2 2
[1] FALSE

Clustering(24) Variable = AMP PEAK 24(XP21.2) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 24(XP21.2) MUTATED    60  33
  AMP PEAK 24(XP21.2) WILD-TYPE 102  49
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                           93                           151 
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                           33                            49 
$`AMP PEAK 24(XP21.2) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ 
       19.69        88.57        44.91        25.25        42.84        31.00 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A240 TCGA-DX-A3LW 
       38.24        12.85        36.69        18.54        60.30       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UE 
       17.10        20.05         4.54        10.68        39.35        34.88 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YS 
       64.18        24.26        15.95        66.05        23.44        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM 
       67.20        23.54        50.50        74.10        64.21        48.36 
TCGA-DX-A7EN TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       15.62        17.95         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       38.17        27.95        35.54        60.66        19.43         1.15 
TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
        8.75        12.39        86.10        13.28        50.40        22.85 
TCGA-DX-AB35 TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
       19.20         0.46        20.32        48.30        34.88         4.57 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A3RQ 
       23.97        41.33        80.48        19.53        19.89        37.12 
TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M6 TCGA-K1-A42W TCGA-K1-A6RV TCGA-MB-A5Y8 
       28.21        13.58        22.62        27.29         4.08         8.32 
TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QC-A6FX TCGA-QC-AA9N 
       14.99         4.08         6.35        38.63        20.94         9.83 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A849 TCGA-UE-A6QU 
       18.08        35.90        98.27        10.52         6.58         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7W8 
       10.72        26.17        72.72        38.27         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       29.92        36.82        18.35        25.71        15.95        16.83 
TCGA-X6-A8C6 TCGA-X9-A971 TCGA-X9-A973 
       35.08        15.58        36.43 

$`AMP PEAK 24(XP21.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HY TCGA-3B-A9I0 
       36.30        53.49        68.55        54.74        10.32        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L1 
       18.64        26.56         0.56        14.04        32.71        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       59.24        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87         6.28        27.81         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3M2 TCGA-DX-A3U5 
       54.77         9.04        23.08        70.49        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A48J 
       17.75        42.77        14.99        44.45        28.80         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U 
       19.30        12.26        27.22        14.96        26.47        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       25.08        25.15        11.47        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6Z2 
       21.63        16.18         3.06        34.55        16.87        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        34.49        75.32       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
       14.07         7.04        14.43        35.77        14.07       124.37 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2P 
       36.69         6.58        12.99         4.67        40.60        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB32 
       49.18         9.21        71.57        96.89       106.45       101.98 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
       60.00        84.66        32.15        50.89        71.31         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         0.07         0.07         2.07        15.91        12.62 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ 
        0.10         9.80        21.37         3.22         1.38        25.22 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE 
       40.08       143.41       116.88        73.28         5.92        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        71.70        36.39       123.78         9.04 
TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA 
       10.85        11.70        22.03        13.35         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        4.34        19.73        17.98        15.65         7.46        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V2 
      120.20        37.55        81.01        18.08         5.03         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG 
       46.82        48.59        30.90       188.15       130.32        62.20 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
        0.72        11.18        18.94         3.88        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ 
       27.22         5.06         9.93        13.22        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C5 
       41.49        65.46        22.62        57.80        18.08        38.96 
TCGA-X6-A8C7 
       17.72 

  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                         0.46                          0.07 
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                       108.13                        188.15 
  AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE 
                        25.25                         21.37 
[1] "0.5 - 108.1 (25.2)" "0.1 - 188.2 (21.4)"
[1] "hr=" "1.1"
D24V2, continuous
D24V3, binary
                               cls
clus                             0  1
  AMP PEAK 24(XP21.2) MUTATED   54 40
  AMP PEAK 24(XP21.2) WILD-TYPE 78 74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.2) MUTATED     54   40
  AMP PEAK 24(XP21.2) WILD-TYPE   78   74
        clus
vv       AMP PEAK 24(XP21.2) MUTATED AMP PEAK 24(XP21.2) WILD-TYPE
  FEMALE                          54                            78
  MALE                            40                            74
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(XP21.2) MUTATED       3                         7    76
  AMP PEAK 24(XP21.2) WILD-TYPE     3                        11   118
D24V4, multiclass
                           clus
vv                          AMP PEAK 24(XP21.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              76
                           clus
vv                          AMP PEAK 24(XP21.2) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               118
[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"
D24V5, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP21.2) MUTATED     1  81
  AMP PEAK 24(XP21.2) WILD-TYPE   4 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP21.2) MUTATED      1   81
  AMP PEAK 24(XP21.2) WILD-TYPE    4  110
                        clus
vv                       AMP PEAK 24(XP21.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          81
                        clus
vv                       AMP PEAK 24(XP21.2) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           110
[1] 2 2
[1] FALSE

Clustering(25) Variable = AMP PEAK 25(XQ21.1) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 25(XQ21.1) MUTATED    23  20
  AMP PEAK 25(XQ21.1) WILD-TYPE 139  62
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           43                           201 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                           20                            62 
$`AMP PEAK 25(XQ21.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY 
       19.69        68.55        44.91         0.56        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A6YU 
       36.69        18.54        54.21         6.28        17.10        23.54 
TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BX 
       16.87        64.21        21.30        59.87        38.17        19.43 
TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 
        8.75        49.18       106.45        13.28        22.85        19.20 
TCGA-FX-A3TO TCGA-HB-A43Z TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A3RQ 
       20.32        15.91        41.33        19.53         3.22        37.12 
TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-LI-A67I TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QQ-A5VA 
       28.21        13.58        22.03         6.35        81.01        18.08 
TCGA-QQ-A8VF TCGA-SG-A6Z7 TCGA-SI-A71Q TCGA-SI-AA8B TCGA-X6-A7WC TCGA-X6-A8C2 
       98.27         3.88        27.22         5.06        36.82        25.71 
TCGA-X9-A973 
       36.43 

$`AMP PEAK 25(XQ21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        88.57        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       32.71        59.24        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       76.41        66.87        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       20.05        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       14.99        10.68        44.45        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       14.96        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       21.63        16.18         3.06        34.55        66.31        67.20 
TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       50.50        74.10        88.31        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
       17.95        14.43         9.34        33.07        44.68        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       14.07       124.37        27.95        35.54        36.69        60.66 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        6.58         1.15        12.99         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        12.07         9.21        71.57        96.89        50.40 
TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
      101.98        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.46         0.10         0.07         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       48.30        34.88         4.57        12.62        23.97         0.10 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ 
        9.80        80.48        21.37         1.38        19.89        25.22 
TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
       40.08       143.41       116.88        73.28         5.92        22.62 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W 
       16.41         1.05         3.91        71.70        36.39        27.29 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH 
      123.78         9.04        10.85         4.08        11.70        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
        8.32         8.28         0.49         4.34        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       37.55        38.63        18.08        20.94         5.03         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        1.84        46.82        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32        62.20        10.52         0.72        11.18        18.94 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        6.58        17.92        19.82         9.93        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT 
       10.72        26.17        11.93         4.80        72.72        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 
       38.27        65.46        22.62         9.04        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       29.92        18.08        18.35        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       35.08        17.72        15.58 

  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                         0.56                          0.07 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                       106.45                        188.15 
  AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE 
                        22.03                         23.97 
[1] "0.6 - 106.5 (22.0)" "0.1 - 188.2 (24.0)"
[1] "hr=" "1.6"
D25V2, continuous
D25V3, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ21.1) MUTATED    26  17
  AMP PEAK 25(XQ21.1) WILD-TYPE 106  97
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED     26   17
  AMP PEAK 25(XQ21.1) WILD-TYPE  106   97
        clus
vv       AMP PEAK 25(XQ21.1) MUTATED AMP PEAK 25(XQ21.1) WILD-TYPE
  FEMALE                          26                           106
  MALE                            17                            97
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(XQ21.1) MUTATED       0                         1    33
  AMP PEAK 25(XQ21.1) WILD-TYPE     6                        17   161
D25V4, multiclass
                           clus
vv                          AMP PEAK 25(XQ21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              33
                           clus
vv                          AMP PEAK 25(XQ21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            17
  WHITE                                               161
[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"
D25V5, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ21.1) MUTATED     2  30
  AMP PEAK 25(XQ21.1) WILD-TYPE   3 161
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ21.1) MUTATED      2   30
  AMP PEAK 25(XQ21.1) WILD-TYPE    3  161
                        clus
vv                       AMP PEAK 25(XQ21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          30
                        clus
vv                       AMP PEAK 25(XQ21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           161
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.32) MUTATED    47  17
  DEL PEAK  1(1P36.32) WILD-TYPE 115  65
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            64                            180 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            17                             65 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A3LW 
       68.55        88.57        25.25        26.56        38.24       108.13 
TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UF 
       15.06        42.77        14.99        10.68        39.35        64.18 
TCGA-DX-A48J TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
        9.73        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6Z2 
       25.15        66.05        23.44        67.20        23.54        88.31 
TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A8BJ TCGA-DX-AB2V TCGA-DX-AB2W 
       21.30        75.32        15.62         9.34        96.89       106.45 
TCGA-DX-AB2X TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N8 
       13.28         0.07         0.07        15.91        12.62         0.10 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K7 
        9.80        21.37         1.38        37.12        40.08       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A42W TCGA-K1-A42X 
      116.88        13.58        73.28        22.62        27.29       123.78 
TCGA-MJ-A68H TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-QQ-A8VB TCGA-SI-A71Q 
       14.99        10.45       120.20        37.55       188.15        27.22 
TCGA-SI-AA8C TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
        9.93        26.17        72.72        41.49        38.27        65.46 
TCGA-WP-A9GB TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X6-A8C6 
        9.04        18.35        38.96        35.08 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX 
       36.30        19.69        53.49        44.91        54.74        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       32.71        12.85        36.69        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        23.08        70.49        17.10        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE 
       34.68        17.75         4.54        44.45        28.80        34.88 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BE 
       19.30        24.26        12.26        15.95        11.47        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.11        17.79        21.63        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI 
       66.31        50.50        16.87        74.10        64.21        34.49 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       48.36       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       17.95        14.43        59.87        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       35.77        14.07       124.37        27.95        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
        9.21        71.57        50.40        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.10        20.32         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
        4.57        23.97        41.33        80.48        19.53         3.22 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
       19.89        25.22        28.21         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV 
        3.91        71.70        36.39         9.04        10.85         4.08 
TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       11.70        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
        4.34        19.73        17.98        15.65         7.46         4.08 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
        6.35        38.63        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        9.83         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       30.90       130.32        98.27        62.20        10.52         0.72 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       11.18        18.94         3.88         6.58        17.92        19.82 
TCGA-SI-AA8B TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ 
        5.06        13.22         0.72        10.72        11.93         4.80 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62        57.80        26.43        29.92        18.08        36.82 
TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       25.71        15.95        16.83        17.72        15.58        36.43 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                        188.15                         135.48 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                         26.89                          19.97 
[1] "0.1 - 188.2 (26.9)" "0.1 - 135.5 (20.0)"
[1] "hr=" "1.9"
D26V2, continuous
D26V3, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED   46 18
  DEL PEAK  1(1P36.32) WILD-TYPE 86 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED     46   18
  DEL PEAK  1(1P36.32) WILD-TYPE   86   96
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                           46                             86
  MALE                             18                             96
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED       2                         6    53
  DEL PEAK  1(1P36.32) WILD-TYPE     4                        12   141
D26V4, multiclass
                           clus
vv                          DEL PEAK  1(1P36.32) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               53
                           clus
vv                          DEL PEAK  1(1P36.32) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                141
[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"
D26V5, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.32) MUTATED     0  55
  DEL PEAK  1(1P36.32) WILD-TYPE   5 136
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      0   55
  DEL PEAK  1(1P36.32) WILD-TYPE    5  136
                        clus
vv                       DEL PEAK  1(1P36.32) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           55
                        clus
vv                       DEL PEAK  1(1P36.32) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            136
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK  2(1Q44) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(1Q44) MUTATED    47  28
  DEL PEAK  2(1Q44) WILD-TYPE 115  54
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         75                         169 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                         28                          54 
$`DEL PEAK  2(1Q44) MUTATED`
TCGA-3B-A9HL TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       19.69        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U7 
       59.24       108.13        17.10        34.68        15.06        42.77 
TCGA-DX-A48J TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR 
        9.73        15.95        66.05         9.11         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A8BG TCGA-DX-A8BH 
       66.31        67.20        64.21        21.30        17.95        14.43 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
        9.34        59.87        35.77       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X 
       36.69        12.07        49.18        71.57        96.89        13.28 
TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A48G 
       50.40        19.20        32.15         0.46        20.32         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A4EJ 
       48.30         4.57        12.62        23.97         9.80         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 
       19.89        37.12        13.58        11.70        13.35         8.32 
TCGA-MB-A8JK TCGA-N1-A6IA TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5VB 
        4.34         4.08        81.01        18.08         9.83        48.59 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P 
       11.18        18.94         3.88         6.58        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XX TCGA-WK-A8XY TCGA-X6-A7W8 
       27.22         5.06        10.72        38.27        65.46        26.43 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C6 
       18.35        25.71        35.08 

$`DEL PEAK  2(1Q44) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A1L4 
       26.56         0.56        14.04        32.71        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 
       23.08        70.49        20.05        17.75         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       10.68        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
       19.30        24.26        12.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        25.15        11.47        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
       17.79        21.63        16.18        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       74.10        88.31        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BL 
      135.48        29.49        48.20        14.07         7.04        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       44.68        38.17        14.07        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       86.10         9.21       106.45        22.85       101.98        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y 
       84.66        50.89        71.31         0.10         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV 
        2.07        34.88        15.91         0.10        41.33        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       21.37        19.53         1.38        25.22        40.08        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      143.41       116.88        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X 
        1.05         3.91        71.70        36.39        27.29       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA 
        9.04        10.85         4.08        22.03         8.28         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        15.65         7.46        10.45 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QC-A6FX TCGA-QC-A7B5 
      120.20        37.55         6.35        38.63        20.94         5.03 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        1.84        46.82        18.08        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SI-AA8C 
      130.32        98.27        62.20        10.52         0.72         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22         0.72        26.17        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       41.49        22.62         9.04        57.80        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 
       36.82        15.95        16.83        38.96        17.72        15.58 
TCGA-X9-A973 
       36.43 

  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                       0.07                        0.07 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                     124.37                      188.15 
  DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE 
                      19.82                       25.08 
[1] "0.1 - 124.4 (19.8)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.3"
D27V2, continuous
D27V3, binary
                             cls
clus                           0  1
  DEL PEAK  2(1Q44) MUTATED   40 36
  DEL PEAK  2(1Q44) WILD-TYPE 92 78
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q44) MUTATED     40   36
  DEL PEAK  2(1Q44) WILD-TYPE   92   78
        clus
vv       DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  FEMALE                        40                          92
  MALE                          36                          78
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1Q44) MUTATED       0                         7    60
  DEL PEAK  2(1Q44) WILD-TYPE     6                        11   134
D27V4, multiclass
                           clus
vv                          DEL PEAK  2(1Q44) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         7
  WHITE                                            60
                           clus
vv                          DEL PEAK  2(1Q44) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                             134
[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"
D27V5, binary
                             cls
clus                            0   1
  DEL PEAK  2(1Q44) MUTATED     1  62
  DEL PEAK  2(1Q44) WILD-TYPE   4 129
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1Q44) MUTATED      1   62
  DEL PEAK  2(1Q44) WILD-TYPE    4  129
                        clus
vv                       DEL PEAK  2(1Q44) MUTATED DEL PEAK  2(1Q44) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        62                         129
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK  3(2P25.3) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2P25.3) MUTATED    59  33
  DEL PEAK  3(2P25.3) WILD-TYPE 103  49
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           92                           152 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                           33                            49 
$`DEL PEAK  3(2P25.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9I1 
       19.69        88.57        44.91        25.25        10.32        18.64 
TCGA-3B-A9I3 TCGA-DX-A1L2 TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U9 
       26.56        59.24        17.10        20.05        34.68        14.99 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48O 
       39.35        28.80        34.88        64.18        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BF 
       14.96        25.08        15.95        11.47        66.05         9.11 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX 
        3.06        34.55        66.31        67.20        23.54        16.87 
TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH 
       21.30        48.36        15.62         7.04        17.95        14.43 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV 
       59.87        44.68        35.77        27.95        36.69        60.66 
TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2P TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W 
        6.58         8.75        12.07        71.57        96.89       106.45 
TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-FX-A48G TCGA-HB-A2OT 
       50.40        19.20        84.66        32.15         0.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
       34.88        15.91        12.62        23.97         0.10        41.33 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 
        3.22        19.89        25.22        40.08        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN TCGA-K1-A42W TCGA-LI-A9QH TCGA-MJ-A68H 
       22.62        16.41        71.70        27.29        13.35        14.99 
TCGA-N1-A6IA TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A8VH 
        4.08        81.01        18.08         9.83        46.82        10.52 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-WK-A8XS TCGA-WK-A8XX 
       11.18        18.94        17.92         5.06        72.72        38.27 
TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       65.46         9.04        26.43        18.08        18.35        25.71 
TCGA-X6-A8C6 TCGA-X9-A971 
       35.08        15.58 

$`DEL PEAK  3(2P25.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9HZ 
       36.30        53.49        68.55        54.74        42.84        31.00 
TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       36.03         0.56        14.04        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       36.69        18.54        54.21        33.53        42.54        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 
        5.26        76.41        66.87         6.28        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49       108.13        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48R 
       10.68        44.45         9.73        19.30        12.26        26.47 
TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       72.72        25.15        23.44        28.96        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       16.18        50.50        74.10        64.21        88.31        34.49 
TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ 
       75.32       135.48        29.49        48.20        14.07         9.34 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX 
       33.07        38.17        14.07       124.37        35.54        19.43 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O 
        1.15        12.99         4.67        12.39        40.60        86.10 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 
       49.18         9.21        13.28        22.85       101.98        60.00 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
        0.07         2.07         4.57         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       19.53         1.38        37.12        28.21       143.41       116.88 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
        5.92         1.05         3.91        36.39       123.78         9.04 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       10.85         4.08        11.70        22.03         8.32         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49         4.34        19.73        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QC-A6FX 
       10.45       120.20        37.55         6.35        38.63        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        5.03         1.84        18.08        48.59        35.90        30.90 
TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 
      188.15       130.32        98.27        62.20         0.72         3.88 
TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        6.58        19.82        27.22         9.93        13.22         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8Y0 
       10.72        26.17        11.93         4.80        41.49        22.62 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       57.80        29.92        36.82        15.95        16.83        38.96 
TCGA-X6-A8C7 TCGA-X9-A973 
       17.72        36.43 

  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       106.45                        188.15 
  DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE 
                       24.115                        22.735 
[1] "0.1 - 106.5 (24.1)" "0.1 - 188.2 (22.7)"
[1] "hr=" "1.1"
D28V2, continuous
D28V3, binary
                               cls
clus                             0  1
  DEL PEAK  3(2P25.3) MUTATED   59 34
  DEL PEAK  3(2P25.3) WILD-TYPE 73 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED     59   34
  DEL PEAK  3(2P25.3) WILD-TYPE   73   80
        clus
vv       DEL PEAK  3(2P25.3) MUTATED DEL PEAK  3(2P25.3) WILD-TYPE
  FEMALE                          59                            73
  MALE                            34                            80
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2P25.3) MUTATED       1                        13    73
  DEL PEAK  3(2P25.3) WILD-TYPE     5                         5   121
D28V4, multiclass
                           clus
vv                          DEL PEAK  3(2P25.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                              73
                           clus
vv                          DEL PEAK  3(2P25.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                               121
[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"
D28V5, binary
                               cls
clus                              0   1
  DEL PEAK  3(2P25.3) MUTATED     0  85
  DEL PEAK  3(2P25.3) WILD-TYPE   5 106
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2P25.3) MUTATED      0   85
  DEL PEAK  3(2P25.3) WILD-TYPE    5  106
                        clus
vv                       DEL PEAK  3(2P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          85
                        clus
vv                       DEL PEAK  3(2P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           106
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    61  41
  DEL PEAK  4(2Q37.3) WILD-TYPE 101  41
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                          102                           142 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           41                            41 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 
       19.69        88.57        44.91        42.84        18.64        26.56 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3M1 
       12.85        18.54        54.21        59.24         6.28        20.05 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD 
       34.68        15.06        42.77        14.99        10.68        28.80 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BF 
       64.18        24.26        26.47        25.08        15.95         9.11 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
       16.18         3.06        34.55        66.31        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET 
       50.50        16.87        21.30        48.36        15.62         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2H 
       38.17        27.95        35.54        36.69        60.66        12.39 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        12.07        49.18        71.57        96.89        50.40 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3L4 
      101.98        19.20        32.15         0.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ 
        4.57        41.33         9.80        80.48        21.37         3.22 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3KA TCGA-IW-A3M6 TCGA-JV-A5VE 
       19.89        37.12        28.21        13.58        22.62        16.41 
TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
        1.05        36.39        27.29        10.85         4.08        11.70 
TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
        4.08         6.35        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
        9.83        10.52        18.94         3.88         6.58        17.92 
TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-WP-A9GB 
        5.06        10.72        72.72        38.27        22.62         9.04 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       57.80        26.43        18.08        18.35        25.71        15.95 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY 
       36.30        53.49        68.55        54.74        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       31.00        36.03         0.56        14.04        32.71        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       36.69        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J 
       17.75         4.54        44.45        39.35        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 
       19.30        12.26        27.22        14.96        72.72        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        66.05        23.44        28.96        17.79        21.63 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EO 
       74.10        64.21        88.31        34.49        75.32       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR 
       29.49        48.20        14.07        35.77        14.07       124.37 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       19.43         6.58         1.15        12.99         8.75         4.67 
TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 
       40.60         9.21       106.45        13.28        22.85        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       84.66        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
       20.32         0.07         2.07        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 
        0.10        19.53         1.38        25.22        40.08       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42X 
      116.88        73.28         5.92         3.91        71.70       123.78 
TCGA-K1-A6RT TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        9.04        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       10.45       120.20        37.55        38.63         1.84        46.82 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       18.08        48.59        35.90        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q 
       98.27        62.20         0.72        11.18        19.82        27.22 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
        9.93        13.22         0.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C5 
       41.49        65.46        29.92        36.82        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       35.08        17.72        15.58        36.43 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       101.98                        188.15 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                       21.335                        25.185 
[1] "0.1 - 102.0 (21.3)" "0.1 - 188.2 (25.2)"
[1] "hr=" "1.6"
D29V2, continuous
D29V3, binary
                               cls
clus                             0  1
  DEL PEAK  4(2Q37.3) MUTATED   55 48
  DEL PEAK  4(2Q37.3) WILD-TYPE 77 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     55   48
  DEL PEAK  4(2Q37.3) WILD-TYPE   77   66
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          55                            77
  MALE                            48                            66
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED       2                        10    82
  DEL PEAK  4(2Q37.3) WILD-TYPE     4                         8   112
D29V4, multiclass
                           clus
vv                          DEL PEAK  4(2Q37.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              82
                           clus
vv                          DEL PEAK  4(2Q37.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               112
[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"
D29V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     1  86
  DEL PEAK  4(2Q37.3) WILD-TYPE   4 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      1   86
  DEL PEAK  4(2Q37.3) WILD-TYPE    4  105
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          86
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           105
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK  5(2Q37.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2Q37.3) MUTATED   64 40
  DEL PEAK  5(2Q37.3) WILD-TYPE 98 42
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                          104                           140 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                           40                            42 
$`DEL PEAK  5(2Q37.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 
       19.69        88.57        44.91        42.84        18.64        26.56 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A3LW 
       12.85        18.54        54.21        59.24         6.28       108.13 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD 
       20.05        34.68        15.06        42.77        14.99        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BF 
       34.88        64.18        26.47        25.08        15.95         9.11 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
       16.18         3.06        34.55        66.31        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET 
       50.50        16.87        21.30        48.36        15.62         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       17.95        14.43        59.87        33.07        44.68        38.17 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2H 
       27.95        35.54        36.69        60.66         8.75        12.39 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z 
       86.10        12.07        49.18        71.57        96.89        50.40 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
      101.98        19.20        32.15         0.07        20.32         0.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       48.30        34.88         4.57        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 
       21.37         3.22        19.89        37.12        28.21       143.41 
TCGA-IS-A3KA TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A42W 
       13.58        22.62        16.41         1.05         3.91        27.29 
TCGA-K1-A6RU TCGA-KF-A41W TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP 
       10.85        11.70         4.08         6.35        81.01        18.08 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 
       20.94         5.03         9.83        10.52        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX 
        6.58        17.92         5.06        10.72        72.72        38.27 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WD 
       22.62         9.04        57.80        26.43        18.08        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C3 
       25.71        15.95 

$`DEL PEAK  5(2Q37.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HY 
       36.30        53.49        68.55        54.74        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX 
       31.00        36.03         0.56        14.04        32.71        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       36.69        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       66.87        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3U6 
       54.77         9.04        23.08        70.49        17.10        17.75 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K 
        4.54        10.68        44.45        39.35         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 
       24.26        12.26        27.22        14.96        72.72        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       11.47        66.05        23.44        28.96        17.79        21.63 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EO 
       74.10        64.21        88.31        34.49        75.32       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BP 
       29.49        48.20        14.07         9.34        35.77        14.07 
TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G 
      124.37        19.43         6.58         1.15        12.99         4.67 
TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 
       40.60         9.21       106.45        13.28        22.85        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y 
       84.66        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A8OO TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EI 
        2.07        15.91        12.62        23.97         0.10        19.53 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 
        1.38        25.22        40.08       116.88        73.28         5.92 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I 
       71.70        36.39       123.78         9.04         4.08        22.03 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL 
       13.35         8.32         8.28         0.49         4.34        19.73 
TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK 
       14.99        17.98        15.65         7.46        10.45       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       37.55        38.63         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG 
       35.90        30.90       188.15       130.32        98.27        62.20 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT 
        0.72        11.18        19.82        27.22         9.93        13.22 
TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY 
        0.72        26.17        11.93         4.80        41.49        65.46 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       29.92        36.82        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       143.41                        188.15 
  DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE 
                       21.335                        24.705 
[1] "0.1 - 143.4 (21.3)" "0.1 - 188.2 (24.7)"
[1] "hr=" "1.4"
D30V2, continuous
D30V3, binary
                               cls
clus                             0  1
  DEL PEAK  5(2Q37.3) MUTATED   58 47
  DEL PEAK  5(2Q37.3) WILD-TYPE 74 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED     58   47
  DEL PEAK  5(2Q37.3) WILD-TYPE   74   67
        clus
vv       DEL PEAK  5(2Q37.3) MUTATED DEL PEAK  5(2Q37.3) WILD-TYPE
  FEMALE                          58                            74
  MALE                            47                            67
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2Q37.3) MUTATED       2                        10    84
  DEL PEAK  5(2Q37.3) WILD-TYPE     4                         8   110
D30V4, multiclass
                           clus
vv                          DEL PEAK  5(2Q37.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              84
                           clus
vv                          DEL PEAK  5(2Q37.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                               110
[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"
D30V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(2Q37.3) MUTATED     2  86
  DEL PEAK  5(2Q37.3) WILD-TYPE   3 105
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2Q37.3) MUTATED      2   86
  DEL PEAK  5(2Q37.3) WILD-TYPE    3  105
                        clus
vv                       DEL PEAK  5(2Q37.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          86
                        clus
vv                       DEL PEAK  5(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           105
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK  6(3P21.31) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  6(3P21.31) MUTATED    45  17
  DEL PEAK  6(3P21.31) WILD-TYPE 117  65
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            62                            182 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                            17                             65 
$`DEL PEAK  6(3P21.31) MUTATED`
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A3LS TCGA-DX-A3LY 
       38.24        12.85        18.54        59.24         9.04        17.10 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YR 
       20.05        34.68        12.26        15.95         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A8BG 
       66.31        23.54        74.10        15.62       135.48        17.95 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BT 
       59.87        33.07        44.68        35.77       124.37        35.54 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2T 
       36.69         6.58         4.67        40.60        86.10        71.57 
TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3B TCGA-DX-AB3C 
       96.89        13.28       101.98        19.20        50.89        71.31 
TCGA-FX-A3RE TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IS-A3K7 
        0.07         4.57         0.10         3.22        19.89       143.41 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A6RU TCGA-LI-A9QH 
        5.92        22.62        16.41         1.05        10.85        13.35 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-QC-AA9N TCGA-QQ-A8VB TCGA-QQ-A8VF 
       10.45         4.08        37.55         9.83       188.15        98.27 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-VT-A80G TCGA-WK-A8XT 
       10.52        11.18        18.94         6.58        10.72        41.49 
TCGA-X6-A8C6 TCGA-X6-A8C7 
       35.08        17.72 

$`DEL PEAK  6(3P21.31) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ 
       18.64        26.56         0.56        14.04        32.71        36.69 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       54.21        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 
       59.47        54.77        23.08        70.49       108.13        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       17.75        42.77         4.54        14.99        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       39.35        28.80        34.88        64.18         9.73        19.30 
TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       24.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.15        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX 
       17.79        21.63        16.18        67.20        50.50        16.87 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       64.21        88.31        21.30        34.49        75.32        48.36 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ 
       29.49        48.20        14.07         7.04        14.43         9.34 
TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       38.17        14.07        27.95        60.66        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.99         8.75        12.39        12.07        49.18         9.21 
TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
      106.45        50.40        22.85        60.00        84.66        32.15 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
        0.46         0.10        20.32         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 
       48.30        34.88        15.91        12.62        23.97        41.33 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ 
        9.80        80.48        21.37        19.53         1.38        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        40.08        28.21       116.88        13.58        73.28 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        4.08        11.70        22.03         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
      120.20         6.35        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC 
        5.03         1.84        46.82        18.08        48.59        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71O 
       30.90       130.32        62.20         0.72         3.88        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       19.82        27.22         5.06         9.93        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       26.17        11.93         4.80        72.72        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       22.62         9.04        57.80        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       36.82        18.35        25.71        15.95        16.83        38.96 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                        188.15                         130.32 
  DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE 
                        19.545                         24.670 
[1] "0.1 - 188.2 (19.5)" "0.1 - 130.3 (24.7)"
[1] "hr=" "1.4"
D31V2, continuous
D31V3, binary
                                cls
clus                              0  1
  DEL PEAK  6(3P21.31) MUTATED   35 29
  DEL PEAK  6(3P21.31) WILD-TYPE 97 85
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3P21.31) MUTATED     35   29
  DEL PEAK  6(3P21.31) WILD-TYPE   97   85
        clus
vv       DEL PEAK  6(3P21.31) MUTATED DEL PEAK  6(3P21.31) WILD-TYPE
  FEMALE                           35                             97
  MALE                             29                             85
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P21.31) MUTATED       2                         6    50
  DEL PEAK  6(3P21.31) WILD-TYPE     4                        12   144
D31V4, multiclass
                           clus
vv                          DEL PEAK  6(3P21.31) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               50
                           clus
vv                          DEL PEAK  6(3P21.31) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                144
[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"
D31V5, binary
                                cls
clus                               0   1
  DEL PEAK  6(3P21.31) MUTATED     1  50
  DEL PEAK  6(3P21.31) WILD-TYPE   4 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3P21.31) MUTATED      1   50
  DEL PEAK  6(3P21.31) WILD-TYPE    4  141
                        clus
vv                       DEL PEAK  6(3P21.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       DEL PEAK  6(3P21.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            141
[1] 2 2
[1] FALSE

Clustering(32) Variable = DEL PEAK  7(3Q13.31) MUTATION ANALYSIS
D32V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(3Q13.31) MUTATED    32  17
  DEL PEAK  7(3Q13.31) WILD-TYPE 130  65
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            49                            195 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                            17                             65 
$`DEL PEAK  7(3Q13.31) MUTATED`
TCGA-3B-A9HL TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R 
       19.69        14.04        32.71        38.24        18.54        74.66 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A6B8 TCGA-DX-A6YR 
       23.08        17.10        20.05        34.68        15.95        34.55 
TCGA-DX-A7EF TCGA-DX-A7EO TCGA-DX-A8BH TCGA-DX-AATS TCGA-DX-AB2W TCGA-DX-AB35 
       21.30       135.48        14.43         1.15       106.45        19.20 
TCGA-DX-AB36 TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A3YV 
       60.00        71.31         0.46        20.32         0.07         4.57 
TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IW-A3M5 TCGA-K1-A42X 
       15.91         0.10         3.22        19.89         5.92       123.78 
TCGA-K1-A6RU TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MO-A47R 
       10.85        13.35         8.32         4.34        14.99        10.45 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QC-A7B5 TCGA-QQ-A8VB TCGA-RN-AAAQ TCGA-SG-A6Z7 
       37.55         6.35         5.03       188.15        11.18         3.88 
TCGA-SI-A71Q TCGA-SI-AA8C TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C4 
       27.22         9.93         9.04        26.43        36.82        16.83 
TCGA-X9-A971 
       15.58 

$`DEL PEAK  7(3Q13.31) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       26.56         0.56        12.85        36.69        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
        9.04        70.49       108.13        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
        4.54        14.99        10.68        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
       21.63        16.18         3.06        66.31        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       50.50        16.87        74.10        64.21        88.31        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       75.32        48.36        15.62        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
        7.04        17.95         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT 
       38.17        35.77        14.07       124.37        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        60.66        19.43         6.58        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        4.67        12.39        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 
        9.21        71.57        96.89        13.28        50.40        22.85 
TCGA-DX-AB32 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A3NJ TCGA-FX-A3RE 
      101.98        84.66        32.15        50.89         0.10         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07         2.07        48.30        34.88        12.62        23.97 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK 
       41.33         9.80        80.48        21.37        19.53         1.38 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       37.12        25.22        40.08        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58        73.28        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W 
       71.70        36.39        27.29         9.04         4.08        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 
       22.03         8.28         0.49        19.73        17.98        15.65 
TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP 
        7.46         4.08       120.20        38.63        81.01        18.08 
TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       20.94         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        30.90       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B 
        0.72        18.94         6.58        17.92        19.82         5.06 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T 
       72.72        41.49        38.27        65.46        22.62        57.80 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 
       29.92        18.08        18.35        25.71        15.95        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       35.08        17.72        36.43 

  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                        188.15                         143.41 
  DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE 
                         16.83                          26.17 
[1] "0.1 - 188.2 (16.8)" "0.1 - 143.4 (26.2)"
[1] "hr=" "1.4"
D32V2, continuous
D32V3, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED    25  26
  DEL PEAK  7(3Q13.31) WILD-TYPE 107  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED     25   26
  DEL PEAK  7(3Q13.31) WILD-TYPE  107   88
        clus
vv       DEL PEAK  7(3Q13.31) MUTATED DEL PEAK  7(3Q13.31) WILD-TYPE
  FEMALE                           25                            107
  MALE                             26                             88
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3Q13.31) MUTATED       1                         2    43
  DEL PEAK  7(3Q13.31) WILD-TYPE     5                        16   151
D32V4, multiclass
                           clus
vv                          DEL PEAK  7(3Q13.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               43
                           clus
vv                          DEL PEAK  7(3Q13.31) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                151
[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"
D32V5, binary
                                cls
clus                               0   1
  DEL PEAK  7(3Q13.31) MUTATED     1  41
  DEL PEAK  7(3Q13.31) WILD-TYPE   4 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(3Q13.31) MUTATED      1   41
  DEL PEAK  7(3Q13.31) WILD-TYPE    4  150
                        clus
vv                       DEL PEAK  7(3Q13.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           41
                        clus
vv                       DEL PEAK  7(3Q13.31) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            150
[1] 2 2
[1] FALSE

Clustering(33) Variable = DEL PEAK  8(3Q29) MUTATION ANALYSIS
D33V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  8(3Q29) MUTATED    32  18
  DEL PEAK  8(3Q29) WILD-TYPE 130  64
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         50                         194 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                         18                          64 
$`DEL PEAK  8(3Q29) MUTATED`
TCGA-3B-A9HL TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 
       19.69        32.71        38.24        12.85        18.54        54.21 
TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3UA 
       74.66        23.08        17.10        20.05        34.68        10.68 
TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6YS 
       64.18        24.26        27.22        26.47        15.95        66.31 
TCGA-DX-A7EO TCGA-DX-A8BL TCGA-DX-A8BR TCGA-DX-AB2W TCGA-DX-AB35 TCGA-DX-AB36 
      135.48        33.07       124.37       106.45        19.20        60.00 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A3YV TCGA-HB-A43Z TCGA-IE-A3OV 
       71.31         0.46        20.32         4.57        15.91        80.48 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3KA TCGA-K1-A6RU TCGA-LI-A9QH 
        3.22        19.89        37.12        13.58        10.85        13.35 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QQ-A5VB TCGA-QQ-A8VB 
        4.34        14.99        37.55         6.35        48.59       188.15 
TCGA-SG-A6Z4 TCGA-SI-A71Q TCGA-VT-A80G TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7WC 
       18.94        27.22        10.72        65.46         9.04        36.82 
TCGA-X6-A8C4 TCGA-X9-A971 
       16.83        15.58 

$`DEL PEAK  8(3Q29) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 
       26.56         0.56        14.04        36.69        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       42.54         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49       108.13        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       14.99        44.45        39.35        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       19.30        12.26        14.96        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG 
       11.47        66.05        23.44        28.96         9.11        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU 
       21.63        16.18         3.06        34.55        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
       50.50        16.87        74.10        64.21        88.31        21.30 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        75.32        48.36        15.62        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK 
       14.07         7.04        17.95        14.43         9.34        59.87 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT 
       44.68        38.17        35.77        14.07        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       36.69        60.66        19.43         6.58         1.15        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
        8.75         4.67        12.39        40.60        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z 
       49.18         9.21        71.57        96.89        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A3NJ 
       22.85       101.98        84.66        32.15        50.89         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.07         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
       12.62        23.97         0.10        41.33         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
       19.53         1.38        25.22        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        73.28         5.92        22.62        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        4.08        11.70        22.03         8.32         8.28         0.49 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       19.73        17.98        15.65         7.46        10.45         4.08 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
      120.20        38.63        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD 
        9.83         1.84        46.82        18.08        35.90        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32        98.27        62.20        10.52         0.72        11.18 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88         6.58        17.92        19.82         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS 
       13.22         0.72        26.17        11.93         4.80        72.72 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       41.49        38.27        22.62        57.80        26.43        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.08        18.35        25.71        15.95        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A973 
       17.72        36.43 

  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                       0.46                        0.07 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                     188.15                      143.41 
  DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE 
                      21.70                       23.49 
[1] "0.5 - 188.2 (21.7)" "0.1 - 143.4 (23.5)"
[1] "hr=" "1"  
D33V2, continuous
D33V3, binary
                             cls
clus                            0   1
  DEL PEAK  8(3Q29) MUTATED    25  27
  DEL PEAK  8(3Q29) WILD-TYPE 107  87
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED     25   27
  DEL PEAK  8(3Q29) WILD-TYPE  107   87
        clus
vv       DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  FEMALE                        25                         107
  MALE                          27                          87
[1] 2 2
[1] FALSE
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3Q29) MUTATED       0                         2    44
  DEL PEAK  8(3Q29) WILD-TYPE     6                        16   150
D33V4, multiclass
                           clus
vv                          DEL PEAK  8(3Q29) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            44
                           clus
vv                          DEL PEAK  8(3Q29) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             150
[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"
D33V5, binary
                             cls
clus                            0   1
  DEL PEAK  8(3Q29) MUTATED     1  40
  DEL PEAK  8(3Q29) WILD-TYPE   4 151
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  8(3Q29) MUTATED      1   40
  DEL PEAK  8(3Q29) WILD-TYPE    4  151
                        clus
vv                       DEL PEAK  8(3Q29) MUTATED DEL PEAK  8(3Q29) WILD-TYPE
  HISPANIC OR LATINO                             1                           4
  NOT HISPANIC OR LATINO                        40                         151
[1] 2 2
[1] FALSE

Clustering(34) Variable = DEL PEAK  9(4Q35.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q35.1) MUTATED    56  35
  DEL PEAK  9(4Q35.1) WILD-TYPE 106  47
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           91                           153 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           35                            47 
$`DEL PEAK  9(4Q35.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY 
       19.69        88.57        26.56         0.56        38.24        12.85 
TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LT 
       54.21        74.66         6.28         8.58         9.04        23.08 
TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE 
      108.13        34.68         4.54        14.99        28.80        34.88 
TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6BA TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       24.26        26.47        66.05         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A8BG 
       67.20        23.54        16.87        64.21        21.30        17.95 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT 
       33.07        44.68        38.17        14.07        27.95        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       36.69        60.66         6.58         1.15        12.99         8.75 
TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z 
       12.39        86.10        12.07        96.89       106.45        50.40 
TCGA-DX-AB32 TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N8 
      101.98         0.46        20.32        48.30        15.91         0.10 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3KA TCGA-IW-A3M5 
       21.37         3.22         1.38        25.22        13.58         5.92 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A6RV TCGA-KF-A41W 
       22.62        16.41         1.05        27.29         4.08        11.70 
TCGA-MB-A8JK TCGA-MO-A47R TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A5V9 
        4.34        10.45         6.35        18.08        20.94        46.82 
TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8C TCGA-UE-A6QU 
      188.15        10.52        18.94        17.92         9.93         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7W8 
       26.17        11.93        72.72        65.46         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       29.92        36.82        18.35        25.71        15.95        16.83 
TCGA-X6-A8C6 
       35.08 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KU 
       42.84        10.32        31.00        36.03        18.64        14.04 
TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       32.71        36.69        18.54        59.24        33.53        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2J0 
        5.26        76.41        66.87        27.81        60.30         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
       59.47        54.77        70.49        17.10        20.05        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UF 
       17.75        42.77        10.68        44.45        39.35        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
        9.73        19.30        12.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        15.95        11.47        23.44        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YV TCGA-DX-A6YZ 
        9.11        17.79        21.63        16.18        50.50        74.10 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       88.31        34.49        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ 
       29.49        48.20        14.07         7.04        14.43         9.34 
TCGA-DX-A8BK TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-AB2G TCGA-DX-AB2J 
       59.87        35.77       124.37        19.43         4.67        40.60 
TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 
       49.18         9.21        71.57        13.28        22.85        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
       60.00        84.66        32.15        50.89        71.31         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.07         0.07         0.07         2.07        34.88         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI 
       12.62        23.97        41.33         9.80        80.48        19.53 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       19.89        37.12        40.08        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
       73.28         3.91        71.70        36.39       123.78         9.04 
TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
       10.85        22.03        13.35         8.32         8.28         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
      120.20        37.55        38.63        81.01         5.03         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        18.08        48.59        35.90        30.90       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 
       98.27        62.20         0.72        11.18         3.88         6.58 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XQ 
       19.82        27.22         5.06        13.22        10.72         4.80 
TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C5 
       41.49        38.27        22.62        57.80        18.08        38.96 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                         0.10                          0.07 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                       188.15                        143.41 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                        21.30                         25.15 
[1] "0.1 - 188.2 (21.3)" "0.1 - 143.4 (25.1)"
[1] "hr=" "1.4"
D34V2, continuous
D34V3, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   51 40
  DEL PEAK  9(4Q35.1) WILD-TYPE 81 74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     51   40
  DEL PEAK  9(4Q35.1) WILD-TYPE   81   74
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          51                            81
  MALE                            40                            74
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q35.1) MUTATED       4                         6    70
  DEL PEAK  9(4Q35.1) WILD-TYPE     2                        12   124
D34V4, multiclass
                           clus
vv                          DEL PEAK  9(4Q35.1) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              70
                           clus
vv                          DEL PEAK  9(4Q35.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               124
[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"
D34V5, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q35.1) MUTATED     0  74
  DEL PEAK  9(4Q35.1) WILD-TYPE   5 117
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED      0   74
  DEL PEAK  9(4Q35.1) WILD-TYPE    5  117
                        clus
vv                       DEL PEAK  9(4Q35.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          74
                        clus
vv                       DEL PEAK  9(4Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           117
[1] 2 2
[1] FALSE

Clustering(35) Variable = DEL PEAK 10(5P15.33) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(5P15.33) MUTATED    20  12
  DEL PEAK 10(5P15.33) WILD-TYPE 142  70
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            32                            212 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                            12                             70 
$`DEL PEAK 10(5P15.33) MUTATED`
TCGA-3B-A9I0 TCGA-DX-A1L3 TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3UA 
       36.03        33.53        74.66        23.08        20.05        10.68 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BZ 
       16.18         3.06        17.95        14.43         9.34         6.58 
TCGA-DX-AB2G TCGA-DX-AB32 TCGA-DX-AB36 TCGA-HB-A5W3 TCGA-IE-A3OV TCGA-IS-A3K7 
        4.67       101.98        60.00        12.62        80.48       143.41 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A8JK TCGA-MB-A8JL TCGA-QC-AA9N 
       10.85         4.08        11.70         4.34        19.73         9.83 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VG TCGA-SG-A849 TCGA-VT-A80G TCGA-VT-A80J 
       48.59        35.90        62.20         6.58        10.72        26.17 
TCGA-WK-A8Y0 TCGA-X6-A8C3 
       22.62        15.95 

$`DEL PEAK 10(5P15.33) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 
       54.74        25.25        42.84        10.32        31.00        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       26.56         0.56        14.04        32.71        38.24        12.85 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L4 TCGA-DX-A23T 
       36.69        18.54        54.21        59.24        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        9.70        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       17.10        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        44.45        39.35        28.80        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
        9.73        19.30        24.26        12.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47        72.72        25.08        25.15        15.95        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
       34.55        66.31        67.20        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        7.04        59.87        33.07        44.68        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       14.07       124.37        27.95        35.54        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2H TCGA-DX-AB2J 
       19.43         1.15        12.99         8.75        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       86.10        12.07        49.18         9.21        71.57        96.89 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB37 
      106.45        13.28        50.40        22.85        19.20        84.66 
TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       32.15        50.89        71.31         0.46         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
       20.32         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        15.91        23.97         0.10        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        40.08        28.21       116.88        13.58        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62        16.41         1.05         3.91        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-LI-A67I TCGA-LI-A9QH 
       36.39        27.29       123.78         9.04        22.03        13.35 
TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        8.32         8.28         0.49        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        7.46        10.45         4.08       120.20        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 
       38.63        81.01        18.08        20.94         5.03         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
       46.82        18.08        30.90       188.15       130.32        98.27 
TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       10.52         0.72        11.18        18.94         3.88        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       19.82        27.22         5.06         9.93        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       11.93         4.80        72.72        41.49        38.27        65.46 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
        9.04        57.80        26.43        29.92        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 
       18.35        25.71        16.83        38.96        35.08        17.72 
TCGA-X9-A971 TCGA-X9-A973 
       15.58        36.43 

  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                          3.06                           0.07 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                        143.41                         188.15 
  DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE 
                        17.065                         25.115 
[1] "3.1 - 143.4 (17.1)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.3"
D35V2, continuous
D35V3, binary
                                cls
clus                               0   1
  DEL PEAK 10(5P15.33) MUTATED    18  15
  DEL PEAK 10(5P15.33) WILD-TYPE 114  99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(5P15.33) MUTATED     18   15
  DEL PEAK 10(5P15.33) WILD-TYPE  114   99
        clus
vv       DEL PEAK 10(5P15.33) MUTATED DEL PEAK 10(5P15.33) WILD-TYPE
  FEMALE                           18                            114
  MALE                             15                             99
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5P15.33) MUTATED       1                         2    27
  DEL PEAK 10(5P15.33) WILD-TYPE     5                        16   167
D35V4, multiclass
                           clus
vv                          DEL PEAK 10(5P15.33) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               27
                           clus
vv                          DEL PEAK 10(5P15.33) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             16
  WHITE                                                167
[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"
D35V5, binary
                                cls
clus                               0   1
  DEL PEAK 10(5P15.33) MUTATED     0  26
  DEL PEAK 10(5P15.33) WILD-TYPE   5 165
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(5P15.33) MUTATED      0   26
  DEL PEAK 10(5P15.33) WILD-TYPE    5  165
                        clus
vv                       DEL PEAK 10(5P15.33) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           26
                        clus
vv                       DEL PEAK 10(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            165
[1] 2 2
[1] FALSE

Clustering(36) Variable = DEL PEAK 11(6P25.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(6P25.3) MUTATED    53  23
  DEL PEAK 11(6P25.3) WILD-TYPE 109  59
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           76                           168 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                           23                            59 
$`DEL PEAK 11(6P25.3) MUTATED`
TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       68.55        44.91        42.84        10.32        31.00        36.03 
TCGA-3B-A9I3 TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3LY 
       26.56        36.69        18.54        74.66        23.08        17.10 
TCGA-DX-A3M1 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF 
       20.05        10.68        39.35        28.80        34.88        64.18 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       19.30        24.26        27.22        14.96        72.72        25.08 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YS 
       66.05        23.44         9.11        16.18         3.06        66.31 
TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BM TCGA-DX-A8BO 
       88.31        34.49        48.36         7.04        44.68        35.77 
TCGA-DX-A8BU TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB32 TCGA-FX-A48G 
       36.69        71.57        96.89        13.28       101.98         0.07 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A3OV 
       34.88         4.57        15.91        12.62        23.97        80.48 
TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN 
       37.12        28.21       143.41        22.62         1.05        71.70 
TCGA-K1-A6RV TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-PC-A5DL TCGA-PC-A5DP 
        4.08         8.32         8.28        19.73        37.55        18.08 
TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-RN-AAAQ TCGA-SG-A6Z4 
        5.03        18.08        30.90       188.15        11.18        18.94 
TCGA-SI-A71O TCGA-SI-A71P TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX 
       17.92        19.82        10.72        26.17        72.72        38.27 
TCGA-WK-A8XY TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C5 
       65.46        26.43        15.95        38.96 

$`DEL PEAK 11(6P25.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        19.69        53.49        88.57        54.74        25.25 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY 
       18.64         0.56        14.04        32.71        38.24        12.85 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        59.24        33.53        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 
       66.87         6.28        27.81        60.30         8.58         9.70 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M2 
       59.47        54.77         9.04        70.49       108.13        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        14.99        44.45 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48R TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
        9.73        12.26        26.47        25.15        15.95        11.47 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU 
       28.96        17.79        21.63        34.55        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EL 
       50.50        16.87        74.10        64.21        21.30        75.32 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG 
       15.62       135.48        29.49        48.20        14.07        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP 
       14.43         9.34        59.87        33.07        38.17        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
      124.37        27.95        35.54        60.66        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        1.15        12.99         8.75         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2Z 
       86.10        12.07        49.18         9.21       106.45        50.40 
TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y 
       71.31         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH 
        2.07        48.30         0.10        41.33         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
       19.53         3.22         1.38        19.89        25.22        40.08 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J 
      116.88        13.58        73.28         5.92        16.41         3.91 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W 
       36.39        27.29       123.78         9.04        10.85        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J 
       22.03        13.35         0.49         4.34        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DM 
       15.65         7.46        10.45         4.08       120.20         6.35 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       38.63        81.01        20.94         9.83         1.84        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       48.59        35.90       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        0.72         3.88         6.58        27.22         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8Y0 
       13.22         0.72        11.93         4.80        41.49        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD 
        9.04        57.80        29.92        18.08        36.82        18.35 
TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       25.71        16.83        35.08        17.72        15.58        36.43 

  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                       188.15                        135.48 
  DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE 
                       26.495                        21.120 
[1] "0.1 - 188.2 (26.5)" "0.1 - 135.5 (21.1)"
[1] "hr=" "1.3"
D36V2, continuous
D36V3, binary
                               cls
clus                             0  1
  DEL PEAK 11(6P25.3) MUTATED   40 36
  DEL PEAK 11(6P25.3) WILD-TYPE 92 78
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED     40   36
  DEL PEAK 11(6P25.3) WILD-TYPE   92   78
        clus
vv       DEL PEAK 11(6P25.3) MUTATED DEL PEAK 11(6P25.3) WILD-TYPE
  FEMALE                          40                            92
  MALE                            36                            78
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6P25.3) MUTATED       2                         4    65
  DEL PEAK 11(6P25.3) WILD-TYPE     4                        14   129
D36V4, multiclass
                           clus
vv                          DEL PEAK 11(6P25.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              65
                           clus
vv                          DEL PEAK 11(6P25.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               129
[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"
D36V5, binary
                               cls
clus                              0   1
  DEL PEAK 11(6P25.3) MUTATED     0  62
  DEL PEAK 11(6P25.3) WILD-TYPE   5 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6P25.3) MUTATED      0   62
  DEL PEAK 11(6P25.3) WILD-TYPE    5  129
                        clus
vv                       DEL PEAK 11(6P25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          62
                        clus
vv                       DEL PEAK 11(6P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 5
  NOT HISPANIC OR LATINO                           129
[1] 2 2
[1] FALSE

Clustering(37) Variable = DEL PEAK 12(6Q14.1) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6Q14.1) MUTATED    51  24
  DEL PEAK 12(6Q14.1) WILD-TYPE 111  58
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                           75                           169 
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                           24                            58 
$`DEL PEAK 12(6Q14.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ 
       19.69        88.57        44.91        25.25        42.84        31.00 
TCGA-3B-A9I3 TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
       26.56        12.85        36.69        17.10        20.05        34.68 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       42.77        14.99        10.68        64.18        19.30        24.26 
TCGA-DX-A48P TCGA-DX-A6BA TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YX 
       14.96        66.05        34.55        66.31        67.20        16.87 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A8BL TCGA-DX-A8BO 
       64.21        21.30        34.49        48.36        33.07        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V 
       14.07       124.37        36.69        49.18        71.57        96.89 
TCGA-DX-AB32 TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A43Z TCGA-IE-A3OV TCGA-IE-A4EJ 
      101.98         0.46        20.32        15.91        80.48         3.22 
TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A6RU 
       37.12        25.22        16.41         1.05        27.29        10.85 
TCGA-K1-A6RV TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QC-A7B5 
        4.08         8.32        19.73         6.35        20.94         5.03 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-AAAQ 
       35.90        30.90       188.15        98.27        10.52        11.18 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
        3.88        17.92        19.82        10.72        26.17        11.93 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WC 
       72.72        65.46        22.62        26.43        18.08        36.82 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       15.95        16.83        38.96 

$`DEL PEAK 12(6Q14.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HY TCGA-3B-A9I0 
       36.30        53.49        68.55        54.74        10.32        36.03 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       18.64         0.56        14.04        32.71        38.24        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T 
       54.21        59.24        33.53        42.54        74.66         5.26 
TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
       76.41        66.87         6.28        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        9.70        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC 
      108.13        15.06        17.75         4.54        44.45        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48R 
       28.80        34.88         9.73        12.26        27.22        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB 
       72.72        25.08        25.15        15.95        11.47        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         9.11        17.79        21.63        16.18         3.06 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EN 
       23.54        50.50        74.10        88.31        75.32        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
      135.48        29.49        48.20        14.07         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BS 
       14.43         9.34        59.87        44.68        38.17        27.95 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       35.54        60.66        19.43         6.58         1.15        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
        8.75         4.67        12.39        40.60        86.10        12.07 
TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 
        9.21       106.45        13.28        50.40        22.85        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ 
       60.00        84.66        32.15        50.89        71.31         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 
        0.07         0.07         0.07         2.07        48.30        34.88 
TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        12.62        23.97         0.10        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 
       21.37        19.53         1.38        19.89        40.08        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 
      143.41       116.88        13.58        73.28         5.92        22.62 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-KF-A41W 
        3.91        71.70        36.39       123.78         9.04        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H 
       22.03        13.35         8.28         0.49         4.34        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 
       37.55        38.63        81.01        18.08         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q 
       46.82        18.08        48.59       130.32        62.20         0.72 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       18.94         6.58        27.22         5.06         9.93        13.22 
TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T 
        0.72         4.80        41.49        38.27         9.04        57.80 
TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 
       29.92        18.35        25.71        35.08        17.72        15.58 
TCGA-X9-A973 
       36.43 

  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                         0.46                          0.07 
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                       188.15                        143.41 
  DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE 
                        25.25                         22.62 
[1] "0.5 - 188.2 (25.2)" "0.1 - 143.4 (22.6)"
[1] "hr=" "1.2"
D37V2, continuous
D37V3, binary
                               cls
clus                             0  1
  DEL PEAK 12(6Q14.1) MUTATED   40 35
  DEL PEAK 12(6Q14.1) WILD-TYPE 92 79
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q14.1) MUTATED     40   35
  DEL PEAK 12(6Q14.1) WILD-TYPE   92   79
        clus
vv       DEL PEAK 12(6Q14.1) MUTATED DEL PEAK 12(6Q14.1) WILD-TYPE
  FEMALE                          40                            92
  MALE                            35                            79
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6Q14.1) MUTATED       1                         6    65
  DEL PEAK 12(6Q14.1) WILD-TYPE     5                        12   129
D37V4, multiclass
                           clus
vv                          DEL PEAK 12(6Q14.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              65
                           clus
vv                          DEL PEAK 12(6Q14.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                               129
[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"
D37V5, binary
                               cls
clus                              0   1
  DEL PEAK 12(6Q14.1) MUTATED     1  64
  DEL PEAK 12(6Q14.1) WILD-TYPE   4 127
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6Q14.1) MUTATED      1   64
  DEL PEAK 12(6Q14.1) WILD-TYPE    4  127
                        clus
vv                       DEL PEAK 12(6Q14.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          64
                        clus
vv                       DEL PEAK 12(6Q14.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           127
[1] 2 2
[1] FALSE

Clustering(38) Variable = DEL PEAK 13(7Q36.3) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 13(7Q36.3) MUTATED    43  24
  DEL PEAK 13(7Q36.3) WILD-TYPE 119  58
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           67                           177 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                           24                            58 
$`DEL PEAK 13(7Q36.3) MUTATED`
TCGA-3B-A9HQ TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L4 
       68.55        10.32        18.64        38.24        18.54        42.54 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A3UD 
       74.66         6.28        17.10        34.68        42.77        28.80 
TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A6BF TCGA-DX-A6BH 
        9.73        12.26        14.96        26.47         9.11        21.63 
TCGA-DX-A6YQ TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A7EF TCGA-DX-A7EN TCGA-DX-A7ET 
        3.06        66.31        23.54        21.30        15.62         7.04 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BP TCGA-DX-A8BT 
       14.43         9.34        33.07        44.68        14.07        35.54 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2E TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2W 
       36.69        60.66        12.99        12.07        49.18       106.45 
TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5NA TCGA-IF-A3RQ TCGA-IF-A4AJ 
       34.88         4.57        15.91         9.80        37.12        25.22 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-K1-A42W TCGA-MB-A5Y8 TCGA-PC-A5DP TCGA-QC-AA9N 
        5.92        22.62        27.29         8.32        18.08         9.83 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-A71O 
       18.08        35.90        98.27        10.52        18.94        17.92 
TCGA-SI-AA8B TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
        5.06         0.72        10.72        72.72        38.27        65.46 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
        9.04        57.80        26.43        25.71        15.95        16.83 
TCGA-X6-A8C6 
       35.08 

$`DEL PEAK 13(7Q36.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-3R-A8YX 
       25.25        42.84        31.00        36.03        26.56         0.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       14.04        32.71        12.85        36.69        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       33.53         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 
       70.49       108.13        20.05        15.06        17.75         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
       14.99        10.68        44.45        39.35        34.88        64.18 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       19.30        24.26        27.22        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG 
       15.95        11.47        66.05        23.44        28.96        17.79 
TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18        34.55        67.20        50.50        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EO 
       64.21        88.31        34.49        75.32        48.36       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BN 
       29.49        48.20        14.07        17.95        59.87        38.17 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       35.77       124.37        27.95        19.43         6.58         1.15 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S 
        8.75         4.67        12.39        40.60        86.10         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       71.57        96.89        13.28        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C 
       19.20        60.00        84.66        32.15        50.89        71.31 
TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
        0.46         0.10         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 
        2.07        48.30        12.62        23.97         0.10        41.33 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       80.48        21.37        19.53         3.22         1.38        19.89 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       40.08        28.21       143.41       116.88        13.58        73.28 
TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       16.41         1.05         3.91        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH 
        9.04        10.85         4.08        11.70        22.03        13.35 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5V2 
        6.35        38.63        81.01        20.94         5.03         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG 
       46.82        48.59        30.90       188.15       130.32        62.20 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q 
        0.72        11.18         3.88         6.58        19.82        27.22 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
        9.93        13.22        26.17        11.93         4.80        41.49 
TCGA-WK-A8Y0 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C5 
       22.62        29.92        18.08        36.82        18.35        38.96 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                         0.72                          0.07 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                       106.45                        188.15 
  DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE 
                        18.94                         25.08 
[1] "0.7 - 106.5 (18.9)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.3"
D38V2, continuous
D38V3, binary
                               cls
clus                             0  1
  DEL PEAK 13(7Q36.3) MUTATED   34 34
  DEL PEAK 13(7Q36.3) WILD-TYPE 98 80
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED     34   34
  DEL PEAK 13(7Q36.3) WILD-TYPE   98   80
        clus
vv       DEL PEAK 13(7Q36.3) MUTATED DEL PEAK 13(7Q36.3) WILD-TYPE
  FEMALE                          34                            98
  MALE                            34                            80
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(7Q36.3) MUTATED       3                         4    54
  DEL PEAK 13(7Q36.3) WILD-TYPE     3                        14   140
D38V4, multiclass
                           clus
vv                          DEL PEAK 13(7Q36.3) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              54
                           clus
vv                          DEL PEAK 13(7Q36.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                            14
  WHITE                                               140
[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"
D38V5, binary
                               cls
clus                              0   1
  DEL PEAK 13(7Q36.3) MUTATED     1  56
  DEL PEAK 13(7Q36.3) WILD-TYPE   4 135
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(7Q36.3) MUTATED      1   56
  DEL PEAK 13(7Q36.3) WILD-TYPE    4  135
                        clus
vv                       DEL PEAK 13(7Q36.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          56
                        clus
vv                       DEL PEAK 13(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           135
[1] 2 2
[1] FALSE

Clustering(39) Variable = DEL PEAK 14(8P23.3) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(8P23.3) MUTATED    47  30
  DEL PEAK 14(8P23.3) WILD-TYPE 115  52
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           77                           167 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                           30                            52 
$`DEL PEAK 14(8P23.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX 
       19.69        88.57        44.91         0.56        32.71        38.24 
TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW 
       36.69        18.54         6.28         9.04        23.08       108.13 
TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD 
       20.05        15.06        42.77        10.68        44.45        28.80 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BK TCGA-DX-A6YQ 
        9.73        19.30        26.47        15.95        16.18         3.06 
TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BG 
       23.54        16.87        21.30        34.49         7.04        17.95 
TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV 
       33.07        38.17        35.77        27.95        35.54        60.66 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2T 
        1.15        12.99         8.75        86.10        12.07        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB35 TCGA-FX-A2QS 
       96.89       106.45        13.28       101.98        19.20         0.46 
TCGA-FX-A3RE TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 
        0.07        34.88         4.57        15.91         0.10        41.33 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K7 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A6RT 
       19.89        37.12       143.41        16.41         3.91         9.04 
TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A8JK TCGA-MB-A8JL TCGA-PC-A5DM TCGA-QQ-A5VB 
        4.08        13.35         4.34        19.73         6.35        48.59 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XS 
        3.88        17.92        27.22         0.72        10.72        72.72 
TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C6 
       26.43        36.82        25.71        16.83        35.08 

$`DEL PEAK 14(8P23.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        68.55        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       10.32        31.00        36.03        18.64        26.56        14.04 
TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R 
       12.85        54.21        59.24        33.53        42.54        74.66 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M2 
        9.70        59.47        54.77        70.49        17.10        34.68 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
       17.75         4.54        14.99        39.35        34.88        64.18 
TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       24.26        12.26        27.22        14.96        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.15        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV 
       17.79        21.63        34.55        66.31        67.20        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       74.10        64.21        88.31        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ 
      135.48        29.49        48.20        14.07        14.43         9.34 
TCGA-DX-A8BK TCGA-DX-A8BM TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BX 
       59.87        44.68        14.07       124.37        36.69        19.43 
TCGA-DX-A8BZ TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S 
        6.58         4.67        12.39        40.60        49.18         9.21 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       50.40        22.85        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO 
       71.31         0.10        20.32         0.07         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       48.30        12.62        23.97         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
       19.53         3.22         1.38        25.22        40.08        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF 
      116.88        13.58        73.28         5.92        22.62         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU TCGA-KF-A41W 
       71.70        36.39        27.29       123.78        10.85        11.70 
TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J 
       22.03         8.32         8.28         0.49        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
       38.63        81.01        18.08        20.94         5.03         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        1.84        46.82        18.08        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32        98.27        62.20        10.52         0.72        11.18 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
       18.94         6.58        19.82         5.06         9.93        13.22 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       26.17        11.93         4.80        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD 
       22.62         9.04        57.80        29.92        18.08        18.35 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       15.95        38.96        17.72        15.58        36.43 

  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                       143.41                        188.15 
  DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE 
                        19.73                         25.15 
[1] "0.1 - 143.4 (19.7)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.5"
D39V2, continuous
D39V3, binary
                               cls
clus                             0  1
  DEL PEAK 14(8P23.3) MUTATED   39 39
  DEL PEAK 14(8P23.3) WILD-TYPE 93 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED     39   39
  DEL PEAK 14(8P23.3) WILD-TYPE   93   75
        clus
vv       DEL PEAK 14(8P23.3) MUTATED DEL PEAK 14(8P23.3) WILD-TYPE
  FEMALE                          39                            93
  MALE                            39                            75
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(8P23.3) MUTATED       1                         7    60
  DEL PEAK 14(8P23.3) WILD-TYPE     5                        11   134
D39V4, multiclass
                           clus
vv                          DEL PEAK 14(8P23.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              60
                           clus
vv                          DEL PEAK 14(8P23.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               134
[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"
D39V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(8P23.3) MUTATED     1  59
  DEL PEAK 14(8P23.3) WILD-TYPE   4 132
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(8P23.3) MUTATED      1   59
  DEL PEAK 14(8P23.3) WILD-TYPE    4  132
                        clus
vv                       DEL PEAK 14(8P23.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          59
                        clus
vv                       DEL PEAK 14(8P23.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           132
[1] 2 2
[1] FALSE

Clustering(40) Variable = DEL PEAK 15(9P24.3) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 15(9P24.3) MUTATED    60  36
  DEL PEAK 15(9P24.3) WILD-TYPE 102  46
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                           96                           148 
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                           36                            46 
$`DEL PEAK 15(9P24.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HZ TCGA-3B-A9I1 
       19.69        88.57        44.91        54.74        31.00        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
       26.56         0.56        14.04        36.69        54.21        59.24 
TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW 
       66.87         6.28        27.81         9.04        23.08       108.13 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3UA 
       17.10        20.05        34.68        15.06        42.77        10.68 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA 
       64.18         9.73        19.30        25.08        25.15        66.05 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX 
        9.11        16.18         3.06        34.55        66.31        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN 
       74.10        64.21        21.30        34.49        75.32        15.62 
TCGA-DX-A7EQ TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       29.49        14.43         9.34        44.68        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2J 
       14.07       124.37        35.54         6.58        12.99        40.60 
TCGA-DX-AB2P TCGA-DX-AB32 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3RE TCGA-HB-A2OT 
       12.07       101.98        32.15         0.46         0.07        48.30 
TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 
        0.10        19.53         3.22       143.41         5.92        22.62 
TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A6RU TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A5Y9 
        3.91        27.29        10.85        11.70         8.32         8.28 
TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX 
       19.73        10.45         4.08        38.63        81.01        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ 
        5.03        18.08        35.90       188.15        10.52        11.18 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS 
       19.82        27.22         5.06        10.72        26.17        72.72 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WC TCGA-X9-A971 
       38.27        65.46        22.62        57.80        36.82        15.58 

$`DEL PEAK 15(9P24.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY 
       36.30        53.49        68.55        25.25        42.84        10.32 
TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L3 
       36.03        32.71        38.24        12.85        18.54        33.53 
TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A240 TCGA-DX-A2IZ 
       42.54        74.66         5.26        76.41        60.30         8.58 
TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U8 
        9.70        59.47        54.77        70.49        17.75         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48L 
       14.99        44.45        39.35        28.80        34.88        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B8 
       12.26        27.22        14.96        26.47        72.72        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YT 
       11.47        23.44        28.96        17.79        21.63        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7ER 
       23.54        50.50        88.31        48.36       135.48        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BS 
       14.07         7.04        17.95        59.87        33.07        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G 
       36.69        60.66        19.43         1.15         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V 
       12.39        86.10        49.18         9.21        71.57        96.89 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
      106.45        13.28        50.40        22.85        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A48G 
       84.66        50.89        71.31         0.10        20.32         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07         2.07        34.88         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK 
       23.97        41.33         9.80        80.48        21.37         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       19.89        37.12        25.22        40.08        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A3PO 
       13.58        73.28        16.41         1.05        71.70        36.39 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5YA 
      123.78         9.04         4.08        22.03        13.35         0.49 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK 
        4.34        14.99        17.98        15.65         7.46       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 
       37.55         6.35        18.08         9.83         1.84        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       48.59        30.90       130.32        98.27        62.20         0.72 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8C TCGA-UE-A6QT 
       18.94         3.88         6.58        17.92         9.93        13.22 
TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WP-A9GB TCGA-X6-A7W8 
        0.72        11.93         4.80        41.49         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       29.92        18.08        18.35        25.71        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       38.96        35.08        17.72        36.43 

  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                       188.15                        135.48 
  DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE 
                       22.620                        23.755 
[1] "0.1 - 188.2 (22.6)" "0.1 - 135.5 (23.8)"
[1] "hr=" "1.2"
D40V2, continuous
D40V3, binary
                               cls
clus                             0  1
  DEL PEAK 15(9P24.3) MUTATED   53 43
  DEL PEAK 15(9P24.3) WILD-TYPE 79 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P24.3) MUTATED     53   43
  DEL PEAK 15(9P24.3) WILD-TYPE   79   71
        clus
vv       DEL PEAK 15(9P24.3) MUTATED DEL PEAK 15(9P24.3) WILD-TYPE
  FEMALE                          53                            79
  MALE                            43                            71
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9P24.3) MUTATED       2                         7    77
  DEL PEAK 15(9P24.3) WILD-TYPE     4                        11   117
D40V4, multiclass
                           clus
vv                          DEL PEAK 15(9P24.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              77
                           clus
vv                          DEL PEAK 15(9P24.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               117
[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"
D40V5, binary
                               cls
clus                              0   1
  DEL PEAK 15(9P24.3) MUTATED     1  74
  DEL PEAK 15(9P24.3) WILD-TYPE   4 117
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(9P24.3) MUTATED      1   74
  DEL PEAK 15(9P24.3) WILD-TYPE    4  117
                        clus
vv                       DEL PEAK 15(9P24.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          74
                        clus
vv                       DEL PEAK 15(9P24.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           117
[1] 2 2
[1] FALSE

Clustering(41) Variable = DEL PEAK 16(9P21.3) MUTATION ANALYSIS
D41V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 16(9P21.3) MUTATED   68 43
  DEL PEAK 16(9P21.3) WILD-TYPE 94 39
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                          111                           133 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                           43                            39 
$`DEL PEAK 16(9P21.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 
       19.69        88.57        44.91        31.00        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        14.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A3LS 
       54.21        59.24        74.66        66.87         6.28         9.04 
TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U7 
      108.13        17.10        20.05        34.68        15.06        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48R 
        4.54        10.68        28.80        64.18         9.73        26.47 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ 
       25.08        25.15        66.05         9.11        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EF 
       34.55        66.31        16.87        74.10        64.21        21.30 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A8BH TCGA-DX-A8BJ 
       34.49        75.32        15.62        29.49        14.43         9.34 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BX TCGA-DX-A8BZ 
       38.17        35.77        14.07       124.37        19.43         6.58 
TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q 
        1.15        12.99         8.75        40.60        12.07        49.18 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB3A TCGA-FX-A2QS 
      106.45        13.28        22.85       101.98        32.15         0.46 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.07         0.07        48.30         0.10        19.53         3.22 
TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-K1-A42W TCGA-K1-A6RU TCGA-KF-A41W 
      143.41         5.92        22.62        27.29        10.85        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA 
       13.35         8.32         8.28        19.73        10.45         4.08 
TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QQ-A5VA TCGA-QQ-A5VB 
       38.63        81.01        20.94         5.03        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A849 
       35.90       188.15        62.20        10.52        11.18         6.58 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J 
       19.82        27.22         9.93         0.72        10.72        26.17 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C4 
       38.27        65.46        22.62        36.82        15.95        16.83 
TCGA-X6-A8C6 TCGA-X9-A971 TCGA-X9-A973 
       35.08        15.58        36.43 

$`DEL PEAK 16(9P21.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX 
       36.30        53.49        68.55        54.74        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T 
       10.32        36.03        32.71        33.53        42.54         5.26 
TCGA-DX-A23U TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
       76.41        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3U6 TCGA-DX-A3U9 TCGA-DX-A3UB 
       54.77        23.08        70.49        17.75        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       39.35        34.88        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       14.96        72.72        15.95        11.47        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6Z2 
       17.79        21.63        67.20        23.54        50.50        88.31 
TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
       48.36       135.48        48.20        14.07         7.04        17.95 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       59.87        33.07        44.68        27.95        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
       60.66         4.67        12.39        86.10         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B 
       96.89        50.40        19.20        60.00        84.66        50.89 
TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       71.31         0.10        20.32         0.07         2.07        34.88 
TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
        4.57        15.91        12.62        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       80.48        21.37         1.38        19.89        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE 
       40.08        28.21       116.88        13.58        73.28        16.41 
TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT 
        1.05         3.91        71.70        36.39       123.78         9.04 
TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J 
        4.08        22.03         0.49         4.34        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DP 
       15.65         7.46       120.20        37.55         6.35        18.08 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
        9.83         1.84        46.82        30.90       130.32        98.27 
TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-UE-A6QT 
        0.72        18.94         3.88        17.92         5.06        13.22 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WP-A9GB TCGA-X2-A95T 
       11.93         4.80        72.72        41.49         9.04        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 
       26.43        29.92        18.08        18.35        25.71        38.96 
TCGA-X6-A8C7 
       17.72 

  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                       188.15                        135.48 
  DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE 
                        20.05                         25.25 
[1] "0.1 - 188.2 (20.1)" "0.1 - 135.5 (25.2)"
[1] "hr=" "1.5"
D41V2, continuous
D41V3, binary
                               cls
clus                             0  1
  DEL PEAK 16(9P21.3) MUTATED   62 50
  DEL PEAK 16(9P21.3) WILD-TYPE 70 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED     62   50
  DEL PEAK 16(9P21.3) WILD-TYPE   70   64
        clus
vv       DEL PEAK 16(9P21.3) MUTATED DEL PEAK 16(9P21.3) WILD-TYPE
  FEMALE                          62                            70
  MALE                            50                            64
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(9P21.3) MUTATED       4                         7    87
  DEL PEAK 16(9P21.3) WILD-TYPE     2                        11   107
D41V4, multiclass
                           clus
vv                          DEL PEAK 16(9P21.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                              87
                           clus
vv                          DEL PEAK 16(9P21.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            11
  WHITE                                               107
[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"
D41V5, binary
                               cls
clus                              0   1
  DEL PEAK 16(9P21.3) MUTATED     2  84
  DEL PEAK 16(9P21.3) WILD-TYPE   3 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(9P21.3) MUTATED      2   84
  DEL PEAK 16(9P21.3) WILD-TYPE    3  107
                        clus
vv                       DEL PEAK 16(9P21.3) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          84
                        clus
vv                       DEL PEAK 16(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           107
[1] 2 2
[1] FALSE

Clustering(42) Variable = DEL PEAK 17(9Q34.3) MUTATION ANALYSIS
D42V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 17(9Q34.3) MUTATED    36  24
  DEL PEAK 17(9Q34.3) WILD-TYPE 126  58
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           60                           184 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                           24                            58 
$`DEL PEAK 17(9Q34.3) MUTATED`
TCGA-3B-A9HR TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A3M1 
       88.57        18.64        26.56         0.56        14.04        20.05 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 
       39.35        28.80         9.73        26.47        25.08        15.95 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX 
        3.06        34.55        66.31        67.20        23.54        16.87 
TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-AB2E TCGA-DX-AB2W 
       64.21        48.36        27.95        36.69        12.99       106.45 
TCGA-DX-AB32 TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HS-A5N7 
      101.98        20.32         0.07        48.30         4.57        23.97 
TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-IS-A3KA 
        0.10         9.80        80.48        21.37        25.22        13.58 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A42W TCGA-K1-A42X 
        5.92        16.41         1.05         3.91        27.29       123.78 
TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R 
        4.08        13.35         8.32        19.73        14.99        10.45 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-SI-A71Q TCGA-VT-A80G 
        6.35        81.01        20.94       188.15        27.22        10.72 
TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X9-A971 
       38.27         9.04        29.92        18.08        25.71        15.58 

$`DEL PEAK 17(9Q34.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KW 
       25.25        42.84        10.32        31.00        36.03        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       38.24        12.85        36.69        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY 
       54.77         9.04        23.08        70.49       108.13        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 
       34.68        15.06        17.75        42.77         4.54        14.99 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       10.68        44.45        34.88        64.18        19.30        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B9 
       12.26        27.22        14.96        72.72        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.18        50.50        74.10        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       75.32        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL 
        7.04        17.95        14.43         9.34        59.87        33.07 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT 
       44.68        38.17        35.77        14.07       124.37        35.54 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2G 
       60.66        19.43         6.58         1.15         8.75         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S 
       12.39        40.60        86.10        12.07        49.18         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 
       71.57        96.89        13.28        50.40        22.85        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A43Z 
        0.10         0.07         0.07         2.07        34.88        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ 
       12.62        41.33        19.53         3.22         1.38        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       37.12        40.08        28.21       143.41       116.88        73.28 
TCGA-IW-A3M6 TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W 
       22.62        71.70        36.39         9.04        10.85        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 
       22.03         8.28         0.49         4.34        17.98        15.65 
TCGA-MO-A47P TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP 
        7.46         4.08       120.20        37.55        38.63        18.08 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH 
       35.90        30.90       130.32        98.27        62.20        10.52 
TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
        0.72        11.18        18.94         3.88         6.58        17.92 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J 
       19.82         5.06         9.93        13.22         0.72        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        72.72        41.49        65.46        22.62 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 
       57.80        26.43        36.82        18.35        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A973 
       38.96        35.08        17.72        36.43 

  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                       188.15                        143.41 
  DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE 
                       20.630                        24.705 
[1] "0.1 - 188.2 (20.6)" "0.1 - 143.4 (24.7)"
[1] "hr=" "1.4"
D42V2, continuous
D42V3, binary
                               cls
clus                             0  1
  DEL PEAK 17(9Q34.3) MUTATED   35 25
  DEL PEAK 17(9Q34.3) WILD-TYPE 97 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.3) MUTATED     35   25
  DEL PEAK 17(9Q34.3) WILD-TYPE   97   89
        clus
vv       DEL PEAK 17(9Q34.3) MUTATED DEL PEAK 17(9Q34.3) WILD-TYPE
  FEMALE                          35                            97
  MALE                            25                            89
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(9Q34.3) MUTATED       1                         9    44
  DEL PEAK 17(9Q34.3) WILD-TYPE     5                         9   150
D42V4, multiclass
                           clus
vv                          DEL PEAK 17(9Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           9
  WHITE                                              44
                           clus
vv                          DEL PEAK 17(9Q34.3) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                             9
  WHITE                                               150
[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"
D42V5, binary
                               cls
clus                              0   1
  DEL PEAK 17(9Q34.3) MUTATED     1  44
  DEL PEAK 17(9Q34.3) WILD-TYPE   4 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 17(9Q34.3) MUTATED      1   44
  DEL PEAK 17(9Q34.3) WILD-TYPE    4  147
                        clus
vv                       DEL PEAK 17(9Q34.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          44
                        clus
vv                       DEL PEAK 17(9Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                           147
[1] 2 2
[1] FALSE

Clustering(43) Variable = DEL PEAK 18(10P15.3) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(10P15.3) MUTATED   84 38
  DEL PEAK 18(10P15.3) WILD-TYPE 78 44
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                           122                            122 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                            38                             44 
$`DEL PEAK 18(10P15.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HY 
       19.69        53.49        68.55        88.57        44.91        10.32 
TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 
       36.03        26.56        32.71        38.24        18.54        59.24 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3UA 
       74.66         6.28       108.13        17.10        15.06        10.68 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48P 
       28.80        34.88        64.18        19.30        12.26        14.96 
TCGA-DX-A48R TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       26.47        25.15        15.95        11.47        66.05        23.44 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YX 
       16.18         3.06        34.55        66.31        23.54        16.87 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET 
       64.21        88.31        75.32        48.36        15.62         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO TCGA-DX-A8BS 
       17.95        14.43         9.34        44.68        35.77        27.95 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2P 
       35.54        60.66         6.58         8.75        86.10        12.07 
TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB3C TCGA-FX-A2QS 
       96.89        50.40        22.85       101.98        71.31         0.46 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        0.07        20.32        48.30         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A6BZ 
       23.97         0.10        80.48        19.53         3.22        19.89 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
       25.22        40.08       143.41         5.92        22.62        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
        3.91        71.70        27.29        10.85         4.08        11.70 
TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA 
        8.32         0.49        19.73        14.99        10.45         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 
      120.20        37.55         6.35        81.01        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        9.83        46.82        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VH TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q 
       10.52         3.88         6.58        17.92        19.82        27.22 
TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XS 
        5.06         9.93         0.72        10.72        11.93        72.72 
TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
        9.04        36.82        18.35        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X9-A971 
       35.08        15.58 

$`DEL PEAK 18(10P15.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I1 
       36.30        54.74        25.25        42.84        31.00        18.64 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        0.56        14.04        12.85        36.69        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49        20.05        34.68        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48O 
       14.99        44.45        39.35         9.73        24.26        27.22 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       72.72        25.08        28.96         9.11        17.79        21.63 
TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EO 
       67.20        50.50        74.10        21.30        34.49       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN 
       29.49        48.20        14.07        59.87        33.07        38.17 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E 
       14.07       124.37        36.69        19.43         1.15        12.99 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        12.39        40.60        49.18         9.21        71.57 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
      106.45        13.28        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-FX-A3NJ TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
       50.89         0.10         0.07         0.07         2.07        34.88 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 
       41.33         9.80        21.37         1.38        37.12        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42X 
      116.88        13.58        73.28         1.05        36.39       123.78 
TCGA-K1-A6RT TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A8JK TCGA-MJ-A68J 
        9.04        22.03        13.35         8.28         4.34        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       15.65         7.46        38.63        18.08         1.84        18.08 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32        98.27        62.20         0.72        11.18        18.94 
TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY 
       13.22        26.17         4.80        41.49        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C2 
       22.62        57.80        26.43        29.92        18.08        25.71 
TCGA-X6-A8C7 TCGA-X9-A973 
       17.72        36.43 

  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        188.15                         135.48 
  DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE 
                        19.855                         26.300 
[1] "0.1 - 188.2 (19.9)" "0.1 - 135.5 (26.3)"
[1] "hr=" "1.1"
D43V2, continuous
D43V3, binary
                                cls
clus                              0  1
  DEL PEAK 18(10P15.3) MUTATED   72 51
  DEL PEAK 18(10P15.3) WILD-TYPE 60 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED     72   51
  DEL PEAK 18(10P15.3) WILD-TYPE   60   63
        clus
vv       DEL PEAK 18(10P15.3) MUTATED DEL PEAK 18(10P15.3) WILD-TYPE
  FEMALE                           72                             60
  MALE                             51                             63
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10P15.3) MUTATED       4                        12    97
  DEL PEAK 18(10P15.3) WILD-TYPE     2                         6    97
D43V4, multiclass
                           clus
vv                          DEL PEAK 18(10P15.3) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                               97
                           clus
vv                          DEL PEAK 18(10P15.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 97
[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"
D43V5, binary
                                cls
clus                               0   1
  DEL PEAK 18(10P15.3) MUTATED     1 102
  DEL PEAK 18(10P15.3) WILD-TYPE   4  89
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10P15.3) MUTATED      1  102
  DEL PEAK 18(10P15.3) WILD-TYPE    4   89
                        clus
vv                       DEL PEAK 18(10P15.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          102
                        clus
vv                       DEL PEAK 18(10P15.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             89
[1] 2 2
[1] FALSE

Clustering(44) Variable = DEL PEAK 19(10Q23.31) MUTATION ANALYSIS
D44V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 19(10Q23.31) MUTATED   86 46
  DEL PEAK 19(10Q23.31) WILD-TYPE 76 36
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                            132                             112 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                             46                              36 
$`DEL PEAK 19(10Q23.31) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU 
       19.69        53.49        68.55        88.57        44.91        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A1KZ 
       10.32        31.00        36.03        26.56        38.24        36.69 
TCGA-DX-A1L0 TCGA-DX-A23Y TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC 
       18.54         6.28        42.77        14.99        10.68        39.35 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L 
       28.80        34.88        64.18         9.73        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 
       27.22        14.96        26.47        72.72        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ 
       11.47        66.05        23.44         9.11        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 
       34.55        23.54        16.87        74.10        64.21        88.31 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ 
       75.32        48.36         7.04        17.95        14.43         9.34 
TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       35.77       124.37        27.95        35.54        36.69        60.66 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2P 
        6.58         1.15        12.99         8.75        86.10        12.07 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       71.57        96.89         0.10         0.07        20.32         0.07 
TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
       48.30         4.57        15.91        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       41.33        80.48        21.37        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3KA 
       19.89        25.22        40.08        28.21       143.41        13.58 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W 
       22.62        16.41         1.05         3.91        71.70        27.29 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5YA 
       10.85         4.08        11.70        13.35         8.32         0.49 
TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM 
        4.34        14.99        10.45         4.08        37.55         6.35 
TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 
       81.01        18.08        20.94         5.03         9.83        46.82 
TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ 
       48.59        35.90        30.90       188.15        10.52        11.18 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XQ 
       18.94         6.58        17.92         5.06        10.72         4.80 
TCGA-WK-A8XS TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       72.72        65.46        22.62        26.43        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X9-A971 
       36.82        18.35        25.71        38.96        35.08        15.58 

$`DEL PEAK 19(10Q23.31) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU 
       36.30        54.74        42.84        18.64         0.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       32.71        12.85        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT 
        8.58         9.70        59.47        54.77         9.04        23.08 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       70.49       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6BE 
       17.75         4.54        44.45        12.26        25.08        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A7EF 
       17.79        21.63        66.31        67.20        50.50        21.30 
TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BX 
       59.87        33.07        44.68        38.17        14.07        19.43 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W 
        4.67        12.39        40.60        49.18         9.21       106.45 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 
       13.28        50.40        22.85       101.98        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A76Y 
       84.66        32.15        50.89        71.31         0.46         0.07 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IF-A3RQ TCGA-IS-A3K8 TCGA-IW-A3M4 
        2.07        34.88         9.80        37.12       116.88        73.28 
TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-LI-A67I TCGA-MB-A5Y9 
        5.92        36.39       123.78         9.04        22.03         8.28 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN 
       19.73        17.98        15.65         7.46       120.20        38.63 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
        1.84        18.08       130.32        98.27        62.20         0.72 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        3.88        19.82        27.22         9.93        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X2-A95T 
       26.17        11.93        41.49        38.27         9.04        57.80 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        16.83        17.72        36.43 

  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         188.15                          135.48 
  DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE 
                         21.155                          27.515 
[1] "0.1 - 188.2 (21.2)" "0.1 - 135.5 (27.5)"
[1] "hr=" "1.3"
D44V2, continuous
D44V3, binary
                                 cls
clus                               0  1
  DEL PEAK 19(10Q23.31) MUTATED   76 57
  DEL PEAK 19(10Q23.31) WILD-TYPE 56 57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED     76   57
  DEL PEAK 19(10Q23.31) WILD-TYPE   56   57
        clus
vv       DEL PEAK 19(10Q23.31) MUTATED DEL PEAK 19(10Q23.31) WILD-TYPE
  FEMALE                            76                              56
  MALE                              57                              57
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(10Q23.31) MUTATED       2                        15   107
  DEL PEAK 19(10Q23.31) WILD-TYPE     4                         3    87
D44V4, multiclass
                           clus
vv                          DEL PEAK 19(10Q23.31) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            15
  WHITE                                               107
                           clus
vv                          DEL PEAK 19(10Q23.31) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                               3
  WHITE                                                  87
[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"
D44V5, binary
                                 cls
clus                                0   1
  DEL PEAK 19(10Q23.31) MUTATED     1 113
  DEL PEAK 19(10Q23.31) WILD-TYPE   4  78
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 19(10Q23.31) MUTATED      1  113
  DEL PEAK 19(10Q23.31) WILD-TYPE    4   78
                        clus
vv                       DEL PEAK 19(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                           113
                        clus
vv                       DEL PEAK 19(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                              78
[1] 2 2
[1] FALSE

Clustering(45) Variable = DEL PEAK 20(10Q26.3) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 20(10Q26.3) MUTATED   86 41
  DEL PEAK 20(10Q26.3) WILD-TYPE 76 41
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                           127                            117 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                            41                             41 
$`DEL PEAK 20(10Q26.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HY 
       19.69        53.49        68.55        44.91        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1KX 
       31.00        36.03        18.64        26.56        32.71        38.24 
TCGA-DX-A1KZ TCGA-DX-A3LY TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC 
       36.69        17.10        42.77        14.99        10.68        39.35 
TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P 
       28.80        64.18        19.30        24.26        27.22        14.96 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       26.47        72.72        25.08        25.15        15.95        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
       66.05        23.44         9.11        16.18         3.06        34.55 
TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM 
       23.54        16.87        74.10        88.31        75.32        48.36 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BS 
        7.04        17.95        14.43         9.34        35.77        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O 
       36.69        60.66         6.58        12.99         8.75        86.10 
TCGA-DX-AB2P TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-FX-A3NJ TCGA-FX-A3RE 
       12.07        71.57        96.89        50.40         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
       20.32         0.07        48.30         4.57        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EK 
       23.97         0.10        41.33        80.48        21.37         1.38 
TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3KA 
       19.89        25.22        40.08        28.21       143.41        13.58 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
        5.92        22.62        16.41         1.05         3.91        71.70 
TCGA-K1-A42W TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 
       27.29        10.85         4.08        11.70        13.35         8.32 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL 
        0.49         4.34        14.99        10.45         4.08        37.55 
TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
        6.35        81.01        18.08        20.94         5.03         9.83 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VF TCGA-RN-AAAQ 
       46.82        48.59        30.90       188.15        98.27        11.18 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B TCGA-VT-A80G TCGA-WK-A8XY 
       18.94         6.58        17.92         5.06        10.72        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC 
       22.62         9.04        26.43        29.92        18.08        36.82 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.35        25.71        15.95        16.83        38.96        35.08 
TCGA-X9-A971 
       15.58 

$`DEL PEAK 20(10Q26.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3R-A8YX TCGA-DX-A1KU 
       36.30        88.57        54.74        42.84         0.56        14.04 
TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        18.54        54.21        59.24        33.53        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       74.66         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       23.08        70.49       108.13        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N 
       17.75         4.54        44.45        34.88         9.73        12.26 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV 
       28.96        17.79        21.63        66.31        67.20        50.50 
TCGA-DX-A6Z0 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       64.21        21.30        34.49        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       48.20        14.07        59.87        33.07        44.68        38.17 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2G 
       14.07       124.37        35.54        19.43         1.15         4.67 
TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X 
       12.39        40.60        49.18         9.21       106.45        13.28 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       22.85       101.98        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A48G TCGA-FX-A8OO TCGA-HB-A3L4 
       50.89        71.31         0.46         0.07         2.07        34.88 
TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IF-A3RQ TCGA-IS-A3K8 TCGA-IW-A3M4 
        9.80        19.53         3.22        37.12       116.88        73.28 
TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A8JL 
       36.39       123.78         9.04        22.03         8.28        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 
       17.98        15.65         7.46       120.20        38.63         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q 
       18.08        35.90       130.32        62.20        10.52         0.72 
TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        3.88        19.82        27.22         9.93        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       26.17        11.93         4.80        72.72        41.49        38.27 
TCGA-X2-A95T TCGA-X6-A8C7 TCGA-X9-A973 
       57.80        17.72        36.43 

  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                        188.15                         135.48 
  DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE 
                         20.94                          28.96 
[1] "0.1 - 188.2 (20.9)" "0.1 - 135.5 (29.0)"
[1] "hr=" "1.2"
D45V2, continuous
D45V3, binary
                                cls
clus                              0  1
  DEL PEAK 20(10Q26.3) MUTATED   72 56
  DEL PEAK 20(10Q26.3) WILD-TYPE 60 58
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED     72   56
  DEL PEAK 20(10Q26.3) WILD-TYPE   60   58
        clus
vv       DEL PEAK 20(10Q26.3) MUTATED DEL PEAK 20(10Q26.3) WILD-TYPE
  FEMALE                           72                             60
  MALE                             56                             58
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(10Q26.3) MUTATED       3                        14   103
  DEL PEAK 20(10Q26.3) WILD-TYPE     3                         4    91
D45V4, multiclass
                           clus
vv                          DEL PEAK 20(10Q26.3) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              103
                           clus
vv                          DEL PEAK 20(10Q26.3) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 91
[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"
D45V5, binary
                                cls
clus                               0   1
  DEL PEAK 20(10Q26.3) MUTATED     1 110
  DEL PEAK 20(10Q26.3) WILD-TYPE   4  81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(10Q26.3) MUTATED      1  110
  DEL PEAK 20(10Q26.3) WILD-TYPE    4   81
                        clus
vv                       DEL PEAK 20(10Q26.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                          110
                        clus
vv                       DEL PEAK 20(10Q26.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             81
[1] 2 2
[1] FALSE

Clustering(46) Variable = DEL PEAK 21(11P15.5) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(11P15.5) MUTATED   67 36
  DEL PEAK 21(11P15.5) WILD-TYPE 95 46
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                           103                            141 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                            36                             46 
$`DEL PEAK 21(11P15.5) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KU 
       19.69        44.91        42.84        36.03        18.64        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A23Y TCGA-DX-A2J0 
       32.71        38.24        36.69        59.24         6.28         9.70 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 
        9.04        23.08       108.13        17.10        20.05        15.06 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L 
       42.77        14.99        28.80        34.88        64.18        24.26 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A6B8 TCGA-DX-A6YQ TCGA-DX-A6YS 
       12.26        27.22        14.96        15.95         3.06        66.31 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7EN 
       67.20        23.54        74.10        34.49        48.36        15.62 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
       17.95        14.43        59.87        33.07        44.68        35.77 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-AB2F TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V 
       36.69        60.66         8.75        49.18        71.57        96.89 
TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A3RE TCGA-FX-A3TO 
       19.20        60.00        32.15        50.89         0.07        20.32 
TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 
        0.07        48.30         4.57        15.91        12.62        23.97 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IF-A4AK 
        0.10        41.33        19.53        19.89        25.22        40.08 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU 
        5.92        22.62         1.05        71.70        27.29        10.85 
TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO 
        4.08        13.35         8.32        37.55         6.35        81.01 
TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       35.90       188.15        10.52        18.94         3.88        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       19.82        27.22         5.06         9.93         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 
       26.17        38.27        65.46        22.62         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       29.92        18.08        36.82        16.83        38.96        35.08 
TCGA-X9-A971 
       15.58 

$`DEL PEAK 21(11P15.5) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        88.57        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KY TCGA-DX-A1L0 
       10.32        31.00        26.56         0.56        12.85        18.54 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U 
       54.21        33.53        42.54        74.66         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81        60.30         8.58        59.47        54.77 
TCGA-DX-A3LU TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       70.49        34.68        17.75         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       39.35         9.73        19.30        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       25.15        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YV TCGA-DX-A6YX 
       17.79        21.63        16.18        34.55        50.50        16.87 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ 
       64.21        88.31        21.30        75.32       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BP 
       48.20        14.07         7.04         9.34        38.17        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
      124.37        27.95        35.54        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P 
       12.99         4.67        12.39        40.60        86.10        12.07 
TCGA-DX-AB2S TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
        9.21       106.45        13.28        50.40        22.85       101.98 
TCGA-DX-AB37 TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO 
       84.66        71.31         0.46         0.10         0.07         2.07 
TCGA-HB-A3L4 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A4EK 
       34.88         9.80        80.48        21.37         3.22         1.38 
TCGA-IF-A3RQ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       37.12        28.21       143.41       116.88        13.58        73.28 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-KF-A41W 
       16.41         3.91        36.39       123.78         9.04        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       22.03         8.28         0.49         4.34        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        18.08        20.94         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF 
       46.82        18.08        48.59        30.90       130.32        98.27 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A849 TCGA-UE-A6QT TCGA-WK-A8XO 
       62.20         0.72        11.18         6.58        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-X2-A95T TCGA-X6-A7WD TCGA-X6-A8C2 
        4.80        72.72        41.49        57.80        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        17.72        36.43 

  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                        188.15                         143.41 
  DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE 
                         23.54                          22.85 
[1] "0.1 - 188.2 (23.5)" "0.1 - 143.4 (22.9)"
[1] "hr=" "1.2"
D46V2, continuous
D46V3, binary
                                cls
clus                              0  1
  DEL PEAK 21(11P15.5) MUTATED   58 46
  DEL PEAK 21(11P15.5) WILD-TYPE 74 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED     58   46
  DEL PEAK 21(11P15.5) WILD-TYPE   74   68
        clus
vv       DEL PEAK 21(11P15.5) MUTATED DEL PEAK 21(11P15.5) WILD-TYPE
  FEMALE                           58                             74
  MALE                             46                             68
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(11P15.5) MUTATED       2                         6    86
  DEL PEAK 21(11P15.5) WILD-TYPE     4                        12   108
D46V4, multiclass
                           clus
vv                          DEL PEAK 21(11P15.5) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               86
                           clus
vv                          DEL PEAK 21(11P15.5) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                108
[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"
D46V5, binary
                                cls
clus                               0   1
  DEL PEAK 21(11P15.5) MUTATED     1  88
  DEL PEAK 21(11P15.5) WILD-TYPE   4 103
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(11P15.5) MUTATED      1   88
  DEL PEAK 21(11P15.5) WILD-TYPE    4  103
                        clus
vv                       DEL PEAK 21(11P15.5) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           88
                        clus
vv                       DEL PEAK 21(11P15.5) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            103
[1] 2 2
[1] FALSE

Clustering(47) Variable = DEL PEAK 22(11Q24.2) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(11Q24.2) MUTATED   80 38
  DEL PEAK 22(11Q24.2) WILD-TYPE 82 44
  DEL PEAK 22(11Q24.2) MUTATED DEL PEAK 22(11Q24.2) WILD-TYPE 
                           118                            126 
  DEL PEAK 22(11Q24.2) MUTATED DEL PEAK 22(11Q24.2) WILD-TYPE 
                            38                             44 
$`DEL PEAK 22(11Q24.2) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ 
       19.69        88.57        44.91        25.25        42.84        31.00 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       26.56         0.56        32.71        38.24        12.85        36.69 
TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23Y TCGA-DX-A2J0 
       18.54        59.24        74.66         5.26         6.28         9.70 
TCGA-DX-A2J1 TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       59.47        23.08        17.10        20.05        34.68        15.06 
TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       42.77        14.99        28.80        19.30        12.26        27.22 
TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ 
       26.47        72.72        66.05         9.11        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EI 
       34.55        66.31        23.54        74.10        64.21        34.49 
TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
       48.36         7.04        17.95        33.07        44.68        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV 
       35.77        14.07        27.95        35.54        36.69        60.66 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T 
        8.75         4.67        86.10        12.07        49.18        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3B 
       96.89       106.45       101.98        19.20        84.66        50.89 
TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N9 
        0.46        20.32        48.30         4.57        12.62        41.33 
TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3KA 
       80.48         3.22        19.89        37.12        40.08        13.58 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RU 
        5.92        22.62         1.05        27.29       123.78        10.85 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
        4.08        11.70        22.03        13.35         8.32         8.28 
TCGA-MB-A8JK TCGA-MO-A47R TCGA-PC-A5DM TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A5VB 
        4.34        10.45         6.35         9.83        18.08        48.59 
TCGA-QQ-A8VB TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
      188.15        11.18        18.94         3.88        17.92        19.82 
TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX 
       27.22         5.06         9.93        10.72        72.72        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WC TCGA-X6-A8C2 
       65.46        22.62         9.04        26.43        36.82        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X9-A971 
       15.95        16.83        35.08        15.58 

$`DEL PEAK 22(11Q24.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HT TCGA-3B-A9HY TCGA-3B-A9I0 
       36.30        53.49        68.55        54.74        10.32        36.03 
TCGA-3B-A9I1 TCGA-DX-A1KU TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23U 
       18.64        14.04        54.21        33.53        42.54        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J4 TCGA-DX-A3LS 
       66.87        27.81        60.30         8.58        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       70.49       108.13        17.75         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48P 
       39.35        34.88        64.18         9.73        24.26        14.96 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        15.95        11.47        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z2 
       17.79        21.63        67.20        50.50        16.87        88.31 
TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        75.32        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BR TCGA-DX-A8BX 
       14.07        14.43         9.34        59.87       124.37        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2S 
        6.58         1.15        12.99        12.39        40.60         9.21 
TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A TCGA-DX-AB3C 
       13.28        50.40        22.85        60.00        32.15        71.31 
TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 
        0.10         0.07         0.07         0.07         2.07        34.88 
TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
       15.91        23.97         0.10         9.80        21.37        19.53 
TCGA-IE-A4EK TCGA-IF-A4AJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
        1.38        25.22        28.21       143.41       116.88        73.28 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A6RT TCGA-MB-A5YA 
       16.41         3.91        71.70        36.39         9.04         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-N1-A6IA 
       19.73        14.99        17.98        15.65         7.46         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
      120.20        37.55        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
        5.03         1.84        46.82        35.90        30.90       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-UE-A6QT 
       98.27        62.20        10.52         0.72         6.58        13.22 
TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X2-A95T 
        0.72        26.17        11.93         4.80        41.49        57.80 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       29.92        18.08        18.35        38.96        17.72        36.43 

  DEL PEAK 22(11Q24.2) MUTATED DEL PEAK 22(11Q24.2) WILD-TYPE 
                          0.46                           0.07 
  DEL PEAK 22(11Q24.2) MUTATED DEL PEAK 22(11Q24.2) WILD-TYPE 
                        188.15                         143.41 
  DEL PEAK 22(11Q24.2) MUTATED DEL PEAK 22(11Q24.2) WILD-TYPE 
                        23.310                         23.145 
[1] "0.5 - 188.2 (23.3)" "0.1 - 143.4 (23.1)"
[1] "hr=" "1.1"
D47V2, continuous
D47V3, binary
                                cls
clus                              0  1
  DEL PEAK 22(11Q24.2) MUTATED   61 57
  DEL PEAK 22(11Q24.2) WILD-TYPE 71 57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q24.2) MUTATED     61   57
  DEL PEAK 22(11Q24.2) WILD-TYPE   71   57
        clus
vv       DEL PEAK 22(11Q24.2) MUTATED DEL PEAK 22(11Q24.2) WILD-TYPE
  FEMALE                           61                             71
  MALE                             57                             57
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(11Q24.2) MUTATED       3                         9    92
  DEL PEAK 22(11Q24.2) WILD-TYPE     3                         9   102
D47V4, multiclass
                           clus
vv                          DEL PEAK 22(11Q24.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                               92
                           clus
vv                          DEL PEAK 22(11Q24.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              9
  WHITE                                                102
[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"
D47V5, binary
                                cls
clus                              0  1
  DEL PEAK 22(11Q24.2) MUTATED    1 92
  DEL PEAK 22(11Q24.2) WILD-TYPE  4 99
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(11Q24.2) MUTATED      1   92
  DEL PEAK 22(11Q24.2) WILD-TYPE    4   99
                        clus
vv                       DEL PEAK 22(11Q24.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           92
                        clus
vv                       DEL PEAK 22(11Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                             99
[1] 2 2
[1] FALSE

Clustering(48) Variable = DEL PEAK 23(12P13.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 23(12P13.1) MUTATED    52  30
  DEL PEAK 23(12P13.1) WILD-TYPE 110  52
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                            82                            162 
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                            30                             52 
$`DEL PEAK 23(12P13.1) MUTATED`
TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 
       18.64        26.56         0.56        32.71        38.24        18.54 
TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LW 
       54.21        74.66         6.28         9.70        23.08       108.13 
TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UD 
       17.10        34.68        15.06        42.77        14.99        28.80 
TCGA-DX-A48N TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6BK TCGA-DX-A6YQ 
       12.26        25.08        25.15        15.95        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF 
       34.55        67.20        23.54        74.10        88.31        21.30 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       48.36        15.62         7.04        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV 
       38.17        35.77       124.37        27.95        36.69        60.66 
TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2H TCGA-DX-AB2T TCGA-DX-AB2Z 
       19.43         6.58         1.15        12.39        71.57        50.40 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-HB-A3L4 TCGA-HS-A5N7 
      101.98        19.20         0.10        20.32        34.88        23.97 
TCGA-HS-A5N9 TCGA-IE-A6BZ TCGA-IS-A3K6 TCGA-JV-A5VF TCGA-K1-A6RV TCGA-KF-A41W 
       41.33        19.89        28.21         1.05         4.08        11.70 
TCGA-LI-A9QH TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 
       13.35        14.99         6.35        81.01        20.94         5.03 
TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-QQ-A8VH 
       46.82        48.59        35.90        30.90        98.27        10.52 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-UE-A6QU TCGA-WK-A8XS TCGA-WK-A8XX 
       18.94         3.88        17.92         0.72        72.72        38.27 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C6 
       57.80        26.43        18.35        35.08 

$`DEL PEAK 23(12P13.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       54.74        25.25        42.84        10.32        31.00        36.03 
TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       14.04        12.85        36.69        59.24        33.53        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3M1 TCGA-DX-A3U6 
       59.47        54.77         9.04        70.49        20.05        17.75 
TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF 
        4.54        10.68        44.45        39.35        34.88        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        24.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       72.72        11.47        66.05        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6Z0 
       17.79        21.63        66.31        50.50        16.87        64.21 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       34.49        75.32       135.48        29.49        48.20        14.07 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BP TCGA-DX-A8BT TCGA-DX-AB2E 
       17.95        14.43         9.34        14.07        35.54        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q 
        8.75         4.67        40.60        86.10        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB36 
        9.21        96.89       106.45        13.28        22.85        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE 
       84.66        32.15        50.89        71.31         0.46         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         0.07         2.07        48.30         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI 
       12.62         0.10         9.80        80.48        21.37        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 
        3.22         1.38        37.12        25.22        40.08       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
      116.88        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT 
        3.91        71.70        36.39        27.29       123.78         9.04 
TCGA-K1-A6RU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
       10.85        22.03         8.32         8.28         0.49         4.34 
TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA 
       19.73        17.98        15.65         7.46        10.45         4.08 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5V2 
      120.20        37.55        38.63        18.08         9.83         1.84 
TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-QQ-A8VD TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
       18.08       188.15       130.32        62.20         0.72        11.18 
TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QT 
        6.58        19.82        27.22         5.06         9.93        13.22 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XY 
       10.72        26.17        11.93         4.80        41.49        65.46 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
       22.62         9.04        29.92        18.08        36.82        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       15.95        16.83        38.96        17.72        15.58        36.43 

  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                        124.37                         188.15 
  DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE 
                        25.115                         22.325 
[1] "0.1 - 124.4 (25.1)" "0.1 - 188.2 (22.3)"
[1] "hr=" "1.1"
D48V2, continuous
D48V3, binary
                                cls
clus                              0  1
  DEL PEAK 23(12P13.1) MUTATED   37 47
  DEL PEAK 23(12P13.1) WILD-TYPE 95 67
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(12P13.1) MUTATED     37   47
  DEL PEAK 23(12P13.1) WILD-TYPE   95   67
        clus
vv       DEL PEAK 23(12P13.1) MUTATED DEL PEAK 23(12P13.1) WILD-TYPE
  FEMALE                           37                             95
  MALE                             47                             67
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(12P13.1) MUTATED       1                         7    65
  DEL PEAK 23(12P13.1) WILD-TYPE     5                        11   129
D48V4, multiclass
                           clus
vv                          DEL PEAK 23(12P13.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               65
                           clus
vv                          DEL PEAK 23(12P13.1) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                129
[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"
D48V5, binary
                                cls
clus                               0   1
  DEL PEAK 23(12P13.1) MUTATED     1  66
  DEL PEAK 23(12P13.1) WILD-TYPE   4 125
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(12P13.1) MUTATED      1   66
  DEL PEAK 23(12P13.1) WILD-TYPE    4  125
                        clus
vv                       DEL PEAK 23(12P13.1) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           66
                        clus
vv                       DEL PEAK 23(12P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            125
[1] 2 2
[1] FALSE

Clustering(49) Variable = DEL PEAK 24(12Q12) MUTATION ANALYSIS
D49V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 24(12Q12) MUTATED    30  23
  DEL PEAK 24(12Q12) WILD-TYPE 132  59
  DEL PEAK 24(12Q12) MUTATED DEL PEAK 24(12Q12) WILD-TYPE 
                          53                          191 
  DEL PEAK 24(12Q12) MUTATED DEL PEAK 24(12Q12) WILD-TYPE 
                          23                           59 
$`DEL PEAK 24(12Q12) MUTATED`
TCGA-3B-A9HU TCGA-3B-A9HZ TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1L1 
       25.25        31.00        18.64        26.56        32.71        54.21 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LY TCGA-DX-A3UC 
       74.66         6.28         8.58         9.70        17.10        39.35 
TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YX 
       64.18        26.47        15.95         9.11         3.06        16.87 
TCGA-DX-A7EF TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BN TCGA-DX-A8BS 
       21.30        48.36         7.04        14.43        38.17        27.95 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB35 TCGA-FX-A3NJ 
       36.69         6.58        86.10        12.07        19.20         0.10 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-JV-A5VF TCGA-K1-A6RU 
       12.62        23.97        21.37        25.22         1.05        10.85 
TCGA-KF-A41W TCGA-MB-A8JK TCGA-MJ-A68H TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N 
       11.70         4.34        14.99        81.01         5.03         9.83 
TCGA-QQ-A5V9 TCGA-SI-AA8B TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       46.82         5.06        26.17        72.72        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WD TCGA-X6-A8C6 TCGA-X9-A971 
       22.62        57.80        18.35        35.08        15.58 

$`DEL PEAK 24(12Q12) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KU 
       54.74        42.84        10.32        36.03         0.56        14.04 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L3 
       38.24        12.85        36.69        18.54        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW 
       59.47        54.77         9.04        23.08        70.49       108.13 
TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       20.05        34.68        15.06        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J 
       14.99        10.68        44.45        28.80        34.88         9.73 
TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U 
       19.30        24.26        12.26        27.22        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE 
       25.08        25.15        11.47        66.05        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       17.79        21.63        16.18        34.55        66.31        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       23.54        50.50        74.10        64.21        88.31        34.49 
TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       75.32        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BO 
       17.95         9.34        59.87        33.07        44.68        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       14.07       124.37        35.54        60.66        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q 
       12.99         8.75         4.67        12.39        40.60        49.18 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
        9.21        71.57        96.89       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85       101.98        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.46         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 
        2.07        48.30        34.88         4.57        15.91         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK 
       41.33         9.80        80.48        19.53         3.22         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
       19.89        37.12        40.08        28.21       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J 
       13.58        73.28         5.92        22.62        16.41         3.91 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV 
       71.70        36.39        27.29       123.78         9.04         4.08 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL 
       22.03        13.35         8.32         8.28         0.49        19.73 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A5V2 
       37.55         6.35        38.63        18.08        20.94         1.84 
TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VD 
       18.08        48.59        35.90        30.90       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
       98.27        62.20        10.52         0.72        11.18        18.94 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C 
        3.88         6.58        17.92        19.82        27.22         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
       13.22         0.72        10.72        11.93         4.80        41.49 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 
        9.04        26.43        29.92        18.08        36.82        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        16.83        38.96        17.72        36.43 

  DEL PEAK 24(12Q12) MUTATED DEL PEAK 24(12Q12) WILD-TYPE 
                        0.10                         0.07 
  DEL PEAK 24(12Q12) MUTATED DEL PEAK 24(12Q12) WILD-TYPE 
                       86.10                       188.15 
  DEL PEAK 24(12Q12) MUTATED DEL PEAK 24(12Q12) WILD-TYPE 
                       21.30                        24.26 
[1] "0.1 - 86.1 (21.3)"  "0.1 - 188.2 (24.3)"
[1] "hr=" "1.8"
D49V2, continuous
D49V3, binary
                              cls
clus                             0   1
  DEL PEAK 24(12Q12) MUTATED    30  23
  DEL PEAK 24(12Q12) WILD-TYPE 102  91
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(12Q12) MUTATED     30   23
  DEL PEAK 24(12Q12) WILD-TYPE  102   91
        clus
vv       DEL PEAK 24(12Q12) MUTATED DEL PEAK 24(12Q12) WILD-TYPE
  FEMALE                         30                          102
  MALE                           23                           91
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(12Q12) MUTATED       0                         8    36
  DEL PEAK 24(12Q12) WILD-TYPE     6                        10   158
D49V4, multiclass
                           clus
vv                          DEL PEAK 24(12Q12) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          8
  WHITE                                             36
                           clus
vv                          DEL PEAK 24(12Q12) WILD-TYPE
  ASIAN                                                6
  BLACK OR AFRICAN AMERICAN                           10
  WHITE                                              158
[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"
D49V5, binary
                              cls
clus                             0   1
  DEL PEAK 24(12Q12) MUTATED     0  41
  DEL PEAK 24(12Q12) WILD-TYPE   5 150
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 24(12Q12) MUTATED      0   41
  DEL PEAK 24(12Q12) WILD-TYPE    5  150
                        clus
vv                       DEL PEAK 24(12Q12) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         41
                        clus
vv                       DEL PEAK 24(12Q12) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                          150
[1] 2 2
[1] FALSE

Clustering(50) Variable = DEL PEAK 25(12Q24.33) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 25(12Q24.33) MUTATED    44  24
  DEL PEAK 25(12Q24.33) WILD-TYPE 118  58
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             68                             176 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                             24                              58 
$`DEL PEAK 25(12Q24.33) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I3 TCGA-DX-A1KW 
       19.69        88.57        31.00        36.03        26.56        32.71 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LY 
       74.66         6.28         8.58         9.70         9.04        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       34.68        14.99        28.80        64.18        19.30        24.26 
TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF TCGA-DX-A6YS TCGA-DX-A6YU 
       26.47        15.95        66.05         9.11        66.31        23.54 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BK 
       21.30        34.49        48.36         7.04        17.95        59.87 
TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BU TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2H 
       44.68        38.17        36.69         1.15        12.99        12.39 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2T TCGA-DX-AB35 TCGA-DX-AB3A TCGA-FX-A3NJ 
       86.10        12.07        71.57        19.20        32.15         0.10 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ 
       23.97         0.10        21.37         3.22        19.89        25.22 
TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A42W TCGA-KF-A41W TCGA-MB-A8JK TCGA-MJ-A68H 
        5.92         1.05        27.29        11.70         4.34        14.99 
TCGA-PC-A5DK TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VD 
      120.20         6.35        81.01         5.03        46.82        30.90 
TCGA-SG-A6Z7 TCGA-VT-A80G TCGA-WK-A8XS TCGA-WK-A8XX TCGA-X6-A7W8 TCGA-X6-A7WC 
        3.88        10.72        72.72        38.27        26.43        36.82 
TCGA-X6-A7WD TCGA-X9-A971 
       18.35        15.58 

$`DEL PEAK 25(12Q24.33) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX 
       42.84        10.32        18.64         0.56        14.04        38.24 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       12.85        36.69        18.54        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 
       59.47        54.77        23.08        70.49       108.13        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75        42.77         4.54        10.68        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P 
       39.35        34.88         9.73        12.26        27.22        14.96 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE 
       72.72        25.08        25.15        11.47        23.44        28.96 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YT 
       17.79        21.63        16.18         3.06        34.55        67.20 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL 
       50.50        16.87        74.10        64.21        88.31        75.32 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BH 
       15.62       135.48        29.49        48.20        14.07        14.43 
TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS 
        9.34        33.07        35.77        14.07       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AB2F TCGA-DX-AB2G 
       35.54        60.66        19.43         6.58         8.75         4.67 
TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X 
       40.60        49.18         9.21        96.89       106.45        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B 
       50.40        22.85       101.98        60.00        84.66        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.46         0.07        20.32         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HB-A5W3 
        2.07        48.30        34.88         4.57        15.91        12.62 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ 
       41.33         9.80        80.48        19.53         1.38        37.12 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       40.08        28.21       143.41       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X 
       22.62        16.41         3.91        71.70        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-K1-A6RV TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
        9.04        10.85         4.08        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        8.28         0.49        19.73        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX 
       10.45         4.08        37.55        38.63        18.08        20.94 
TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB 
        9.83         1.84        18.08        48.59        35.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32        98.27        62.20        10.52         0.72        11.18 
TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B 
       18.94         6.58        17.92        19.82        27.22         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
        9.93        13.22         0.72        26.17        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       41.49        65.46        22.62         9.04        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.08        25.71        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A973 
       17.72        36.43 

  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                           0.10                            0.07 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                         120.20                          188.15 
  DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE 
                         22.455                          23.260 
[1] "0.1 - 120.2 (22.5)" "0.1 - 188.2 (23.3)"
[1] "hr=" "1.2"
D50V2, continuous
D50V3, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED    31  37
  DEL PEAK 25(12Q24.33) WILD-TYPE 101  77
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED     31   37
  DEL PEAK 25(12Q24.33) WILD-TYPE  101   77
        clus
vv       DEL PEAK 25(12Q24.33) MUTATED DEL PEAK 25(12Q24.33) WILD-TYPE
  FEMALE                            31                             101
  MALE                              37                              77
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(12Q24.33) MUTATED       0                         5    56
  DEL PEAK 25(12Q24.33) WILD-TYPE     6                        13   138
D50V4, multiclass
                           clus
vv                          DEL PEAK 25(12Q24.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                56
                           clus
vv                          DEL PEAK 25(12Q24.33) WILD-TYPE
  ASIAN                                                   6
  BLACK OR AFRICAN AMERICAN                              13
  WHITE                                                 138
[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"
D50V5, binary
                                 cls
clus                                0   1
  DEL PEAK 25(12Q24.33) MUTATED     0  55
  DEL PEAK 25(12Q24.33) WILD-TYPE   5 136
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(12Q24.33) MUTATED      0   55
  DEL PEAK 25(12Q24.33) WILD-TYPE    5  136
                        clus
vv                       DEL PEAK 25(12Q24.33) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            55
                        clus
vv                       DEL PEAK 25(12Q24.33) WILD-TYPE
  HISPANIC OR LATINO                                   5
  NOT HISPANIC OR LATINO                             136
[1] 2 2
[1] FALSE

Clustering(51) Variable = DEL PEAK 26(13Q14.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(13Q14.2) MUTATED   116  57
  DEL PEAK 26(13Q14.2) WILD-TYPE  46  25
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                           173                             71 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                            57                             25 
$`DEL PEAK 26(13Q14.2) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       19.69        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        31.00        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 
        0.56        14.04        38.24        12.85        36.69        18.54 
TCGA-DX-A1L1 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LS TCGA-DX-A3LT 
       54.21        74.66         6.28         9.70         9.04        23.08 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UC TCGA-DX-A3UD 
       17.10        20.05        42.77        14.99        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       34.88        64.18         9.73        19.30        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       14.96        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR 
       66.05        23.44         9.11        16.18         3.06        34.55 
TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 
       66.31        67.20        23.54        16.87        74.10        64.21 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET 
       88.31        21.30        75.32        48.36        15.62         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN 
       17.95        14.43         9.34        59.87        33.07        38.17 
TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       35.77        14.07       124.37        27.95        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2P 
       60.66         1.15        12.99         8.75        86.10        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB32 
       49.18        71.57        96.89       106.45        50.40       101.98 
TCGA-DX-AB35 TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       19.20        50.89         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         0.07        48.30        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
       21.37        19.53         3.22         1.38        19.89        37.12 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 
       25.22        40.08        28.21       143.41        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W 
       22.62        16.41         1.05         3.91        71.70        27.29 
TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 
       10.85         4.08        11.70        13.35         8.32         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
        0.49         4.34        19.73        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
       37.55         6.35        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A8VB 
        9.83        46.82        18.08        48.59        35.90       188.15 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O 
       10.52        11.18        18.94         3.88         6.58        17.92 
TCGA-SI-A71P TCGA-SI-AA8B TCGA-SI-AA8C TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
       19.82         5.06         9.93        10.72        26.17        11.93 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T 
       72.72        38.27        65.46        22.62         9.04        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       26.43        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X9-A971 
       15.95        16.83        38.96        35.08        15.58 

$`DEL PEAK 26(13Q14.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-DX-A1KW TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 
       36.30        53.49        32.71        59.24        33.53        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ 
        5.26        76.41        66.87        27.81        60.30         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U5 
       59.47        54.77        70.49       108.13        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A48N TCGA-DX-A6B9 
       17.75         4.54        10.68        44.45        12.26        11.47 
TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YV TCGA-DX-A7EI TCGA-DX-A7EO 
       28.96        17.79        21.63        50.50        34.49       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BM TCGA-DX-A8BX TCGA-DX-A8BZ 
       29.49        48.20        14.07        44.68        19.43         6.58 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2X TCGA-DX-AB30 
        4.67        12.39        40.60         9.21        13.28        22.85 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3C TCGA-FX-A8OO TCGA-IS-A3K8 
       60.00        84.66        32.15        71.31         2.07       116.88 
TCGA-IW-A3M5 TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-LI-A67I TCGA-MJ-A68H 
        5.92        36.39       123.78         9.04        22.03        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VD 
       17.98        15.65         7.46        38.63         1.84        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SI-A71Q TCGA-UE-A6QT 
      130.32        98.27        62.20         0.72        27.22        13.22 
TCGA-UE-A6QU TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-X6-A8C7 TCGA-X9-A973 
        0.72         4.80        41.49        17.72        36.43 

  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                          0.07                           0.72 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                        188.15                         135.48 
  DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE 
                         21.37                          29.49 
[1] "0.1 - 188.2 (21.4)" "0.7 - 135.5 (29.5)"
[1] "hr=" "1.1"
D51V2, continuous
D51V3, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED   100  75
  DEL PEAK 26(13Q14.2) WILD-TYPE  32  39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED    100   75
  DEL PEAK 26(13Q14.2) WILD-TYPE   32   39
        clus
vv       DEL PEAK 26(13Q14.2) MUTATED DEL PEAK 26(13Q14.2) WILD-TYPE
  FEMALE                          100                             32
  MALE                             75                             39
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(13Q14.2) MUTATED       3                        13   144
  DEL PEAK 26(13Q14.2) WILD-TYPE     3                         5    50
D51V4, multiclass
                           clus
vv                          DEL PEAK 26(13Q14.2) MUTATED
  ASIAN                                                3
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              144
                           clus
vv                          DEL PEAK 26(13Q14.2) WILD-TYPE
  ASIAN                                                  3
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 50
[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"
D51V5, binary
                                cls
clus                               0   1
  DEL PEAK 26(13Q14.2) MUTATED     2 145
  DEL PEAK 26(13Q14.2) WILD-TYPE   3  46
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(13Q14.2) MUTATED      2  145
  DEL PEAK 26(13Q14.2) WILD-TYPE    3   46
                        clus
vv                       DEL PEAK 26(13Q14.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          145
                        clus
vv                       DEL PEAK 26(13Q14.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             46
[1] 2 2
[1] FALSE

Clustering(52) Variable = DEL PEAK 27(14Q24.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(14Q24.1) MUTATED    55  22
  DEL PEAK 27(14Q24.1) WILD-TYPE 107  60
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                            77                            167 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                            22                             60 
$`DEL PEAK 27(14Q24.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KU 
       19.69        53.49        42.84        18.64        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A23R 
       32.71        38.24        12.85        36.69        18.54        74.66 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3UE 
       23.08        70.49        17.10        34.68        15.06        34.88 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 
       12.26        27.22        14.96        72.72        25.15        15.95 
TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A8BM TCGA-DX-A8BN 
       23.54        74.10        64.21        88.31        44.68        38.17 
TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AB2O TCGA-DX-AB2P 
       35.54        36.69        60.66         6.58        86.10        12.07 
TCGA-DX-AB2T TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-FX-A2QS TCGA-FX-A3NJ 
       71.57       101.98        19.20        84.66         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N8 
        0.07         0.07         0.07        34.88        15.91         0.10 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 
        9.80        21.37         3.22        28.21       143.41       116.88 
TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A42X TCGA-K1-A6RU 
       73.28        22.62        16.41         1.05       123.78        10.85 
TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 
       11.70        13.35         8.32         5.03         9.83        46.82 
TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SI-A71P TCGA-SI-AA8B TCGA-VT-A80G TCGA-WP-A9GB 
       10.52        11.18        19.82         5.06        10.72         9.04 
TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C5 
       57.80        18.08        36.82        25.71        38.96 

$`DEL PEAK 27(14Q24.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        68.55        88.57        44.91        54.74        25.25 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1L1 TCGA-DX-A1L2 
       10.32        31.00        36.03         0.56        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y 
       33.53        42.54         5.26        76.41        66.87         6.28 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
        9.04       108.13        20.05        17.75        42.77         4.54 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF 
       14.99        10.68        44.45        39.35        28.80        64.18 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B9 
        9.73        19.30        24.26        26.47        25.08        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV 
       16.18         3.06        34.55        66.31        67.20        50.50 
TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN 
       16.87        21.30        34.49        75.32        48.36        15.62 
TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BG 
      135.48        29.49        48.20        14.07         7.04        17.95 
TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BO TCGA-DX-A8BP 
       14.43         9.34        59.87        33.07        35.77        14.07 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BX TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
      124.37        27.95        19.43         1.15        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V 
        4.67        12.39        40.60        49.18         9.21        96.89 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB3A 
      106.45        13.28        50.40        22.85        60.00        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3YV 
       50.89        71.31        20.32         2.07        48.30         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EK 
       12.62        23.97        41.33        80.48        19.53         1.38 
TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M5 
       19.89        37.12        25.22        40.08        13.58         5.92 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV 
        3.91        71.70        36.39        27.29         9.04         4.08 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H 
       22.03         8.28         0.49         4.34        19.73        14.99 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK 
       17.98        15.65         7.46        10.45         4.08       120.20 
TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
       37.55         6.35        38.63        81.01        18.08        20.94 
TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        1.84        18.08        48.59        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 
      130.32        98.27        62.20         0.72        18.94         3.88 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
        6.58        17.92        27.22         9.93        13.22         0.72 
TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX 
       26.17        11.93         4.80        72.72        41.49        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 
       65.46        22.62        26.43        29.92        18.35        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        35.08        17.72        15.58        36.43 

  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                          0.07                           0.49 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                        143.41                         188.15 
  DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE 
                         22.62                          23.97 
[1] "0.1 - 143.4 (22.6)" "0.5 - 188.2 (24.0)"
[1] "hr=" "1.3"
D52V2, continuous
D52V3, binary
                                cls
clus                              0  1
  DEL PEAK 27(14Q24.1) MUTATED   46 31
  DEL PEAK 27(14Q24.1) WILD-TYPE 86 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED     46   31
  DEL PEAK 27(14Q24.1) WILD-TYPE   86   83
        clus
vv       DEL PEAK 27(14Q24.1) MUTATED DEL PEAK 27(14Q24.1) WILD-TYPE
  FEMALE                           46                             86
  MALE                             31                             83
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(14Q24.1) MUTATED       1                         7    61
  DEL PEAK 27(14Q24.1) WILD-TYPE     5                        11   133
D52V4, multiclass
                           clus
vv                          DEL PEAK 27(14Q24.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               61
                           clus
vv                          DEL PEAK 27(14Q24.1) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                133
[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"
D52V5, binary
                                cls
clus                               0   1
  DEL PEAK 27(14Q24.1) MUTATED     0  59
  DEL PEAK 27(14Q24.1) WILD-TYPE   5 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(14Q24.1) MUTATED      0   59
  DEL PEAK 27(14Q24.1) WILD-TYPE    5  132
                        clus
vv                       DEL PEAK 27(14Q24.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           59
                        clus
vv                       DEL PEAK 27(14Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            132
[1] 2 2
[1] FALSE

Clustering(53) Variable = DEL PEAK 28(16Q11.2) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(16Q11.2) MUTATED   85 39
  DEL PEAK 28(16Q11.2) WILD-TYPE 77 43
  DEL PEAK 28(16Q11.2) MUTATED DEL PEAK 28(16Q11.2) WILD-TYPE 
                           124                            120 
  DEL PEAK 28(16Q11.2) MUTATED DEL PEAK 28(16Q11.2) WILD-TYPE 
                            39                             43 
$`DEL PEAK 28(16Q11.2) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 
       19.69        88.57        25.25        10.32        31.00        18.64 
TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1L0 TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 
       26.56         0.56        18.54        74.66         6.28         9.70 
TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA 
       23.08        17.10        15.06        42.77        14.99        10.68 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O 
       39.35        28.80        64.18        19.30        24.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BB 
       14.96        26.47        25.08        15.95        66.05        23.44 
TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM 
       67.20        23.54        16.87        74.10        64.21        48.36 
TCGA-DX-A7EO TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BO 
      135.48         7.04        17.95         9.34        59.87        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ 
       14.07       124.37        27.95        35.54        36.69         6.58 
TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T 
        1.15         8.75        40.60        12.07        49.18        71.57 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-FX-A3NJ TCGA-FX-A3RE 
      106.45        13.28        50.40       101.98         0.10         0.07 
TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV TCGA-HB-A43Z 
       20.32         0.07         0.07        48.30         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI 
       12.62        23.97         0.10         9.80        21.37        19.53 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK 
        3.22         1.38        19.89        37.12        25.22        40.08 
TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN 
       13.58        73.28        16.41         1.05         3.91        71.70 
TCGA-K1-A42X TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MB-A8JL 
      123.78         4.08        11.70         8.32         4.34        19.73 
TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP 
       14.99         4.08        37.55         6.35        81.01        18.08 
TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC 
       20.94         5.03         9.83        46.82        48.59        35.90 
TCGA-QQ-A5VD TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B 
       30.90        11.18        18.94         6.58        17.92         5.06 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
        9.93         0.72        26.17        72.72        38.27        65.46 
TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        26.43        29.92        18.08        18.35        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X9-A973 
       16.83        38.96        35.08        36.43 

$`DEL PEAK 28(16Q11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX 
       36.30        53.49        68.55        44.91        54.74        42.84 
TCGA-3B-A9I0 TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       36.03        14.04        32.71        38.24        12.85        36.69 
TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U 
       54.21        59.24        33.53        42.54         5.26        76.41 
TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
       66.87        27.81        60.30         8.58        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U6 
        9.04        70.49       108.13        20.05        34.68        17.75 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48U 
        4.54        44.45        34.88         9.73        12.26        72.72 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       25.15        11.47        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6Z2 
       16.18         3.06        34.55        66.31        50.50        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER 
       21.30        34.49        75.32        15.62        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BV 
       14.07        14.43        33.07        44.68        38.17        60.66 
TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2S 
       19.43        12.99         4.67        12.39        86.10         9.21 
TCGA-DX-AB2V TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       96.89        22.85        19.20        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N9 
       50.89        71.31         0.46         2.07        34.88        41.33 
TCGA-IE-A3OV TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-IW-A3M6 
       80.48        28.21       143.41       116.88         5.92        22.62 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH 
       36.39        27.29         9.04        10.85        22.03        13.35 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        8.28         0.49        17.98        15.65         7.46        10.45 
TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VB TCGA-QQ-A8VD 
      120.20        38.63         1.84        18.08       188.15       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71P 
       98.27        62.20        10.52         0.72         3.88        19.82 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
       27.22        13.22        10.72        11.93         4.80        41.49 
TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 
       22.62         9.04        36.82        15.95        17.72        15.58 

  DEL PEAK 28(16Q11.2) MUTATED DEL PEAK 28(16Q11.2) WILD-TYPE 
                          0.07                           0.46 
  DEL PEAK 28(16Q11.2) MUTATED DEL PEAK 28(16Q11.2) WILD-TYPE 
                        135.48                         188.15 
  DEL PEAK 28(16Q11.2) MUTATED DEL PEAK 28(16Q11.2) WILD-TYPE 
                        20.105                         28.010 
[1] "0.1 - 135.5 (20.1)" "0.5 - 188.2 (28.0)"
[1] "hr=" "1.1"
D53V2, continuous
D53V3, binary
                                cls
clus                              0  1
  DEL PEAK 28(16Q11.2) MUTATED   74 51
  DEL PEAK 28(16Q11.2) WILD-TYPE 58 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16Q11.2) MUTATED     74   51
  DEL PEAK 28(16Q11.2) WILD-TYPE   58   63
        clus
vv       DEL PEAK 28(16Q11.2) MUTATED DEL PEAK 28(16Q11.2) WILD-TYPE
  FEMALE                           74                             58
  MALE                             51                             63
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(16Q11.2) MUTATED       1                        14   101
  DEL PEAK 28(16Q11.2) WILD-TYPE     5                         4    93
D53V4, multiclass
                           clus
vv                          DEL PEAK 28(16Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                           14
  WHITE                                              101
                           clus
vv                          DEL PEAK 28(16Q11.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 93
[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"
D53V5, binary
                                cls
clus                               0   1
  DEL PEAK 28(16Q11.2) MUTATED     3 103
  DEL PEAK 28(16Q11.2) WILD-TYPE   2  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(16Q11.2) MUTATED      3  103
  DEL PEAK 28(16Q11.2) WILD-TYPE    2   88
                        clus
vv                       DEL PEAK 28(16Q11.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          103
                        clus
vv                       DEL PEAK 28(16Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             88
[1] 2 2
[1] FALSE

Clustering(54) Variable = DEL PEAK 29(16Q23.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 29(16Q23.1) MUTATED   86 43
  DEL PEAK 29(16Q23.1) WILD-TYPE 76 39
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                           129                            115 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                            43                             39 
$`DEL PEAK 29(16Q23.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I1 
       19.69        88.57        25.25        10.32        31.00        18.64 
TCGA-3B-A9I3 TCGA-DX-A1KU TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
       26.56        14.04        18.54        59.24        74.66         6.28 
TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U7 TCGA-DX-A3U9 
        9.70        23.08        17.10        15.06        42.77        14.99 
TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L 
       10.68        39.35        28.80        64.18        19.30        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48V TCGA-DX-A6B8 TCGA-DX-A6BA 
       27.22        14.96        26.47        25.08        15.95        66.05 
TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6YZ 
       23.44         3.06        67.20        23.54        16.87        74.10 
TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A7EO TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BJ 
       64.21        48.36       135.48         7.04        14.43         9.34 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU 
       38.17        35.77        14.07       124.37        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2J TCGA-DX-AB2P 
       60.66         6.58         1.15         8.75        40.60        12.07 
TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-FX-A3NJ 
       49.18        71.57        13.28        50.40       101.98         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A3YV 
        0.07        20.32         0.07         0.07        48.30         4.57 
TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5NA TCGA-IE-A4EH 
       15.91        12.62        23.97         0.10         9.80        21.37 
TCGA-IE-A4EI TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ 
       19.53         3.22         1.38        19.89        37.12        25.22 
TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
       40.08        13.58        73.28         5.92        22.62        16.41 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42X TCGA-K1-A6RU TCGA-K1-A6RV TCGA-KF-A41W 
        1.05        71.70       123.78        10.85         4.08        11.70 
TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MO-A47R 
       13.35         8.32         8.28        19.73        14.99        10.45 
TCGA-N1-A6IA TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
        4.08        37.55         6.35        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        5.03         9.83        46.82        48.59        35.90        30.90 
TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G 
       11.18         6.58         5.06         9.93         0.72        10.72 
TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X6-A7W8 
       26.17        72.72        38.27        65.46         9.04        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C4 
       29.92        18.08        18.35        25.71        15.95        16.83 
TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X9-A973 
       38.96        35.08        36.43 

$`DEL PEAK 29(16Q23.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HX 
       36.30        53.49        68.55        44.91        54.74        42.84 
TCGA-3B-A9I0 TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
       36.03         0.56        32.71        38.24        12.85        36.69 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       54.21        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U8 
       70.49       108.13        20.05        34.68        17.75         4.54 
TCGA-DX-A3UB TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48N TCGA-DX-A48U TCGA-DX-A6B7 
       44.45        34.88         9.73        12.26        72.72        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       34.55        66.31        50.50        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG 
       75.32        15.62        29.49        48.20        14.07        17.95 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS TCGA-DX-A8BX TCGA-DX-AB2E 
       59.87        33.07        44.68        27.95        19.43        12.99 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W 
        4.67        12.39        86.10         9.21        96.89       106.45 
TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HS-A5N9 TCGA-IE-A3OV 
       71.31         0.46         2.07        34.88        41.33        80.48 
TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42W 
       28.21       143.41       116.88         3.91        36.39        27.29 
TCGA-K1-A6RT TCGA-LI-A67I TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 
        9.04        22.03         0.49         4.34        17.98        15.65 
TCGA-MO-A47P TCGA-PC-A5DK TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A8VB 
        7.46       120.20        38.63         1.84        18.08       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A6Z4 
      130.32        98.27        62.20        10.52         0.72        18.94 
TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-WK-A8XO 
        3.88        17.92        19.82        27.22        13.22        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7WC TCGA-X6-A8C7 
        4.80        41.49        22.62        57.80        36.82        17.72 
TCGA-X9-A971 
       15.58 

  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                          0.07                           0.46 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                        135.48                         188.15 
  DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE 
                         19.69                          29.49 
[1] "0.1 - 135.5 (19.7)" "0.5 - 188.2 (29.5)"
[1] "hr=" "1.3"
D54V2, continuous
D54V3, binary
                                cls
clus                              0  1
  DEL PEAK 29(16Q23.1) MUTATED   77 53
  DEL PEAK 29(16Q23.1) WILD-TYPE 55 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.1) MUTATED     77   53
  DEL PEAK 29(16Q23.1) WILD-TYPE   55   61
        clus
vv       DEL PEAK 29(16Q23.1) MUTATED DEL PEAK 29(16Q23.1) WILD-TYPE
  FEMALE                           77                             55
  MALE                             53                             61
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(16Q23.1) MUTATED       4                        13   103
  DEL PEAK 29(16Q23.1) WILD-TYPE     2                         5    91
D54V4, multiclass
                           clus
vv                          DEL PEAK 29(16Q23.1) MUTATED
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              103
                           clus
vv                          DEL PEAK 29(16Q23.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 91
[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"
D54V5, binary
                                cls
clus                               0   1
  DEL PEAK 29(16Q23.1) MUTATED     2 109
  DEL PEAK 29(16Q23.1) WILD-TYPE   3  82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(16Q23.1) MUTATED      2  109
  DEL PEAK 29(16Q23.1) WILD-TYPE    3   82
                        clus
vv                       DEL PEAK 29(16Q23.1) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                          109
                        clus
vv                       DEL PEAK 29(16Q23.1) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                             82
[1] 2 2
[1] FALSE

Clustering(55) Variable = DEL PEAK 30(17P13.1) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 30(17P13.1) MUTATED   89 34
  DEL PEAK 30(17P13.1) WILD-TYPE 73 48
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                           123                            121 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                            34                             48 
$`DEL PEAK 30(17P13.1) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HU TCGA-3B-A9HX 
       19.69        53.49        68.55        88.57        25.25        42.84 
TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-DX-A1KZ 
       10.32        31.00        36.03        18.64        26.56        36.69 
TCGA-DX-A23R TCGA-DX-A3LT TCGA-DX-A3U7 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UE 
       74.66        23.08        42.77        14.99        10.68        34.88 
TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R 
        9.73        19.30        24.26        27.22        14.96        26.47 
TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB 
       72.72        25.08        25.15        11.47        66.05        23.44 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ 
       16.18        66.31        67.20        50.50        16.87        74.10 
TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EO 
       88.31        21.30        34.49        75.32        48.36       135.48 
TCGA-DX-A7ET TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM TCGA-DX-A8BO 
        7.04        17.95        14.43         9.34        44.68        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E 
       14.07       124.37        35.54         6.58         1.15        12.99 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2Z TCGA-DX-AB32 
       86.10        12.07        49.18        71.57        50.40       101.98 
TCGA-DX-AB35 TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-HB-A2OT TCGA-HB-A5W3 
       19.20         0.10        20.32         0.07        48.30        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
        3.22         1.38        19.89        40.08        28.21       143.41 
TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU 
        5.92        16.41         3.91        71.70        27.29        10.85 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5YA TCGA-MB-A8JK 
        4.08        11.70        22.03         8.32         0.49         4.34 
TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5VC 
      120.20        37.55        18.08        20.94         9.83        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 
       30.90       188.15        10.52        11.18         3.88         6.58 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C TCGA-UE-A6QU 
       17.92        19.82        27.22         5.06         9.93         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY 
       10.72        26.17        11.93        72.72        38.27        65.46 
TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C3 
       22.62        57.80        26.43        18.08        18.35        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X9-A971 
       16.83        38.96        15.58 

$`DEL PEAK 30(17P13.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.30        44.91        54.74         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 TCGA-DX-A1L3 
       38.24        12.85        18.54        54.21        59.24        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z 
       42.54         5.26        76.41        66.87         6.28        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U5 
       70.49       108.13        17.10        20.05        34.68        15.06 
TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UF 
       17.75         4.54        44.45        39.35        28.80        64.18 
TCGA-DX-A48N TCGA-DX-A6B8 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       12.26        15.95        28.96         9.11        17.79        21.63 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YU TCGA-DX-A6Z0 TCGA-DX-A7EN TCGA-DX-A7EQ 
        3.06        34.55        23.54        64.21        15.62        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BS 
       48.20        14.07        59.87        33.07        38.17        27.95 
TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
       36.69        60.66        19.43         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB30 
       40.60         9.21        96.89       106.45        13.28        22.85 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS 
       60.00        84.66        32.15        50.89        71.31         0.46 
TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         0.07         2.07        34.88         4.57        15.91 
TCGA-IE-A4EI TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 
       19.53        37.12        25.22       116.88        13.58        73.28 
TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-LI-A9QH 
       22.62         1.05        36.39       123.78         9.04        13.35 
TCGA-MB-A5Y9 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        8.28        19.73        14.99        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-QC-A7B5 
       10.45         4.08         6.35        38.63        81.01         5.03 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A8VD TCGA-QQ-A8VF 
        1.84        46.82        18.08        48.59       130.32        98.27 
TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-UE-A6QT TCGA-WK-A8XQ TCGA-WK-A8XT 
       62.20         0.72        18.94        13.22         4.80        41.49 
TCGA-WP-A9GB TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A8C2 TCGA-X6-A8C6 TCGA-X6-A8C7 
        9.04        29.92        36.82        25.71        35.08        17.72 
TCGA-X9-A973 
       36.43 

  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                        188.15                         130.32 
  DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE 
                         22.62                          25.22 
[1] "0.1 - 188.2 (22.6)" "0.1 - 130.3 (25.2)"
[1] "hr=" "1.4"
D55V2, continuous
D55V3, binary
                                cls
clus                              0  1
  DEL PEAK 30(17P13.1) MUTATED   75 49
  DEL PEAK 30(17P13.1) WILD-TYPE 57 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED     75   49
  DEL PEAK 30(17P13.1) WILD-TYPE   57   65
        clus
vv       DEL PEAK 30(17P13.1) MUTATED DEL PEAK 30(17P13.1) WILD-TYPE
  FEMALE                           75                             57
  MALE                             49                             65
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(17P13.1) MUTATED       2                        13   102
  DEL PEAK 30(17P13.1) WILD-TYPE     4                         5    92
D55V4, multiclass
                           clus
vv                          DEL PEAK 30(17P13.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                           13
  WHITE                                              102
                           clus
vv                          DEL PEAK 30(17P13.1) WILD-TYPE
  ASIAN                                                  4
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 92
[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"
D55V5, binary
                                cls
clus                               0   1
  DEL PEAK 30(17P13.1) MUTATED     3 103
  DEL PEAK 30(17P13.1) WILD-TYPE   2  88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(17P13.1) MUTATED      3  103
  DEL PEAK 30(17P13.1) WILD-TYPE    2   88
                        clus
vv                       DEL PEAK 30(17P13.1) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                          103
                        clus
vv                       DEL PEAK 30(17P13.1) WILD-TYPE
  HISPANIC OR LATINO                                  2
  NOT HISPANIC OR LATINO                             88
[1] 2 2
[1] FALSE

Clustering(56) Variable = DEL PEAK 31(17Q11.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(17Q11.2) MUTATED    50  28
  DEL PEAK 31(17Q11.2) WILD-TYPE 112  54
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                            78                            166 
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                            28                             54 
$`DEL PEAK 31(17Q11.2) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KZ TCGA-DX-A23R 
       19.69        42.84        26.56         0.56        36.69        74.66 
TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3M2 
        6.28         9.70        23.08       108.13        20.05        34.68 
TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UD TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 
       14.99        10.68        28.80        64.18        24.26        15.95 
TCGA-DX-A6BF TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU 
        9.11         3.06        34.55        66.31        67.20        23.54 
TCGA-DX-A6YV TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7ET 
       50.50        16.87        74.10        21.30        34.49         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BP 
       17.95        14.43         9.34        59.87        33.07        14.07 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AB2E TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2W 
       36.69         6.58        12.99        86.10        71.57       106.45 
TCGA-DX-AB2X TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3A TCGA-HB-A2OT TCGA-HB-A43Z 
       13.28       101.98        19.20        32.15        48.30        15.91 
TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IW-A3M5 TCGA-JV-A75J TCGA-K1-A42W 
        3.22        19.89        25.22         5.92         3.91        27.29 
TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JK TCGA-MB-A8JL TCGA-N1-A6IA 
        4.08        13.35         8.32         4.34        19.73         4.08 
TCGA-PC-A5DM TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A8VB 
        6.35        20.94         9.83        46.82        35.90       188.15 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QU 
       18.94         3.88        17.92        27.22         9.93         0.72 
TCGA-VT-A80G TCGA-WK-A8XX TCGA-WK-A8Y0 TCGA-X6-A7WC TCGA-X6-A8C4 TCGA-X6-A8C6 
       10.72        38.27        22.62        36.82        16.83        35.08 

$`DEL PEAK 31(17Q11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-DX-A1KU 
       25.25        10.32        31.00        36.03        18.64        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       32.71        38.24        12.85        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU 
       60.30         8.58        59.47        54.77         9.04        70.49 
TCGA-DX-A3LY TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB 
       17.10        15.06        17.75        42.77         4.54        44.45 
TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O 
       39.35        34.88         9.73        19.30        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       66.05        23.44        28.96        17.79        21.63        16.18 
TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO 
       64.21        88.31        75.32        48.36        15.62       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       29.49        48.20        14.07        44.68        38.17        35.77 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
      124.37        27.95        35.54        60.66        19.43         1.15 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q 
        8.75         4.67        12.39        40.60        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 
        9.21        96.89        50.40        22.85        60.00        84.66 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       50.89        71.31         0.46         0.10         0.07        20.32 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 
        0.07         0.07         2.07        34.88         4.57        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH 
       23.97         0.10        41.33         9.80        80.48        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 
       19.53         1.38        37.12        40.08        28.21       143.41 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF 
      116.88        13.58        73.28        22.62        16.41         1.05 
TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W 
       71.70        36.39       123.78         9.04        10.85        11.70 
TCGA-LI-A67I TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       22.03         8.28         0.49        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DO 
        7.46        10.45       120.20        37.55        38.63        81.01 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD 
       18.08         5.03         1.84        18.08        48.59        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ 
      130.32        98.27        62.20        10.52         0.72        11.18 
TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-AA8B TCGA-UE-A6QT TCGA-VT-A80J TCGA-WK-A8XO 
        6.58        19.82         5.06        13.22        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
        4.80        72.72        41.49        65.46         9.04        57.80 
TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 
       26.43        29.92        18.08        18.35        25.71        15.95 
TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       38.96        17.72        15.58        36.43 

  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                          0.56                           0.07 
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                        188.15                         143.41 
  DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE 
                         19.97                          25.48 
[1] "0.6 - 188.2 (20.0)" "0.1 - 143.4 (25.5)"
[1] "hr=" "1.3"
D56V2, continuous
D56V3, binary
                                cls
clus                              0  1
  DEL PEAK 31(17Q11.2) MUTATED   39 39
  DEL PEAK 31(17Q11.2) WILD-TYPE 93 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17Q11.2) MUTATED     39   39
  DEL PEAK 31(17Q11.2) WILD-TYPE   93   75
        clus
vv       DEL PEAK 31(17Q11.2) MUTATED DEL PEAK 31(17Q11.2) WILD-TYPE
  FEMALE                           39                             93
  MALE                             39                             75
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(17Q11.2) MUTATED       1                         7    63
  DEL PEAK 31(17Q11.2) WILD-TYPE     5                        11   131
D56V4, multiclass
                           clus
vv                          DEL PEAK 31(17Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               63
                           clus
vv                          DEL PEAK 31(17Q11.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             11
  WHITE                                                131
[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"
D56V5, binary
                                cls
clus                               0   1
  DEL PEAK 31(17Q11.2) MUTATED     1  63
  DEL PEAK 31(17Q11.2) WILD-TYPE   4 128
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(17Q11.2) MUTATED      1   63
  DEL PEAK 31(17Q11.2) WILD-TYPE    4  128
                        clus
vv                       DEL PEAK 31(17Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           63
                        clus
vv                       DEL PEAK 31(17Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            128
[1] 2 2
[1] FALSE

Clustering(57) Variable = DEL PEAK 32(17Q25.3) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(17Q25.3) MUTATED    36  25
  DEL PEAK 32(17Q25.3) WILD-TYPE 126  57
  DEL PEAK 32(17Q25.3) MUTATED DEL PEAK 32(17Q25.3) WILD-TYPE 
                            61                            183 
  DEL PEAK 32(17Q25.3) MUTATED DEL PEAK 32(17Q25.3) WILD-TYPE 
                            25                             57 
$`DEL PEAK 32(17Q25.3) MUTATED`
TCGA-3B-A9HR TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A23R 
       88.57        26.56        32.71        38.24        18.54        74.66 
TCGA-DX-A23Y TCGA-DX-A3LT TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 TCGA-DX-A3U9 
        6.28        23.08        17.10        20.05        34.68        14.99 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6B8 TCGA-DX-A6BA 
       28.80        34.88        64.18        24.26        15.95        66.05 
TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A7EI TCGA-DX-A7ET TCGA-DX-A8BJ TCGA-DX-A8BK 
       23.44         3.06        34.49         7.04         9.34        59.87 
TCGA-DX-A8BL TCGA-DX-A8BP TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2H 
       33.07        14.07        36.69         6.58         1.15        12.39 
TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB35 TCGA-FX-A3NJ TCGA-HB-A5W3 
       86.10        71.57       106.45        19.20         0.10        12.62 
TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IF-A4AJ TCGA-IS-A3KA 
       23.97        80.48        21.37         3.22        25.22        13.58 
TCGA-JV-A5VE TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH 
       16.41        27.29       123.78         4.08        11.70        13.35 
TCGA-MB-A8JK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VB 
        4.34        37.55         6.35         9.83        46.82        48.59 
TCGA-QQ-A8VH TCGA-SI-A71O TCGA-WK-A8XX TCGA-WP-A9GB TCGA-X6-A7WC TCGA-X6-A8C3 
       10.52        17.92        38.27         9.04        36.82        15.95 
TCGA-X6-A8C4 
       16.83 

$`DEL PEAK 32(17Q25.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 
       25.25        42.84        10.32        31.00        36.03        18.64 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L2 
        0.56        14.04        12.85        36.69        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z 
       33.53        42.54         5.26        76.41        66.87        27.81 
TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       60.30         8.58         9.70        59.47        54.77         9.04 
TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 
       70.49       108.13        15.06        17.75        42.77         4.54 
TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48N 
       10.68        44.45        39.35         9.73        19.30        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B9 TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK 
       11.47        28.96         9.11        17.79        21.63        16.18 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YX 
       34.55        66.31        67.20        23.54        50.50        16.87 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EL TCGA-DX-A7EM 
       74.10        64.21        88.31        21.30        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG 
       15.62       135.48        29.49        48.20        14.07        17.95 
TCGA-DX-A8BH TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       14.43        44.68        38.17        35.77       124.37        27.95 
TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G 
       35.54        60.66        19.43        12.99         8.75         4.67 
TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2X 
       40.60        12.07        49.18         9.21        96.89        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A 
       50.40        22.85       101.98        60.00        84.66        32.15 
TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       50.89        71.31         0.46         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         2.07        48.30        34.88         4.57        15.91 
TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ 
        0.10        41.33         9.80        19.53         1.38        19.89 
TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M4 
       37.12        40.08        28.21       143.41       116.88        73.28 
TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO 
        5.92        22.62         1.05         3.91        71.70        36.39 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        9.04        10.85        22.03         8.32         8.28         0.49 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX 
        4.08       120.20        38.63        81.01        18.08        20.94 
TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VB 
        5.03         1.84        18.08        35.90        30.90       188.15 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z4 
      130.32        98.27        62.20         0.72        11.18        18.94 
TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-SI-AA8C 
        3.88         6.58        19.82        27.22         5.06         9.93 
TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO TCGA-WK-A8XQ 
       13.22         0.72        10.72        26.17        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-X2-A95T TCGA-X6-A7W8 
       72.72        41.49        65.46        22.62        57.80        26.43 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C5 TCGA-X6-A8C6 
       29.92        18.08        18.35        25.71        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  DEL PEAK 32(17Q25.3) MUTATED DEL PEAK 32(17Q25.3) WILD-TYPE 
                          0.10                           0.07 
  DEL PEAK 32(17Q25.3) MUTATED DEL PEAK 32(17Q25.3) WILD-TYPE 
                        123.78                         188.15 
  DEL PEAK 32(17Q25.3) MUTATED DEL PEAK 32(17Q25.3) WILD-TYPE 
                         21.37                          25.08 
[1] "0.1 - 123.8 (21.4)" "0.1 - 188.2 (25.1)"
[1] "hr=" "1.5"
D57V2, continuous
D57V3, binary
                                cls
clus                               0   1
  DEL PEAK 32(17Q25.3) MUTATED    31  30
  DEL PEAK 32(17Q25.3) WILD-TYPE 101  84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17Q25.3) MUTATED     31   30
  DEL PEAK 32(17Q25.3) WILD-TYPE  101   84
        clus
vv       DEL PEAK 32(17Q25.3) MUTATED DEL PEAK 32(17Q25.3) WILD-TYPE
  FEMALE                           31                            101
  MALE                             30                             84
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(17Q25.3) MUTATED       1                         6    47
  DEL PEAK 32(17Q25.3) WILD-TYPE     5                        12   147
D57V4, multiclass
                           clus
vv                          DEL PEAK 32(17Q25.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               47
                           clus
vv                          DEL PEAK 32(17Q25.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                147
[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"
D57V5, binary
                                cls
clus                               0   1
  DEL PEAK 32(17Q25.3) MUTATED     0  50
  DEL PEAK 32(17Q25.3) WILD-TYPE   5 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(17Q25.3) MUTATED      0   50
  DEL PEAK 32(17Q25.3) WILD-TYPE    5  141
                        clus
vv                       DEL PEAK 32(17Q25.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           50
                        clus
vv                       DEL PEAK 32(17Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            141
[1] 2 2
[1] FALSE

Clustering(58) Variable = DEL PEAK 33(18Q23) MUTATION ANALYSIS
D58V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 33(18Q23) MUTATED    47  34
  DEL PEAK 33(18Q23) WILD-TYPE 115  48
  DEL PEAK 33(18Q23) MUTATED DEL PEAK 33(18Q23) WILD-TYPE 
                          81                          163 
  DEL PEAK 33(18Q23) MUTATED DEL PEAK 33(18Q23) WILD-TYPE 
                          34                           48 
$`DEL PEAK 33(18Q23) MUTATED`
TCGA-3B-A9HS TCGA-3B-A9HX TCGA-3R-A8YX TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L1 
       44.91        42.84         0.56        38.24        12.85        54.21 
TCGA-DX-A1L3 TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LT TCGA-DX-A3M1 TCGA-DX-A3U5 
       33.53         6.28         9.70        23.08        20.05        15.06 
TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48P TCGA-DX-A6BA 
       42.77        10.68        64.18        19.30        14.96        66.05 
TCGA-DX-A6BF TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX 
        9.11        16.18         3.06        67.20        23.54        16.87 
TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A7ET TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BS 
       64.21        48.36         7.04         9.34        59.87        27.95 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2P TCGA-DX-AB2Q 
       36.69         6.58         1.15        12.99        12.07        49.18 
TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A48G 
      106.45        13.28        50.40        60.00        32.15         0.07 
TCGA-HB-A2OT TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IF-A4AJ 
       48.30        12.62        23.97        80.48         3.22        25.22 
TCGA-IS-A3K7 TCGA-IW-A3M6 TCGA-JV-A5VF TCGA-K1-A42X TCGA-K1-A6RV TCGA-KF-A41W 
      143.41        22.62         1.05       123.78         4.08        11.70 
TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A8JK TCGA-PC-A5DM 
       22.03        13.35         8.32         8.28         4.34         6.35 
TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V9 TCGA-QQ-A5VB TCGA-QQ-A8VB TCGA-QQ-A8VH 
       18.08         5.03        46.82        48.59       188.15        10.52 
TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-AA8B 
       11.18        18.94         3.88        17.92        19.82         5.06 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8Y0 TCGA-X6-A7W8 
        9.93         0.72        26.17        72.72        22.62        26.43 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       16.83        38.96        35.08 

$`DEL PEAK 33(18Q23) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        88.57        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       25.25        10.32        31.00        36.03        18.64        26.56 
TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A1L4 
       14.04        32.71        36.69        18.54        59.24        42.54 
TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       74.66         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW 
        8.58        59.47        54.77         9.04        70.49       108.13 
TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB 
       17.10        34.68        17.75         4.54        14.99        44.45 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48L TCGA-DX-A48N 
       39.35        28.80        34.88         9.73        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       27.22        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6YR 
       11.47        23.44        28.96        17.79        21.63        34.55 
TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       66.31        50.50        74.10        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       75.32        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
       17.95        14.43        33.07        44.68        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2F 
       14.07       124.37        35.54        60.66        19.43         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2S TCGA-DX-AB2T 
        4.67        12.39        40.60        86.10         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3B 
       96.89        22.85       101.98        19.20        84.66        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A76Y 
       71.31         0.46         0.10         0.07        20.32         0.07 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 
        2.07        34.88         4.57        15.91         0.10        41.33 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ 
        9.80        21.37        19.53         1.38        19.89        37.12 
TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M5 
       40.08        28.21       116.88        13.58        73.28         5.92 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT 
       16.41         3.91        71.70        36.39        27.29         9.04 
TCGA-K1-A6RU TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
       10.85         0.49        19.73        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN 
        7.46        10.45         4.08       120.20        37.55        38.63 
TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5VA TCGA-QQ-A5VC 
       81.01        20.94         9.83         1.84        18.08        35.90 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A849 
       30.90       130.32        98.27        62.20         0.72         6.58 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT 
       27.22        13.22        10.72        11.93         4.80        41.49 
TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB 
       38.27        65.46         9.04        57.80        29.92        18.08 
TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A971 
       36.82        18.35        25.71        15.95        17.72        15.58 
TCGA-X9-A973 
       36.43 

  DEL PEAK 33(18Q23) MUTATED DEL PEAK 33(18Q23) WILD-TYPE 
                        0.07                         0.07 
  DEL PEAK 33(18Q23) MUTATED DEL PEAK 33(18Q23) WILD-TYPE 
                      188.15                       135.48 
  DEL PEAK 33(18Q23) MUTATED DEL PEAK 33(18Q23) WILD-TYPE 
                       19.30                        26.47 
[1] "0.1 - 188.2 (19.3)" "0.1 - 135.5 (26.5)"
[1] "hr=" "1.7"
D58V2, continuous
D58V3, binary
                              cls
clus                            0  1
  DEL PEAK 33(18Q23) MUTATED   47 35
  DEL PEAK 33(18Q23) WILD-TYPE 85 79
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(18Q23) MUTATED     47   35
  DEL PEAK 33(18Q23) WILD-TYPE   85   79
        clus
vv       DEL PEAK 33(18Q23) MUTATED DEL PEAK 33(18Q23) WILD-TYPE
  FEMALE                         47                           85
  MALE                           35                           79
[1] 2 2
[1] FALSE
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(18Q23) MUTATED       2                         6    64
  DEL PEAK 33(18Q23) WILD-TYPE     4                        12   130
D58V4, multiclass
                           clus
vv                          DEL PEAK 33(18Q23) MUTATED
  ASIAN                                              2
  BLACK OR AFRICAN AMERICAN                          6
  WHITE                                             64
                           clus
vv                          DEL PEAK 33(18Q23) WILD-TYPE
  ASIAN                                                4
  BLACK OR AFRICAN AMERICAN                           12
  WHITE                                              130
[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"
D58V5, binary
                              cls
clus                             0   1
  DEL PEAK 33(18Q23) MUTATED     1  65
  DEL PEAK 33(18Q23) WILD-TYPE   4 126
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 33(18Q23) MUTATED      1   65
  DEL PEAK 33(18Q23) WILD-TYPE    4  126
                        clus
vv                       DEL PEAK 33(18Q23) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         65
                        clus
vv                       DEL PEAK 33(18Q23) WILD-TYPE
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                          126
[1] 2 2
[1] FALSE

Clustering(59) Variable = DEL PEAK 34(19P13.3) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 34(19P13.3) MUTATED    50  20
  DEL PEAK 34(19P13.3) WILD-TYPE 112  62
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            70                            174 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                            20                             62 
$`DEL PEAK 34(19P13.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HQ TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-DX-A3LW 
       19.69        68.55        25.25        42.84        10.32       108.13 
TCGA-DX-A3M2 TCGA-DX-A3U7 TCGA-DX-A3UC TCGA-DX-A3UF TCGA-DX-A48R TCGA-DX-A6B8 
       34.68        42.77        39.35        64.18        26.47        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6Z0 
       11.47        66.05        67.20        23.54        16.87        64.21 
TCGA-DX-A7EM TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP 
       48.36        17.95         9.34        38.17        35.77        14.07 
TCGA-DX-AB2W TCGA-DX-AB3A TCGA-FX-A48G TCGA-FX-A76Y TCGA-HB-A43Z TCGA-HB-A5W3 
      106.45        32.15         0.07         0.07        15.91        12.62 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A6BZ 
       23.97         0.10        41.33        21.37        19.53        19.89 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 
       25.22        40.08       143.41        13.58         5.92        22.62 
TCGA-JV-A5VF TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A67I 
        1.05        71.70        27.29         4.08        11.70        22.03 
TCGA-N1-A6IA TCGA-PC-A5DM TCGA-PC-A5DO TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5VB 
        4.08         6.35        81.01         5.03         9.83        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VF TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       30.90        98.27        11.18        18.94         3.88        17.92 
TCGA-SI-A71Q TCGA-VT-A80G TCGA-WK-A8XO TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       27.22        10.72        11.93        38.27        65.46        22.62 
TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A8C4 
       29.92        18.08        36.82        16.83 

$`DEL PEAK 34(19P13.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HZ 
       36.30        53.49        88.57        44.91        54.74        31.00 
TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       36.03        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L2 
       38.24        12.85        36.69        18.54        54.21        59.24 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 
        6.28        27.81        60.30         8.58         9.70        59.47 
TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY TCGA-DX-A3M1 
       54.77         9.04        23.08        70.49        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UB 
       15.06        17.75         4.54        14.99        10.68        44.45 
TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       28.80        34.88         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6BB 
       27.22        14.96        72.72        25.08        25.15        23.44 
TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ 
       28.96         9.11        17.79        21.63        16.18         3.06 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 TCGA-DX-A7EF 
       34.55        66.31        50.50        74.10        88.31        21.30 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       34.49        75.32        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       14.07         7.04        14.43        59.87        33.07        44.68 
TCGA-DX-A8BR TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
      124.37        27.95        35.54        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H 
        6.58         1.15        12.99         8.75         4.67        12.39 
TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2T 
       40.60        86.10        12.07        49.18         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 TCGA-DX-AB35 
       96.89        13.28        50.40        22.85       101.98        19.20 
TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ 
       60.00        84.66        50.89        71.31         0.46         0.10 
TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.07        20.32         2.07        48.30        34.88         4.57 
TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EJ TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IS-A3K6 
        9.80        80.48         3.22         1.38        37.12        28.21 
TCGA-IS-A3K8 TCGA-IW-A3M4 TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PO TCGA-K1-A42X 
      116.88        73.28        16.41         3.91        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A5Y9 TCGA-MB-A5YA 
        9.04        10.85        13.35         8.32         8.28         0.49 
TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        4.34        19.73        14.99        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX 
       10.45       120.20        37.55        38.63        18.08        20.94 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VD 
        1.84        46.82        18.08        35.90       188.15       130.32 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-SG-A849 TCGA-SI-A71P TCGA-SI-AA8B 
       62.20        10.52         0.72         6.58        19.82         5.06 
TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80J TCGA-WK-A8XQ TCGA-WK-A8XS 
        9.93        13.22         0.72        26.17         4.80        72.72 
TCGA-WK-A8XT TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WD TCGA-X6-A8C2 
       41.49         9.04        57.80        26.43        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       15.95        38.96        35.08        17.72        15.58        36.43 

  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                          0.07                           0.07 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                        143.41                         188.15 
  DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE 
                         22.62                          23.85 
[1] "0.1 - 143.4 (22.6)" "0.1 - 188.2 (23.9)"
[1] "hr=" "1.2"
D59V2, continuous
D59V3, binary
                                cls
clus                              0  1
  DEL PEAK 34(19P13.3) MUTATED   47 23
  DEL PEAK 34(19P13.3) WILD-TYPE 85 91
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(19P13.3) MUTATED     47   23
  DEL PEAK 34(19P13.3) WILD-TYPE   85   91
        clus
vv       DEL PEAK 34(19P13.3) MUTATED DEL PEAK 34(19P13.3) WILD-TYPE
  FEMALE                           47                             85
  MALE                             23                             91
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(19P13.3) MUTATED       1                         6    59
  DEL PEAK 34(19P13.3) WILD-TYPE     5                        12   135
D59V4, multiclass
                           clus
vv                          DEL PEAK 34(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               59
                           clus
vv                          DEL PEAK 34(19P13.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             12
  WHITE                                                135
[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"
D59V5, binary
                                cls
clus                               0   1
  DEL PEAK 34(19P13.3) MUTATED     0  60
  DEL PEAK 34(19P13.3) WILD-TYPE   5 131
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(19P13.3) MUTATED      0   60
  DEL PEAK 34(19P13.3) WILD-TYPE    5  131
                        clus
vv                       DEL PEAK 34(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           60
                        clus
vv                       DEL PEAK 34(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  5
  NOT HISPANIC OR LATINO                            131
[1] 2 2
[1] FALSE

Clustering(60) Variable = DEL PEAK 35(19Q13.43) MUTATION ANALYSIS
D60V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 35(19Q13.43) MUTATED   74 26
  DEL PEAK 35(19Q13.43) WILD-TYPE 88 56
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                            100                             144 
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                             26                              56 
$`DEL PEAK 35(19Q13.43) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HU TCGA-3B-A9HY 
       19.69        53.49        68.55        44.91        25.25        10.32 
TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A23R TCGA-DX-A2J0 
       31.00        36.03        32.71        12.85        74.66         9.70 
TCGA-DX-A3LT TCGA-DX-A3UD TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48P TCGA-DX-A48U 
       23.08        28.80        24.26        12.26        14.96        72.72 
TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BH TCGA-DX-A6BK 
       25.08        25.15        11.47        66.05        21.63        16.18 
TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z2 
       34.55        66.31        67.20        50.50        74.10        88.31 
TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7ET 
       21.30        34.49        75.32        48.36        15.62         7.04 
TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR 
       59.87        33.07        44.68        38.17        35.77       124.37 
TCGA-DX-A8BT TCGA-DX-AATS TCGA-DX-AB2F TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2W 
       35.54         1.15         8.75        86.10        49.18       106.45 
TCGA-DX-AB36 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO TCGA-FX-A48G 
       60.00        32.15         0.46         0.07        20.32         0.07 
TCGA-FX-A76Y TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV 
        0.07         4.57        12.62        23.97         9.80        80.48 
TCGA-IE-A4EJ TCGA-IF-A4AK TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A3PN 
        3.22        40.08        13.58        73.28        22.62        71.70 
TCGA-K1-A42X TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JK 
      123.78        10.85        22.03        13.35         8.32         4.34 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
        4.08       120.20        81.01        18.08        20.94         5.03 
TCGA-QC-AA9N TCGA-QQ-A5V9 TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ 
        9.83        46.82        35.90       188.15        10.52        11.18 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C 
       18.94         3.88         6.58        17.92         5.06         9.93 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB 
       10.72        26.17        22.62        26.43        29.92        18.08 
TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.35        25.71        16.83        38.96 

$`DEL PEAK 35(19Q13.43) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HX TCGA-3B-A9I1 TCGA-3B-A9I3 
       36.30        88.57        54.74        42.84        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
        0.56        14.04        38.24        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       59.24        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 
        6.28        27.81        60.30         8.58        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
        9.04        70.49       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       15.06        17.75        42.77         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        34.88        64.18         9.73        19.30 
TCGA-DX-A48O TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF 
       27.22        26.47        15.95        23.44        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6YQ TCGA-DX-A6YU TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A7EO 
       17.79         3.06        23.54        16.87        64.21       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ 
       29.49        48.20        14.07        17.95        14.43         9.34 
TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ 
       14.07        27.95        36.69        60.66        19.43         6.58 
TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2S 
       12.99         4.67        12.39        40.60        12.07         9.21 
TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB32 
       71.57        96.89        13.28        50.40        22.85       101.98 
TCGA-DX-AB35 TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A8OO 
       19.20        84.66        50.89        71.31         0.10         2.07 
TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A4EH 
       48.30        34.88        15.91         0.10        41.33        21.37 
TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 
       19.53         1.38        19.89        37.12        25.22        28.21 
TCGA-IS-A3K7 TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
      143.41       116.88         5.92        16.41         1.05         3.91 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y9 
       36.39        27.29         9.04         4.08        11.70         8.28 
TCGA-MB-A5YA TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P 
        0.49        19.73        14.99        17.98        15.65         7.46 
TCGA-MO-A47R TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-QQ-A5V2 TCGA-QQ-A5VA 
       10.45        37.55         6.35        38.63         1.84        18.08 
TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q 
       48.59        30.90       130.32        98.27        62.20         0.72 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.82        27.22        13.22         0.72        11.93         4.80 
TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T 
       72.72        41.49        38.27        65.46         9.04        57.80 
TCGA-X6-A7WC TCGA-X6-A8C3 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       36.82        15.95        35.08        17.72        15.58        36.43 

  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                           0.07                            0.10 
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                         188.15                          143.41 
  DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE 
                         24.115                          22.110 
[1] "0.1 - 188.2 (24.1)" "0.1 - 143.4 (22.1)"
[1] "hr=" "1.6"
D60V2, continuous
D60V3, binary
                                 cls
clus                               0  1
  DEL PEAK 35(19Q13.43) MUTATED   59 43
  DEL PEAK 35(19Q13.43) WILD-TYPE 73 71
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(19Q13.43) MUTATED     59   43
  DEL PEAK 35(19Q13.43) WILD-TYPE   73   71
        clus
vv       DEL PEAK 35(19Q13.43) MUTATED DEL PEAK 35(19Q13.43) WILD-TYPE
  FEMALE                            59                              73
  MALE                              43                              71
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(19Q13.43) MUTATED       1                         6    89
  DEL PEAK 35(19Q13.43) WILD-TYPE     5                        12   105
D60V4, multiclass
                           clus
vv                          DEL PEAK 35(19Q13.43) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                89
                           clus
vv                          DEL PEAK 35(19Q13.43) WILD-TYPE
  ASIAN                                                   5
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 105
[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"
D60V5, binary
                                 cls
clus                                0   1
  DEL PEAK 35(19Q13.43) MUTATED     1  89
  DEL PEAK 35(19Q13.43) WILD-TYPE   4 102
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(19Q13.43) MUTATED      1   89
  DEL PEAK 35(19Q13.43) WILD-TYPE    4  102
                        clus
vv                       DEL PEAK 35(19Q13.43) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            89
                        clus
vv                       DEL PEAK 35(19Q13.43) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             102
[1] 2 2
[1] FALSE

Clustering(61) Variable = DEL PEAK 36(21Q11.2) MUTATION ANALYSIS
D61V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(21Q11.2) MUTATED    33  15
  DEL PEAK 36(21Q11.2) WILD-TYPE 129  67
  DEL PEAK 36(21Q11.2) MUTATED DEL PEAK 36(21Q11.2) WILD-TYPE 
                            48                            196 
  DEL PEAK 36(21Q11.2) MUTATED DEL PEAK 36(21Q11.2) WILD-TYPE 
                            15                             67 
$`DEL PEAK 36(21Q11.2) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HR TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A23Y 
       19.69        88.57        18.54        59.24        74.66         6.28 
TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U5 TCGA-DX-A3UA TCGA-DX-A48R TCGA-DX-A48V 
       17.10        20.05        15.06        10.68        26.47        25.08 
TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BM 
        3.06        16.87        17.95        14.43         9.34        44.68 
TCGA-DX-A8BO TCGA-DX-A8BZ TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB32 TCGA-FX-A3TO 
       35.77         6.58        86.10        49.18       101.98        20.32 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-JV-A5VE TCGA-JV-A5VF 
       48.30        15.91       143.41         5.92        16.41         1.05 
TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RV TCGA-PC-A5DO TCGA-QQ-A8VB 
        3.91        71.70        27.29         4.08        81.01       188.15 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A6Z4 TCGA-SG-A849 TCGA-SI-AA8B 
       62.20        10.52        11.18        18.94         6.58         5.06 
TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS TCGA-X6-A8C2 
        9.93         0.72        10.72        26.17        72.72        25.71 

$`DEL PEAK 36(21Q11.2) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        44.91        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        31.00        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ 
        0.56        14.04        32.71        38.24        12.85        36.69 
TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       54.21        33.53        42.54         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 
       27.81        60.30         8.58         9.70        59.47        54.77 
TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3M2 TCGA-DX-A3U6 
        9.04        23.08        70.49       108.13        34.68        17.75 
TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD 
       42.77         4.54        14.99        44.45        39.35        28.80 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N 
       34.88        64.18         9.73        19.30        24.26        12.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 
       27.22        14.96        72.72        25.15        15.95        11.47 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV 
       16.18        34.55        66.31        67.20        23.54        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL 
       74.10        64.21        88.31        21.30        34.49        75.32 
TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES 
       48.36        15.62       135.48        29.49        48.20        14.07 
TCGA-DX-A7ET TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BN TCGA-DX-A8BP TCGA-DX-A8BR 
        7.04        59.87        33.07        38.17        14.07       124.37 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AATS 
       27.95        35.54        36.69        60.66        19.43         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2P 
       12.99         8.75         4.67        12.39        40.60        12.07 
TCGA-DX-AB2S TCGA-DX-AB2T TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2X TCGA-DX-AB2Z 
        9.21        71.57        96.89       106.45        13.28        50.40 
TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       22.85        19.20        60.00        84.66        32.15        50.89 
TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A48G TCGA-FX-A76Y 
       71.31         0.46         0.10         0.07         0.07         0.07 
TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 
        2.07        34.88         4.57        12.62        23.97         0.10 
TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EJ 
       41.33         9.80        80.48        21.37        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K6 
        1.38        19.89        37.12        25.22        40.08        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-K1-A3PO TCGA-K1-A42X 
      116.88        13.58        73.28        22.62        36.39       123.78 
TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A5Y8 
        9.04        10.85        11.70        22.03        13.35         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N 
        6.35        38.63        18.08        20.94         5.03         9.83 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        35.90        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-RN-A68Q TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-A71P 
      130.32        98.27         0.72         3.88        17.92        19.82 
TCGA-SI-A71Q TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX 
       27.22        13.22        11.93         4.80        41.49        38.27 
TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA 
       65.46        22.62         9.04        57.80        26.43        29.92 
TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 
       18.08        36.82        18.35        15.95        16.83        38.96 
TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       35.08        17.72        15.58        36.43 

  DEL PEAK 36(21Q11.2) MUTATED DEL PEAK 36(21Q11.2) WILD-TYPE 
                          0.72                           0.07 
  DEL PEAK 36(21Q11.2) MUTATED DEL PEAK 36(21Q11.2) WILD-TYPE 
                        188.15                         135.48 
  DEL PEAK 36(21Q11.2) MUTATED DEL PEAK 36(21Q11.2) WILD-TYPE 
                        18.740                         24.705 
[1] "0.7 - 188.2 (18.7)" "0.1 - 135.5 (24.7)"
[1] "hr=" "1.1"
D61V2, continuous
D61V3, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q11.2) MUTATED    27  21
  DEL PEAK 36(21Q11.2) WILD-TYPE 105  93
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q11.2) MUTATED     27   21
  DEL PEAK 36(21Q11.2) WILD-TYPE  105   93
        clus
vv       DEL PEAK 36(21Q11.2) MUTATED DEL PEAK 36(21Q11.2) WILD-TYPE
  FEMALE                           27                            105
  MALE                             21                             93
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 36(21Q11.2) MUTATED       1                         5    36
  DEL PEAK 36(21Q11.2) WILD-TYPE     5                        13   158
D61V4, multiclass
                           clus
vv                          DEL PEAK 36(21Q11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               36
                           clus
vv                          DEL PEAK 36(21Q11.2) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             13
  WHITE                                                158
[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"
D61V5, binary
                                cls
clus                               0   1
  DEL PEAK 36(21Q11.2) MUTATED     2  36
  DEL PEAK 36(21Q11.2) WILD-TYPE   3 155
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(21Q11.2) MUTATED      2   36
  DEL PEAK 36(21Q11.2) WILD-TYPE    3  155
                        clus
vv                       DEL PEAK 36(21Q11.2) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       DEL PEAK 36(21Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  3
  NOT HISPANIC OR LATINO                            155
[1] 2 2
[1] FALSE

Clustering(62) Variable = DEL PEAK 37(21Q22.3) MUTATION ANALYSIS
D62V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 37(21Q22.3) MUTATED    45  20
  DEL PEAK 37(21Q22.3) WILD-TYPE 117  62
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                            65                            179 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                            20                             62 
$`DEL PEAK 37(21Q22.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HS TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1L0 TCGA-DX-A1L2 
       19.69        44.91        14.04        38.24        18.54        59.24 
TCGA-DX-A23R TCGA-DX-A23Y TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 
       74.66         6.28         9.70       108.13        17.10        20.05 
TCGA-DX-A3U5 TCGA-DX-A3UF TCGA-DX-A48L TCGA-DX-A6BB TCGA-DX-A6BF TCGA-DX-A6YX 
       15.06        64.18        24.26        23.44         9.11        16.87 
TCGA-DX-A7EF TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BS 
       21.30        17.95         9.34        33.07        44.68        27.95 
TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2Q 
       36.69         6.58         1.15        12.39        86.10        49.18 
TCGA-DX-AB2X TCGA-DX-AB32 TCGA-FX-A2QS TCGA-FX-A3TO TCGA-HB-A2OT TCGA-IE-A4EJ 
       13.28       101.98         0.46        20.32        48.30         3.22 
TCGA-IF-A4AJ TCGA-IF-A4AK TCGA-IS-A3K7 TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE 
       25.22        40.08       143.41         5.92        22.62        16.41 
TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5YA 
       71.70        27.29        10.85        11.70        13.35         0.49 
TCGA-MB-A8JK TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QQ-A8VB TCGA-QQ-A8VG TCGA-RN-AAAQ 
        4.34        18.08        20.94       188.15        62.20        11.18 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SG-A849 TCGA-SI-AA8B TCGA-VT-A80G TCGA-VT-A80J 
       18.94         3.88         6.58         5.06        10.72        26.17 
TCGA-WK-A8XS TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C6 
       72.72        36.82        18.35        25.71        35.08 

$`DEL PEAK 37(21Q22.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HT TCGA-3B-A9HU 
       36.30        53.49        68.55        88.57        54.74        25.25 
TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3B-A9I3 
       42.84        10.32        31.00        36.03        18.64        26.56 
TCGA-3R-A8YX TCGA-DX-A1KW TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L1 TCGA-DX-A1L3 
        0.56        32.71        12.85        36.69        54.21        33.53 
TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Z TCGA-DX-A240 
       42.54         5.26        76.41        66.87        27.81        60.30 
TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU 
        8.58        59.47        54.77         9.04        23.08        70.49 
TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UA 
       34.68        17.75        42.77         4.54        14.99        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A48J TCGA-DX-A48K 
       44.45        39.35        28.80        34.88         9.73        19.30 
TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V 
       12.26        27.22        14.96        26.47        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BE TCGA-DX-A6BG 
       25.15        15.95        11.47        66.05        28.96        17.79 
TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT 
       21.63        16.18         3.06        34.55        66.31        67.20 
TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI 
       23.54        50.50        74.10        64.21        88.31        34.49 
TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER 
       75.32        48.36        15.62       135.48        29.49        48.20 
TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BN TCGA-DX-A8BO 
       14.07         7.04        14.43        59.87        38.17        35.77 
TCGA-DX-A8BP TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E 
       14.07       124.37        35.54        60.66        19.43        12.99 
TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2T 
        8.75         4.67        40.60        12.07         9.21        71.57 
TCGA-DX-AB2V TCGA-DX-AB2W TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
       96.89       106.45        50.40        22.85        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A3RE 
       84.66        32.15        50.89        71.31         0.10         0.07 
TCGA-FX-A48G TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         0.07         2.07        34.88         4.57        15.91 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-HS-A5NA TCGA-IE-A3OV 
       12.62        23.97         0.10        41.33         9.80        80.48 
TCGA-IE-A4EH TCGA-IE-A4EI TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IS-A3K6 
       21.37        19.53         1.38        19.89        37.12        28.21 
TCGA-IS-A3K8 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-JV-A5VF TCGA-JV-A75J TCGA-K1-A3PO 
      116.88        13.58        73.28         1.05         3.91        36.39 
TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RV TCGA-LI-A67I TCGA-MB-A5Y8 TCGA-MB-A5Y9 
      123.78         9.04         4.08        22.03         8.32         8.28 
TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
       19.73        14.99        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO 
        4.08       120.20        37.55         6.35        38.63        81.01 
TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB 
        5.03         9.83         1.84        46.82        18.08        48.59 
TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VH TCGA-RN-A68Q 
       35.90        30.90       130.32        98.27        10.52         0.72 
TCGA-SI-A71O TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8C TCGA-UE-A6QT TCGA-UE-A6QU 
       17.92        19.82        27.22         9.93        13.22         0.72 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 
       11.93         4.80        41.49        38.27        65.46        22.62 
TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A8C3 
        9.04        57.80        26.43        29.92        18.08        15.95 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        17.72        15.58        36.43 

  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                          0.46                           0.07 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                        188.15                         135.48 
  DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE 
                         20.05                          25.25 
[1] "0.5 - 188.2 (20.1)" "0.1 - 135.5 (25.2)"
[1] "hr=" "1"  
D62V2, continuous
D62V3, binary
                                cls
clus                              0  1
  DEL PEAK 37(21Q22.3) MUTATED   34 31
  DEL PEAK 37(21Q22.3) WILD-TYPE 98 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(21Q22.3) MUTATED     34   31
  DEL PEAK 37(21Q22.3) WILD-TYPE   98   83
        clus
vv       DEL PEAK 37(21Q22.3) MUTATED DEL PEAK 37(21Q22.3) WILD-TYPE
  FEMALE                           34                             98
  MALE                             31                             83
[1] 2 2
[1] FALSE
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 37(21Q22.3) MUTATED       1                         4    53
  DEL PEAK 37(21Q22.3) WILD-TYPE     5                        14   141
D62V4, multiclass
                           clus
vv                          DEL PEAK 37(21Q22.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               53
                           clus
vv                          DEL PEAK 37(21Q22.3) WILD-TYPE
  ASIAN                                                  5
  BLACK OR AFRICAN AMERICAN                             14
  WHITE                                                141
[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"
D62V5, binary
                                cls
clus                               0   1
  DEL PEAK 37(21Q22.3) MUTATED     1  52
  DEL PEAK 37(21Q22.3) WILD-TYPE   4 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 37(21Q22.3) MUTATED      1   52
  DEL PEAK 37(21Q22.3) WILD-TYPE    4  139
                        clus
vv                       DEL PEAK 37(21Q22.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           52
                        clus
vv                       DEL PEAK 37(21Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  4
  NOT HISPANIC OR LATINO                            139
[1] 2 2
[1] FALSE

Clustering(63) Variable = DEL PEAK 38(22Q13.32) MUTATION ANALYSIS
D63V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 38(22Q13.32) MUTATED    55  24
  DEL PEAK 38(22Q13.32) WILD-TYPE 107  58
  DEL PEAK 38(22Q13.32) MUTATED DEL PEAK 38(22Q13.32) WILD-TYPE 
                             79                             165 
  DEL PEAK 38(22Q13.32) MUTATED DEL PEAK 38(22Q13.32) WILD-TYPE 
                             24                              58 
$`DEL PEAK 38(22Q13.32) MUTATED`
TCGA-3B-A9HR TCGA-3B-A9HX TCGA-3B-A9I3 TCGA-DX-A1KW TCGA-DX-A23R TCGA-DX-A23V 
       88.57        42.84        26.56        32.71        74.66        66.87 
TCGA-DX-A23Y TCGA-DX-A2IZ TCGA-DX-A3LS TCGA-DX-A3LW TCGA-DX-A3M1 TCGA-DX-A3U7 
        6.28         8.58         9.04       108.13        20.05        42.77 
TCGA-DX-A3U9 TCGA-DX-A48L TCGA-DX-A48R TCGA-DX-A6B8 TCGA-DX-A6BA TCGA-DX-A6BF 
       14.99        24.26        26.47        15.95        66.05         9.11 
TCGA-DX-A6BK TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV TCGA-DX-A6YZ 
       16.18        66.31        67.20        23.54        50.50        74.10 
TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN 
        7.04        14.43        59.87        33.07        44.68        38.17 
TCGA-DX-A8BR TCGA-DX-A8BV TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2T TCGA-DX-AB2W 
      124.37        60.66        12.39        86.10        71.57       106.45 
TCGA-DX-AB2Z TCGA-DX-AB32 TCGA-DX-AB3A TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A3TO 
       50.40       101.98        32.15         0.46         0.07        20.32 
TCGA-FX-A48G TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A5W3 TCGA-HS-A5N9 TCGA-HS-A5NA 
        0.07        34.88         4.57        12.62        41.33         9.80 
TCGA-IE-A4EH TCGA-IE-A4EJ TCGA-IE-A6BZ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IS-A3K8 
       21.37         3.22        19.89        25.22       143.41       116.88 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-JV-A75J 
       13.58         5.92        22.62        16.41         1.05         3.91 
TCGA-K1-A3PN TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 TCGA-QC-AA9N TCGA-QQ-A8VB 
       71.70         4.08        11.70         8.32         9.83       188.15 
TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-SG-A6Z4 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C 
       62.20        10.52        18.94        17.92         5.06         9.93 
TCGA-UE-A6QU TCGA-WK-A8XS TCGA-X2-A95T TCGA-X6-A7W8 TCGA-X6-A7WB TCGA-X6-A7WC 
        0.72        72.72        57.80        26.43        18.08        36.82 
TCGA-X6-A8C2 
       25.71 

$`DEL PEAK 38(22Q13.32) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        19.69        53.49        68.55        44.91        54.74 
TCGA-3B-A9HU TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX 
       25.25        10.32        31.00        36.03        18.64         0.56 
TCGA-DX-A1KU TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       14.04        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L2 TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23Z 
       59.24        33.53        42.54         5.26        76.41        27.81 
TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LT TCGA-DX-A3LU 
       60.30         9.70        59.47        54.77        23.08        70.49 
TCGA-DX-A3LY TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U8 TCGA-DX-A3UA 
       17.10        34.68        15.06        17.75         4.54        10.68 
TCGA-DX-A3UB TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J 
       44.45        39.35        28.80        34.88        64.18         9.73 
TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48U TCGA-DX-A48V 
       19.30        12.26        27.22        14.96        72.72        25.08 
TCGA-DX-A6B7 TCGA-DX-A6B9 TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BG TCGA-DX-A6BH 
       25.15        11.47        23.44        28.96        17.79        21.63 
TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YX TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF 
        3.06        34.55        16.87        64.21        88.31        21.30 
TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ 
       34.49        75.32        48.36        15.62       135.48        29.49 
TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BO TCGA-DX-A8BP 
       48.20        14.07        17.95         9.34        35.77        14.07 
TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS 
       27.95        35.54        36.69        19.43         6.58         1.15 
TCGA-DX-AB2E TCGA-DX-AB2F TCGA-DX-AB2G TCGA-DX-AB2J TCGA-DX-AB2P TCGA-DX-AB2Q 
       12.99         8.75         4.67        40.60        12.07        49.18 
TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
        9.21        96.89        13.28        22.85        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3B TCGA-DX-AB3C TCGA-FX-A3NJ TCGA-FX-A76Y TCGA-FX-A8OO 
       84.66        50.89        71.31         0.10         0.07         2.07 
TCGA-HB-A2OT TCGA-HB-A43Z TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-IE-A3OV TCGA-IE-A4EI 
       48.30        15.91        23.97         0.10        80.48        19.53 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IW-A3M4 TCGA-K1-A3PO 
        1.38        37.12        40.08        28.21        73.28        36.39 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RT TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH 
       27.29       123.78         9.04        10.85        22.03        13.35 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MB-A8JL TCGA-MJ-A68H TCGA-MJ-A68J 
        8.28         0.49         4.34        19.73        14.99        17.98 
TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL 
       15.65         7.46        10.45         4.08       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DO TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 
        6.35        38.63        81.01        18.08        20.94         5.03 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD 
        1.84        46.82        18.08        48.59        35.90        30.90 
TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A6Z7 TCGA-SG-A849 
      130.32        98.27         0.72        11.18         3.88         6.58 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XO 
       19.82        27.22        13.22        10.72        26.17        11.93 
TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WK-A8Y0 TCGA-WP-A9GB 
        4.80        41.49        38.27        65.46        22.62         9.04 
TCGA-X6-A7WA TCGA-X6-A7WD TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       29.92        18.35        15.95        16.83        38.96        35.08 
TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       17.72        15.58        36.43 

  DEL PEAK 38(22Q13.32) MUTATED DEL PEAK 38(22Q13.32) WILD-TYPE 
                           0.07                            0.07 
  DEL PEAK 38(22Q13.32) MUTATED DEL PEAK 38(22Q13.32) WILD-TYPE 
                         188.15                          135.48 
  DEL PEAK 38(22Q13.32) MUTATED DEL PEAK 38(22Q13.32) WILD-TYPE 
                          24.26                           22.85 
[1] "0.1 - 188.2 (24.3)" "0.1 - 135.5 (22.9)"
[1] "hr=" "1.4"
D63V2, continuous
D63V3, binary
                                 cls
clus                               0  1
  DEL PEAK 38(22Q13.32) MUTATED   49 30
  DEL PEAK 38(22Q13.32) WILD-TYPE 83 84
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(22Q13.32) MUTATED     49   30
  DEL PEAK 38(22Q13.32) WILD-TYPE   83   84
        clus
vv       DEL PEAK 38(22Q13.32) MUTATED DEL PEAK 38(22Q13.32) WILD-TYPE
  FEMALE                            49                              83
  MALE                              30                              84
[1] 2 2
[1] FALSE
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 38(22Q13.32) MUTATED       2                         6    64
  DEL PEAK 38(22Q13.32) WILD-TYPE     4                        12   130
D63V4, multiclass
                           clus
vv                          DEL PEAK 38(22Q13.32) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                64
                           clus
vv                          DEL PEAK 38(22Q13.32) WILD-TYPE
  ASIAN                                                   4
  BLACK OR AFRICAN AMERICAN                              12
  WHITE                                                 130
[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"
D63V5, binary
                                 cls
clus                                0   1
  DEL PEAK 38(22Q13.32) MUTATED     1  61
  DEL PEAK 38(22Q13.32) WILD-TYPE   4 130
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 38(22Q13.32) MUTATED      1   61
  DEL PEAK 38(22Q13.32) WILD-TYPE    4  130
                        clus
vv                       DEL PEAK 38(22Q13.32) MUTATED
  HISPANIC OR LATINO                                 1
  NOT HISPANIC OR LATINO                            61
                        clus
vv                       DEL PEAK 38(22Q13.32) WILD-TYPE
  HISPANIC OR LATINO                                   4
  NOT HISPANIC OR LATINO                             130
[1] 2 2
[1] FALSE

Clustering(64) Variable = DEL PEAK 39(XP21.1) MUTATION ANALYSIS
D64V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 39(XP21.1) MUTATED    35  17
  DEL PEAK 39(XP21.1) WILD-TYPE 127  65
  DEL PEAK 39(XP21.1) MUTATED DEL PEAK 39(XP21.1) WILD-TYPE 
                           52                           192 
  DEL PEAK 39(XP21.1) MUTATED DEL PEAK 39(XP21.1) WILD-TYPE 
                           17                            65 
$`DEL PEAK 39(XP21.1) MUTATED`
TCGA-3B-A9HY TCGA-3B-A9I0 TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1L2 TCGA-DX-A23Y 
       10.32        36.03        18.64         0.56        59.24         6.28 
TCGA-DX-A2J0 TCGA-DX-A3U8 TCGA-DX-A3U9 TCGA-DX-A3UD TCGA-DX-A48J TCGA-DX-A48O 
        9.70         4.54        14.99        28.80         9.73        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B9 
       14.96        26.47        72.72        25.08        25.15        11.47 
TCGA-DX-A6YQ TCGA-DX-A6YX TCGA-DX-A7EF TCGA-DX-A8BR TCGA-DX-AB2Q TCGA-DX-AB2T 
        3.06        16.87        21.30       124.37        49.18        71.57 
TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB3C TCGA-FX-A2QS TCGA-FX-A48G TCGA-HB-A5W3 
      106.45       101.98        71.31         0.46         0.07        12.62 
TCGA-HS-A5NA TCGA-IE-A4EH TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-JV-A75J 
        9.80        21.37        25.22       143.41        73.28         3.91 
TCGA-K1-A42X TCGA-K1-A6RU TCGA-LI-A67I TCGA-LI-A9QH TCGA-MB-A8JL TCGA-PC-A5DO 
      123.78        10.85        22.03        13.35        19.73        81.01 
TCGA-QQ-A8VB TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O TCGA-SI-AA8B TCGA-SI-AA8C 
      188.15        18.94         3.88        17.92         5.06         9.93 
TCGA-WK-A8XY TCGA-X2-A95T TCGA-X6-A7WB TCGA-X6-A8C5 
       65.46        57.80        18.08        38.96 

$`DEL PEAK 39(XP21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HZ TCGA-3B-A9I3 TCGA-DX-A1KU 
       54.74        25.25        42.84        31.00        26.56        14.04 
TCGA-DX-A1KW TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 
       32.71        38.24        12.85        36.69        18.54        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Z TCGA-DX-A240 TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
       27.81        60.30         8.58        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3M2 
       23.08        70.49       108.13        17.10        20.05        34.68 
TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3UA TCGA-DX-A3UB TCGA-DX-A3UC 
       15.06        17.75        42.77        10.68        44.45        39.35 
TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A6B8 
       34.88        64.18        19.30        24.26        12.26        15.95 
TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6BE TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH 
       66.05        23.44        28.96         9.11        17.79        21.63 
TCGA-DX-A6BK TCGA-DX-A6YR TCGA-DX-A6YS TCGA-DX-A6YT TCGA-DX-A6YU TCGA-DX-A6YV 
       16.18        34.55        66.31        67.20        23.54        50.50 
TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EM 
       74.10        64.21        88.31        34.49        75.32        48.36 
TCGA-DX-A7EN TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       15.62       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BG TCGA-DX-A8BH TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM 
       17.95        14.43         9.34        59.87        33.07        44.68 
TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BP TCGA-DX-A8BS TCGA-DX-A8BT TCGA-DX-A8BU 
       38.17        35.77        14.07        27.95        35.54        36.69 
TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2F 
       60.66        19.43         6.58         1.15        12.99         8.75 
TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2S 
        4.67        12.39        40.60        86.10        12.07         9.21 
TCGA-DX-AB2V TCGA-DX-AB2X TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB35 TCGA-DX-AB36 
       96.89        13.28        50.40        22.85        19.20        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A3NJ TCGA-FX-A3RE TCGA-FX-A3TO 
       84.66        32.15        50.89         0.10         0.07        20.32 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV TCGA-HB-A43Z 
        0.07         2.07        48.30        34.88         4.57        15.91 
TCGA-HS-A5N7 TCGA-HS-A5N8 TCGA-HS-A5N9 TCGA-IE-A3OV TCGA-IE-A4EI TCGA-IE-A4EJ 
       23.97         0.10        41.33        80.48        19.53         3.22 
TCGA-IE-A4EK TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
        1.38        19.89        37.12        40.08        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-JV-A5VF TCGA-K1-A3PN 
       13.58         5.92        22.62        16.41         1.05        71.70 
TCGA-K1-A3PO TCGA-K1-A42W TCGA-K1-A6RT TCGA-K1-A6RV TCGA-KF-A41W TCGA-MB-A5Y8 
       36.39        27.29         9.04         4.08        11.70         8.32 
TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68H TCGA-MJ-A68J TCGA-MJ-A850 
        8.28         0.49         4.34        14.99        17.98        15.65 
TCGA-MO-A47P TCGA-MO-A47R TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DM 
        7.46        10.45         4.08       120.20        37.55         6.35 
TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-A6FX TCGA-QC-A7B5 TCGA-QC-AA9N TCGA-QQ-A5V2 
       38.63        18.08        20.94         5.03         9.83         1.84 
TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VC TCGA-QQ-A5VD TCGA-QQ-A8VD 
       46.82        18.08        48.59        35.90        30.90       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-QQ-A8VH TCGA-RN-A68Q TCGA-RN-AAAQ TCGA-SG-A849 
       98.27        62.20        10.52         0.72        11.18         6.58 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-UE-A6QT TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J 
       19.82        27.22        13.22         0.72        10.72        26.17 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XS TCGA-WK-A8XT TCGA-WK-A8XX TCGA-WK-A8Y0 
       11.93         4.80        72.72        41.49        38.27        22.62 
TCGA-WP-A9GB TCGA-X6-A7W8 TCGA-X6-A7WA TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
        9.04        26.43        29.92        36.82        18.35        25.71 
TCGA-X6-A8C3 TCGA-X6-A8C4 TCGA-X6-A8C6 TCGA-X6-A8C7 TCGA-X9-A971 TCGA-X9-A973 
       15.95        16.83        35.08        17.72        15.58        36.43 

  DEL PEAK 39(XP21.1) MUTATED DEL PEAK 39(XP21.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 39(XP21.1) MUTATED DEL PEAK 39(XP21.1) WILD-TYPE 
                       188.15                        135.48 
  DEL PEAK 39(XP21.1) MUTATED DEL PEAK 39(XP21.1) WILD-TYPE 
                       20.515                        24.115 
[1] "0.1 - 188.2 (20.5)" "0.1 - 135.5 (24.1)"
[1] "hr=" "1.1"
D64V2, continuous
D64V3, binary
                               cls
clus                             0  1
  DEL PEAK 39(XP21.1) MUTATED   33 19
  DEL PEAK 39(XP21.1) WILD-TYPE 99 95
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 39(XP21.1) MUTATED     33   19
  DEL PEAK 39(XP21.1) WILD-TYPE   99   95
        clus
vv       DEL PEAK 39(XP21.1) MUTATED DEL PEAK 39(XP21.1) WILD-TYPE
  FEMALE                          33                            99
  MALE                            19                            95
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 39(XP21.1) MUTATED       0                         5    39
  DEL PEAK 39(XP21.1) WILD-TYPE     6                        13   155
D64V4, multiclass
                           clus
vv                          DEL PEAK 39(XP21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              39
                           clus
vv                          DEL PEAK 39(XP21.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            13
  WHITE                                               155
[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"
D64V5, binary
                               cls
clus                              0   1
  DEL PEAK 39(XP21.1) MUTATED     2  35
  DEL PEAK 39(XP21.1) WILD-TYPE   3 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 39(XP21.1) MUTATED      2   35
  DEL PEAK 39(XP21.1) WILD-TYPE    3  156
                        clus
vv                       DEL PEAK 39(XP21.1) MUTATED
  HISPANIC OR LATINO                               2
  NOT HISPANIC OR LATINO                          35
                        clus
vv                       DEL PEAK 39(XP21.1) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                           156
[1] 2 2
[1] FALSE

Clustering(65) Variable = DEL PEAK 40(XQ21.1) MUTATION ANALYSIS
D65V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 40(XQ21.1) MUTATED   83 26
  DEL PEAK 40(XQ21.1) WILD-TYPE 79 56
  DEL PEAK 40(XQ21.1) MUTATED DEL PEAK 40(XQ21.1) WILD-TYPE 
                          109                           135 
  DEL PEAK 40(XQ21.1) MUTATED DEL PEAK 40(XQ21.1) WILD-TYPE 
                           26                            56 
$`DEL PEAK 40(XQ21.1) MUTATED`
TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 TCGA-DX-A1KX 
       25.25        42.84        10.32        31.00        36.03        38.24 
TCGA-DX-A1L2 TCGA-DX-A23R TCGA-DX-A240 TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3M1 
       59.24        74.66        60.30         9.70       108.13        20.05 
TCGA-DX-A3U5 TCGA-DX-A3U9 TCGA-DX-A3UA TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE 
       15.06        14.99        10.68        39.35        28.80        34.88 
TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48K TCGA-DX-A48L TCGA-DX-A48N TCGA-DX-A48O 
       64.18         9.73        19.30        24.26        12.26        27.22 
TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 TCGA-DX-A6B8 
       14.96        26.47        72.72        25.08        25.15        15.95 
TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YS 
       11.47        66.05        23.44         3.06        34.55        66.31 
TCGA-DX-A6YT TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BG TCGA-DX-A8BJ TCGA-DX-A8BK 
       67.20        48.36        15.62        17.95         9.34        59.87 
TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO TCGA-DX-A8BR TCGA-DX-A8BS 
       33.07        44.68        38.17        35.77       124.37        27.95 
TCGA-DX-AB2F TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3C 
        8.75        71.57       106.45       101.98        19.20        71.31 
TCGA-FX-A2QS TCGA-FX-A3RE TCGA-FX-A48G TCGA-HB-A2OT TCGA-HB-A3L4 TCGA-HB-A3YV 
        0.46         0.07         0.07        48.30        34.88         4.57 
TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5NA TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A4EJ 
       12.62        23.97         9.80        80.48        21.37         3.22 
TCGA-IE-A4EK TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K7 TCGA-IW-A3M4 TCGA-IW-A3M6 
        1.38        37.12        25.22       143.41        73.28        22.62 
TCGA-JV-A5VE TCGA-JV-A75J TCGA-K1-A3PN TCGA-K1-A42W TCGA-K1-A42X TCGA-LI-A67I 
       16.41         3.91        71.70        27.29       123.78        22.03 
TCGA-MB-A5Y8 TCGA-MB-A8JL TCGA-MJ-A68H TCGA-N1-A6IA TCGA-PC-A5DN TCGA-PC-A5DO 
        8.32        19.73        14.99         4.08        38.63        81.01 
TCGA-QC-A6FX TCGA-QC-AA9N TCGA-QQ-A5VA TCGA-QQ-A5VC TCGA-QQ-A8VB TCGA-QQ-A8VH 
       20.94         9.83        18.08        35.90       188.15        10.52 
TCGA-SG-A849 TCGA-SI-A71O TCGA-SI-AA8C TCGA-UE-A6QU TCGA-VT-A80G TCGA-VT-A80J 
        6.58        17.92         9.93         0.72        10.72        26.17 
TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB TCGA-X2-A95T TCGA-X6-A7WA 
       72.72        38.27        65.46         9.04        57.80        29.92 
TCGA-X6-A7WB TCGA-X6-A7WD TCGA-X6-A8C2 TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 
       18.08        18.35        25.71        16.83        38.96        35.08 
TCGA-X9-A971 
       15.58 

$`DEL PEAK 40(XQ21.1) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HL TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS 
       36.30        19.69        53.49        68.55        88.57        44.91 
TCGA-3B-A9HT TCGA-3B-A9I1 TCGA-3B-A9I3 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW 
       54.74        18.64        26.56         0.56        14.04        32.71 
TCGA-DX-A1KY TCGA-DX-A1KZ TCGA-DX-A1L0 TCGA-DX-A1L1 TCGA-DX-A1L3 TCGA-DX-A1L4 
       12.85        36.69        18.54        54.21        33.53        42.54 
TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ 
        5.26        76.41        66.87         6.28        27.81         8.58 
TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3LY 
       59.47        54.77         9.04        23.08        70.49        17.10 
TCGA-DX-A3M2 TCGA-DX-A3U6 TCGA-DX-A3U7 TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A6BE 
       34.68        17.75        42.77         4.54        44.45        28.96 
TCGA-DX-A6BF TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YU TCGA-DX-A6YV 
        9.11        17.79        21.63        16.18        23.54        50.50 
TCGA-DX-A6YX TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI 
       16.87        74.10        64.21        88.31        21.30        34.49 
TCGA-DX-A7EL TCGA-DX-A7EO TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET 
       75.32       135.48        29.49        48.20        14.07         7.04 
TCGA-DX-A8BH TCGA-DX-A8BP TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BV TCGA-DX-A8BX 
       14.43        14.07        35.54        36.69        60.66        19.43 
TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2H TCGA-DX-AB2J 
        6.58         1.15        12.99         4.67        12.39        40.60 
TCGA-DX-AB2O TCGA-DX-AB2P TCGA-DX-AB2Q TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2X 
       86.10        12.07        49.18         9.21        96.89        13.28 
TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B 
       50.40        22.85        60.00        84.66        32.15        50.89 
TCGA-FX-A3NJ TCGA-FX-A3TO TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A43Z TCGA-HS-A5N8 
        0.10        20.32         0.07         2.07        15.91         0.10 
TCGA-HS-A5N9 TCGA-IE-A4EI TCGA-IE-A6BZ TCGA-IF-A4AK TCGA-IS-A3K6 TCGA-IS-A3K8 
       41.33        19.53        19.89        40.08        28.21       116.88 
TCGA-IS-A3KA TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU 
       13.58         5.92         1.05        36.39         9.04        10.85 
TCGA-K1-A6RV TCGA-KF-A41W TCGA-LI-A9QH TCGA-MB-A5Y9 TCGA-MB-A5YA TCGA-MB-A8JK 
        4.08        11.70        13.35         8.28         0.49         4.34 
TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R TCGA-PC-A5DK TCGA-PC-A5DL 
       17.98        15.65         7.46        10.45       120.20        37.55 
TCGA-PC-A5DM TCGA-PC-A5DP TCGA-QC-A7B5 TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VB 
        6.35        18.08         5.03         1.84        46.82        48.59 
TCGA-QQ-A5VD TCGA-QQ-A8VD TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-RN-AAAQ 
       30.90       130.32        98.27        62.20         0.72        11.18 
TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT 
       18.94         3.88        19.82        27.22         5.06        13.22 
TCGA-WK-A8XO TCGA-WK-A8XQ TCGA-WK-A8XT TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A7WC 
       11.93         4.80        41.49        22.62        26.43        36.82 
TCGA-X6-A8C3 TCGA-X6-A8C7 TCGA-X9-A973 
       15.95        17.72        36.43 

  DEL PEAK 40(XQ21.1) MUTATED DEL PEAK 40(XQ21.1) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 40(XQ21.1) MUTATED DEL PEAK 40(XQ21.1) WILD-TYPE 
                       188.15                        135.48 
  DEL PEAK 40(XQ21.1) MUTATED DEL PEAK 40(XQ21.1) WILD-TYPE 
                        25.22                         20.32 
[1] "0.1 - 188.2 (25.2)" "0.1 - 135.5 (20.3)"
[1] "hr=" "1.9"
D65V2, continuous
D65V3, binary
                               cls
clus                             0  1
  DEL PEAK 40(XQ21.1) MUTATED   69 42
  DEL PEAK 40(XQ21.1) WILD-TYPE 63 72
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 40(XQ21.1) MUTATED     69   42
  DEL PEAK 40(XQ21.1) WILD-TYPE   63   72
        clus
vv       DEL PEAK 40(XQ21.1) MUTATED DEL PEAK 40(XQ21.1) WILD-TYPE
  FEMALE                          69                            63
  MALE                            42                            72
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 40(XQ21.1) MUTATED       2                        11    90
  DEL PEAK 40(XQ21.1) WILD-TYPE     4                         7   104
D65V4, multiclass
                           clus
vv                          DEL PEAK 40(XQ21.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          11
  WHITE                                              90
                           clus
vv                          DEL PEAK 40(XQ21.1) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             7
  WHITE                                               104
[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"
D65V5, binary
                               cls
clus                             0  1
  DEL PEAK 40(XQ21.1) MUTATED    1 93
  DEL PEAK 40(XQ21.1) WILD-TYPE  4 98
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 40(XQ21.1) MUTATED      1   93
  DEL PEAK 40(XQ21.1) WILD-TYPE    4   98
                        clus
vv                       DEL PEAK 40(XQ21.1) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          93
                        clus
vv                       DEL PEAK 40(XQ21.1) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            98
[1] 2 2
[1] FALSE

Clustering(66) Variable = DEL PEAK 41(XQ22.3) MUTATION ANALYSIS
D66V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 41(XQ22.3) MUTATED   87 32
  DEL PEAK 41(XQ22.3) WILD-TYPE 75 50
  DEL PEAK 41(XQ22.3) MUTATED DEL PEAK 41(XQ22.3) WILD-TYPE 
                          119                           125 
  DEL PEAK 41(XQ22.3) MUTATED DEL PEAK 41(XQ22.3) WILD-TYPE 
                           32                            50 
$`DEL PEAK 41(XQ22.3) MUTATED`
TCGA-3B-A9HL TCGA-3B-A9HU TCGA-3B-A9HX TCGA-3B-A9HY TCGA-3B-A9HZ TCGA-3B-A9I0 
       19.69        25.25        42.84        10.32        31.00        36.03 
TCGA-3B-A9I3 TCGA-DX-A1KX TCGA-DX-A1KY TCGA-DX-A1L0 TCGA-DX-A1L2 TCGA-DX-A240 
       26.56        38.24        12.85        18.54        59.24        60.30 
TCGA-DX-A2J0 TCGA-DX-A3LW TCGA-DX-A3LY TCGA-DX-A3M1 TCGA-DX-A3U9 TCGA-DX-A3UA 
        9.70       108.13        17.10        20.05        14.99        10.68 
TCGA-DX-A3UC TCGA-DX-A3UD TCGA-DX-A3UE TCGA-DX-A3UF TCGA-DX-A48J TCGA-DX-A48L 
       39.35        28.80        34.88        64.18         9.73        24.26 
TCGA-DX-A48O TCGA-DX-A48P TCGA-DX-A48R TCGA-DX-A48U TCGA-DX-A48V TCGA-DX-A6B7 
       27.22        14.96        26.47        72.72        25.08        25.15 
TCGA-DX-A6B8 TCGA-DX-A6B9 TCGA-DX-A6BA TCGA-DX-A6BB TCGA-DX-A6YS TCGA-DX-A6YT 
       15.95        11.47        66.05        23.44        66.31        67.20 
TCGA-DX-A6YU TCGA-DX-A6YZ TCGA-DX-A6Z0 TCGA-DX-A7EM TCGA-DX-A7EN TCGA-DX-A8BG 
       23.54        74.10        64.21        48.36        15.62        17.95 
TCGA-DX-A8BJ TCGA-DX-A8BK TCGA-DX-A8BL TCGA-DX-A8BM TCGA-DX-A8BN TCGA-DX-A8BO 
        9.34        59.87        33.07        44.68        38.17        35.77 
TCGA-DX-A8BR TCGA-DX-A8BT TCGA-DX-A8BU TCGA-DX-A8BZ TCGA-DX-AATS TCGA-DX-AB2F 
      124.37        35.54        36.69         6.58         1.15         8.75 
TCGA-DX-AB2H TCGA-DX-AB2O TCGA-DX-AB2Q TCGA-DX-AB2T TCGA-DX-AB2W TCGA-DX-AB2X 
       12.39        86.10        49.18        71.57       106.45        13.28 
TCGA-DX-AB32 TCGA-DX-AB35 TCGA-DX-AB3C TCGA-FX-A3TO TCGA-FX-A48G TCGA-HB-A2OT 
      101.98        19.20        71.31        20.32         0.07        48.30 
TCGA-HB-A3L4 TCGA-HB-A43Z TCGA-HB-A5W3 TCGA-HS-A5N7 TCGA-HS-A5N9 TCGA-HS-A5NA 
       34.88        15.91        12.62        23.97        41.33         9.80 
TCGA-IE-A3OV TCGA-IE-A4EH TCGA-IE-A6BZ TCGA-IF-A3RQ TCGA-IF-A4AJ TCGA-IS-A3K6 
       80.48        21.37        19.89        37.12        25.22        28.21 
TCGA-IS-A3K7 TCGA-IS-A3KA TCGA-IW-A3M4 TCGA-IW-A3M6 TCGA-JV-A5VE TCGA-K1-A3PN 
      143.41        13.58        73.28        22.62        16.41        71.70 
TCGA-K1-A42W TCGA-K1-A42X TCGA-K1-A6RV TCGA-LI-A9QH TCGA-MB-A5Y8 TCGA-MB-A8JL 
       27.29       123.78         4.08        13.35         8.32        19.73 
TCGA-MJ-A68H TCGA-PC-A5DM TCGA-PC-A5DN TCGA-PC-A5DP TCGA-QC-AA9N TCGA-QQ-A5VC 
       14.99         6.35        38.63        18.08         9.83        35.90 
TCGA-QQ-A8VB TCGA-QQ-A8VH TCGA-RN-AAAQ TCGA-SG-A849 TCGA-SI-AA8C TCGA-UE-A6QU 
      188.15        10.52        11.18         6.58         9.93         0.72 
TCGA-VT-A80G TCGA-VT-A80J TCGA-WK-A8XS TCGA-WK-A8XX TCGA-WK-A8XY TCGA-WP-A9GB 
       10.72        26.17        72.72        38.27        65.46         9.04 
TCGA-X2-A95T TCGA-X6-A7WA TCGA-X6-A7WB TCGA-X6-A7WC TCGA-X6-A7WD TCGA-X6-A8C2 
       57.80        29.92        18.08        36.82        18.35        25.71 
TCGA-X6-A8C4 TCGA-X6-A8C5 TCGA-X6-A8C6 TCGA-X9-A971 TCGA-X9-A973 
       16.83        38.96        35.08        15.58        36.43 

$`DEL PEAK 41(XQ22.3) WILD-TYPE`
TCGA-3B-A9HJ TCGA-3B-A9HP TCGA-3B-A9HQ TCGA-3B-A9HR TCGA-3B-A9HS TCGA-3B-A9HT 
       36.30        53.49        68.55        88.57        44.91        54.74 
TCGA-3B-A9I1 TCGA-3R-A8YX TCGA-DX-A1KU TCGA-DX-A1KW TCGA-DX-A1KZ TCGA-DX-A1L1 
       18.64         0.56        14.04        32.71        36.69        54.21 
TCGA-DX-A1L3 TCGA-DX-A1L4 TCGA-DX-A23R TCGA-DX-A23T TCGA-DX-A23U TCGA-DX-A23V 
       33.53        42.54        74.66         5.26        76.41        66.87 
TCGA-DX-A23Y TCGA-DX-A23Z TCGA-DX-A2IZ TCGA-DX-A2J1 TCGA-DX-A2J4 TCGA-DX-A3LS 
        6.28        27.81         8.58        59.47        54.77         9.04 
TCGA-DX-A3LT TCGA-DX-A3LU TCGA-DX-A3M2 TCGA-DX-A3U5 TCGA-DX-A3U6 TCGA-DX-A3U7 
       23.08        70.49        34.68        15.06        17.75        42.77 
TCGA-DX-A3U8 TCGA-DX-A3UB TCGA-DX-A48K TCGA-DX-A48N TCGA-DX-A6BE TCGA-DX-A6BF 
        4.54        44.45        19.30        12.26        28.96         9.11 
TCGA-DX-A6BG TCGA-DX-A6BH TCGA-DX-A6BK TCGA-DX-A6YQ TCGA-DX-A6YR TCGA-DX-A6YV 
       17.79        21.63        16.18         3.06        34.55        50.50 
TCGA-DX-A6YX TCGA-DX-A6Z2 TCGA-DX-A7EF TCGA-DX-A7EI TCGA-DX-A7EL TCGA-DX-A7EO 
       16.87        88.31        21.30        34.49        75.32       135.48 
TCGA-DX-A7EQ TCGA-DX-A7ER TCGA-DX-A7ES TCGA-DX-A7ET TCGA-DX-A8BH TCGA-DX-A8BP 
       29.49        48.20        14.07         7.04        14.43        14.07 
TCGA-DX-A8BS TCGA-DX-A8BV TCGA-DX-A8BX TCGA-DX-AB2E TCGA-DX-AB2G TCGA-DX-AB2J 
       27.95        60.66        19.43        12.99         4.67        40.60 
TCGA-DX-AB2P TCGA-DX-AB2S TCGA-DX-AB2V TCGA-DX-AB2Z TCGA-DX-AB30 TCGA-DX-AB36 
       12.07         9.21        96.89        50.40        22.85        60.00 
TCGA-DX-AB37 TCGA-DX-AB3A TCGA-DX-AB3B TCGA-FX-A2QS TCGA-FX-A3NJ TCGA-FX-A3RE 
       84.66        32.15        50.89         0.46         0.10         0.07 
TCGA-FX-A76Y TCGA-FX-A8OO TCGA-HB-A3YV TCGA-HS-A5N8 TCGA-IE-A4EI TCGA-IE-A4EJ 
        0.07         2.07         4.57         0.10        19.53         3.22 
TCGA-IE-A4EK TCGA-IF-A4AK TCGA-IS-A3K8 TCGA-IW-A3M5 TCGA-JV-A5VF TCGA-JV-A75J 
        1.38        40.08       116.88         5.92         1.05         3.91 
TCGA-K1-A3PO TCGA-K1-A6RT TCGA-K1-A6RU TCGA-KF-A41W TCGA-LI-A67I TCGA-MB-A5Y9 
       36.39         9.04        10.85        11.70        22.03         8.28 
TCGA-MB-A5YA TCGA-MB-A8JK TCGA-MJ-A68J TCGA-MJ-A850 TCGA-MO-A47P TCGA-MO-A47R 
        0.49         4.34        17.98        15.65         7.46        10.45 
TCGA-N1-A6IA TCGA-PC-A5DK TCGA-PC-A5DL TCGA-PC-A5DO TCGA-QC-A6FX TCGA-QC-A7B5 
        4.08       120.20        37.55        81.01        20.94         5.03 
TCGA-QQ-A5V2 TCGA-QQ-A5V9 TCGA-QQ-A5VA TCGA-QQ-A5VB TCGA-QQ-A5VD TCGA-QQ-A8VD 
        1.84        46.82        18.08        48.59        30.90       130.32 
TCGA-QQ-A8VF TCGA-QQ-A8VG TCGA-RN-A68Q TCGA-SG-A6Z4 TCGA-SG-A6Z7 TCGA-SI-A71O 
       98.27        62.20         0.72        18.94         3.88        17.92 
TCGA-SI-A71P TCGA-SI-A71Q TCGA-SI-AA8B TCGA-UE-A6QT TCGA-WK-A8XO TCGA-WK-A8XQ 
       19.82        27.22         5.06        13.22        11.93         4.80 
TCGA-WK-A8XT TCGA-WK-A8Y0 TCGA-X6-A7W8 TCGA-X6-A8C3 TCGA-X6-A8C7 
       41.49        22.62        26.43        15.95        17.72 

  DEL PEAK 41(XQ22.3) MUTATED DEL PEAK 41(XQ22.3) WILD-TYPE 
                         0.07                          0.07 
  DEL PEAK 41(XQ22.3) MUTATED DEL PEAK 41(XQ22.3) WILD-TYPE 
                       188.15                        135.48 
  DEL PEAK 41(XQ22.3) MUTATED DEL PEAK 41(XQ22.3) WILD-TYPE 
                        25.71                         19.53 
[1] "0.1 - 188.2 (25.7)" "0.1 - 135.5 (19.5)"
[1] "hr=" "1.7"
D66V2, continuous
D66V3, binary
                               cls
clus                             0  1
  DEL PEAK 41(XQ22.3) MUTATED   73 47
  DEL PEAK 41(XQ22.3) WILD-TYPE 59 67
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 41(XQ22.3) MUTATED     73   47
  DEL PEAK 41(XQ22.3) WILD-TYPE   59   67
        clus
vv       DEL PEAK 41(XQ22.3) MUTATED DEL PEAK 41(XQ22.3) WILD-TYPE
  FEMALE                          73                            59
  MALE                            47                            67
[1] 2 2
[1] FALSE
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 41(XQ22.3) MUTATED       2                        10    99
  DEL PEAK 41(XQ22.3) WILD-TYPE     4                         8    95
D66V4, multiclass
                           clus
vv                          DEL PEAK 41(XQ22.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                          10
  WHITE                                              99
                           clus
vv                          DEL PEAK 41(XQ22.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                             8
  WHITE                                                95
[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"
D66V5, binary
                               cls
clus                             0  1
  DEL PEAK 41(XQ22.3) MUTATED    1 97
  DEL PEAK 41(XQ22.3) WILD-TYPE  4 94
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 41(XQ22.3) MUTATED      1   97
  DEL PEAK 41(XQ22.3) WILD-TYPE    4   94
                        clus
vv                       DEL PEAK 41(XQ22.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          97
                        clus
vv                       DEL PEAK 41(XQ22.3) WILD-TYPE
  HISPANIC OR LATINO                                 4
  NOT HISPANIC OR LATINO                            94
[1] 2 2
[1] FALSE
