[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTREAD-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/READ-TP/10006188/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/10013786/transformed.cor.cli.txt"

nPatients in clinical file=171, in cluster file=162, common to both=162
[1]  60 162
[1] "AMP PEAK  1(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           48                           114 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           48                           114 
[1] "AMP PEAK  2(1Q32.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                           48                           114 
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                           48                           114 
[1] "AMP PEAK  3(5Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           20                           142 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           20                           142 
[1] "AMP PEAK  4(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           53                           109 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           53                           109 
[1] "AMP PEAK  5(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            52                            110 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            52                            110 
[1] "AMP PEAK  6(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            69                             93 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            69                             93 
[1] "AMP PEAK  7(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                           107                             55 
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                           107                             55 
[1] "AMP PEAK  8(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                            11                            151 
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                            11                            151 
[1] "AMP PEAK  9(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            44                            118 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            44                            118 
[1] "AMP PEAK 10(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            27                            135 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            27                            135 
[1] "AMP PEAK 11(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             41                             121 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             41                             121 
[1] "AMP PEAK 12(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                            40                            122 
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                            40                            122 
[1] "AMP PEAK 13(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            123                              39 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            123                              39 
[1] "AMP PEAK 14(13Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           122                             40 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           122                             40 
[1] "AMP PEAK 15(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           117                             45 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           117                             45 
[1] "AMP PEAK 16(15Q26.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            13                            149 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            13                            149 
[1] "AMP PEAK 17(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            45                            117 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            45                            117 
[1] "AMP PEAK 18(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          43                          119 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          43                          119 
[1] "AMP PEAK 19(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            37                            125 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            37                            125 
[1] "AMP PEAK 20(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            34                            128 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            34                            128 
[1] "AMP PEAK 21(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            143                              19 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            143                              19 
[1] "AMP PEAK 22(20Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                            144                              18 
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                            144                              18 
[1] "AMP PEAK 23(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE 
                            143                              19 
  AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE 
                            143                              19 
[1] "AMP PEAK 24(XP22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                           31                           131 
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                           31                           131 
[1] "AMP PEAK 25(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                           36                           126 
  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                           36                           126 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            72                             90 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            72                             90 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         50                         112 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         50                         112 
[1] "DEL PEAK  3(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           52                           110 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           52                           110 
[1] "DEL PEAK  4(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         18                         144 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         18                         144 
[1] "DEL PEAK  5(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           29                           133 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           29                           133 
[1] "DEL PEAK  6(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            16                            146 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            16                            146 
[1] "DEL PEAK  7(4P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         59                         103 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         59                         103 
[1] "DEL PEAK  8(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           72                            90 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           72                            90 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           71                            91 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           71                            91 
[1] "DEL PEAK 10(5Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                           51                           111 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                           51                           111 
[1] "DEL PEAK 11(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           57                           105 
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           57                           105 
[1] "DEL PEAK 12(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           24                           138 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           24                           138 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         30                         132 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         30                         132 
[1] "DEL PEAK 14(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            4                           158 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            4                           158 
[1] "DEL PEAK 15(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           99                            63 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           99                            63 
[1] "DEL PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            24                            138 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            24                            138 
[1] "DEL PEAK 17(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            37                            125 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            37                            125 
[1] "DEL PEAK 18(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            47                            115 
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            47                            115 
[1] "DEL PEAK 19(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            38                            124 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            38                            124 
[1] "DEL PEAK 20(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                            33                            129 
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                            33                            129 
[1] "DEL PEAK 21(12Q22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                          24                          138 
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                          24                          138 
[1] "DEL PEAK 22(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                            68                             94 
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                            68                             94 
[1] "DEL PEAK 23(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                            70                             92 
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                            70                             92 
[1] "DEL PEAK 24(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             76                              86 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             76                              86 
[1] "DEL PEAK 25(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                            13                            149 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                            13                            149 
[1] "DEL PEAK 26(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            23                            139 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            23                            139 
[1] "DEL PEAK 27(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           110                             52 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           110                             52 
[1] "DEL PEAK 28(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                           143                             19 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                           143                             19 
[1] "DEL PEAK 29(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE 
                           138                             24 
  DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE 
                           138                             24 
[1] "DEL PEAK 30(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                            36                            126 
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                            36                            126 
[1] "DEL PEAK 31(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            60                            102 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            60                            102 
[1] "DEL PEAK 32(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                            60                            102 
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                            60                            102 
[1] "DEL PEAK 33(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                            71                             91 
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                            71                             91 
[1] "DEL PEAK 34(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             67                              95 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             67                              95 
[1] "DEL PEAK 35(XP22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                            33                            129 
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                            33                            129 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "NUMBER.OF.LYMPH.NODES"                 
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 162 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
         734          546          524         1309          412          581 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
         387         1148           NA          441          257          468 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
         609          316           NA          365          974          244 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
         215           31           61           NA           31         1400 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
          NA           NA         1035           NA         1522          366 
TCGA-AG-3600 TCGA-AG-3601 TCGA-AG-3602 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
         184           NA           NA           30          485          608 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
          NA          608           NA          243           30          912 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
          31         1003           30           30           NA          608 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
          31           NA         1124          518          396         1065 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
         426           31         1461           NA          974          608 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4015 
         853         1096          427           31          518           NA 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
          NA           30          638          424          183          790 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
         700         1126          485         1096          276           31 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
         365          943         2130         1947          334           NA 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
        1520           NA           NA         1885         1247         1157 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
          15           44           21           22          140           55 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
         310          184          184           NA          212          285 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
         144          425         1826          243          334          335 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
         457          395          365          425          457         1095 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
         216          914          394          397          306          161 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        3846         1258         1741         3932          734         1566 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
         992           15           73          625          607          636 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
         517          556          482          538          497          496 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
         499          262          350          328          415          531 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
         364          257           NA         1141          952          452 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
          12           31           20           21           16           34 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
          23           14           NA         1696           NA          804 
Variable 1:'AGE':	nDistinctValues=47,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=111,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=11,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL.TYPE"                     
 [8] "RADIATIONS.RADIATION.REGIMENINDICATION"
 [9] "COMPLETENESS.OF.RESECTION"             
[10] "NUMBER.OF.LYMPH.NODES"                 
[11] "RACE"                                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 162 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=47, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
  9  29 109  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  29 109  14 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  29 109  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  29 109  14 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
83 45 32 
[1] "table(vv)"
vv
N0 N1 N2 
83 45 32 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
83 45 32 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
83 45 32 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=2, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=17, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q21.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1Q21.3) MUTATED   37  6
  AMP PEAK  1(1Q21.3) WILD-TYPE 91 16
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           43                           107 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                            6                            16 
$`AMP PEAK  1(1Q21.3) MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       24.13        13.55        19.10        14.50        15.39        10.39 
TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3882 TCGA-AG-3999 
       32.02        46.03        34.03        19.99        19.99        28.04 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       23.01        37.02        36.03        31.00        70.03        64.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
        1.94        38.96        38.04         0.69         0.72        10.19 
TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE 
        9.37         4.73        11.01        13.97        15.02       129.27 
TCGA-DY-A1DF TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       24.13        20.55         8.61        10.78        13.64        11.97 
TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 
        9.96         0.39         0.69         0.76        18.28        47.08 
TCGA-G5-6641 
       26.43 

$`AMP PEAK  1(1Q21.3) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        43.04        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
        8.45        20.02        36.03        12.00         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
        1.02         2.01        24.00         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A020 
       25.97        15.95         9.07         1.02        12.00        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       51.98        49.97        61.97        41.00         0.49         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        4.60         1.81         6.05         6.05         6.97        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.03         7.99        10.98        15.02        12.99        12.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       17.46         8.45        37.51        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.53         1.12         0.46        55.76 

  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                         0.39                          0.46 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                       129.27                        126.44 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                        18.28                         13.94 
[1] "0.4 - 129.3 (18.3)" "0.5 - 126.4 (13.9)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  1(1Q21.3) MUTATED         7        3        12         0         1
  AMP PEAK  1(1Q21.3) WILD-TYPE      23        5        26         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  1(1Q21.3) MUTATED           1          3          5          7
  AMP PEAK  1(1Q21.3) WILD-TYPE         4          6         18          7
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK  1(1Q21.3) MUTATED          5         2
  AMP PEAK  1(1Q21.3) WILD-TYPE       13         7
D1V3, multiclass
            clus
vv           AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  STAGE I                              7                            23
  STAGE II                             3                             5
  STAGE IIA                           12                            26
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           3                             6
  STAGE IIIB                           5                            18
  STAGE IIIC                           7                             7
  STAGE IV                             5                            13
  STAGE IVA                            2                             7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  1(1Q21.3) MUTATED    3  8 28  8
  AMP PEAK  1(1Q21.3) WILD-TYPE  6 21 81  6
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  T1                           3                             6
  T2                           8                            21
  T3                          28                            81
  T4                           8                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK  1(1Q21.3) MUTATED   23 11 12
  AMP PEAK  1(1Q21.3) WILD-TYPE 60 34 20
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  N0                          23                            60
  N1                          11                            34
  N2                          12                            20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  1(1Q21.3) MUTATED   34  4   1  7
  AMP PEAK  1(1Q21.3) WILD-TYPE 89 18   1  6
D1V6, multiclass
     clus
vv    AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  M0                           34                            89
  M1                            4                            18
  M1A                           1                             1
  MX                            7                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.3) MUTATED   21 27
  AMP PEAK  1(1Q21.3) WILD-TYPE 53 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     21   27
  AMP PEAK  1(1Q21.3) WILD-TYPE   53   61
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  FEMALE                          21                            53
  MALE                            27                            61
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.3) MUTATED    41   3
  AMP PEAK  1(1Q21.3) WILD-TYPE 102  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     41    3
  AMP PEAK  1(1Q21.3) WILD-TYPE  102   10
                                clus
vv                               AMP PEAK  1(1Q21.3) MUTATED
  RECTAL ADENOCARCINOMA                                   41
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               AMP PEAK  1(1Q21.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    102
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 2 2
[1] FALSE
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.3) MUTATED     4  44
  AMP PEAK  1(1Q21.3) WILD-TYPE   2 112
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED      4   44
  AMP PEAK  1(1Q21.3) WILD-TYPE    2  112
     clus
vv    AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  NO                            4                             2
  YES                          44                           112
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  1(1Q21.3) MUTATED   33  1  3  0
  AMP PEAK  1(1Q21.3) WILD-TYPE 88  1  9  3
D1V10, multiclass
    clus
vv   AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  R0                          33                            88
  R1                           1                             1
  R2                           3                             9
  RX                           0                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q21.3) MUTATED       0                         0    29
  AMP PEAK  1(1Q21.3) WILD-TYPE     1                         3    52
D1V12, multiclass
                           clus
vv                          AMP PEAK  1(1Q21.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              29
                           clus
vv                          AMP PEAK  1(1Q21.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1Q32.2) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q32.2) MUTATED   36  8
  AMP PEAK  2(1Q32.2) WILD-TYPE 92 14
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                           44                           106 
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                            8                            14 
$`AMP PEAK  2(1Q32.2) MUTATED`
TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 
       13.55        14.50        15.39        10.39        32.02        46.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3882 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-A00Y 
       34.03         6.05        19.99        48.03        28.04        23.01 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       36.03        31.00        70.03        51.98         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6623 
       38.04         0.49         0.69         0.72        10.19         9.37 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF 
        4.73        11.01        13.97        15.02       129.27        24.13 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       32.61        20.55         8.61        10.78        13.64        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 
        8.45         9.96         0.39         0.69         0.76        18.28 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK  2(1Q32.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       37.74        10.39         8.45        20.02        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
       35.01        14.01         1.02        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        25.97        37.02        15.95         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
       12.00        64.01        10.98        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45         4.60         1.81         6.05         6.05         6.97 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       13.97        60.03         7.99        10.98        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.00        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       10.06         5.29       126.44        41.36        57.24        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       17.46        37.51        31.30        14.86         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
        0.53         1.12         0.46        55.76 

  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                         0.39                          0.46 
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                       129.27                        126.44 
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                       14.760                        14.025 
[1] "0.4 - 129.3 (14.8)" "0.5 - 126.4 (14.0)"
[1] "hr=" "1.2"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  2(1Q32.2) MUTATED         6        2        12         0         1
  AMP PEAK  2(1Q32.2) WILD-TYPE      24        6        26         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  2(1Q32.2) MUTATED           1          4          4          6
  AMP PEAK  2(1Q32.2) WILD-TYPE         4          5         19          8
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK  2(1Q32.2) MUTATED          6         3
  AMP PEAK  2(1Q32.2) WILD-TYPE       12         6
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  STAGE I                              6                            24
  STAGE II                             2                             6
  STAGE IIA                           12                            26
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           4                             5
  STAGE IIIB                           4                            19
  STAGE IIIC                           6                             8
  STAGE IV                             6                            12
  STAGE IVA                            3                             6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  2(1Q32.2) MUTATED    3  8 27  9
  AMP PEAK  2(1Q32.2) WILD-TYPE  6 21 82  5
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  T1                           3                             6
  T2                           8                            21
  T3                          27                            82
  T4                           9                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK  2(1Q32.2) MUTATED   21 12 13
  AMP PEAK  2(1Q32.2) WILD-TYPE 62 33 19
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  N0                          21                            62
  N1                          12                            33
  N2                          13                            19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  2(1Q32.2) MUTATED   33  6   1  6
  AMP PEAK  2(1Q32.2) WILD-TYPE 90 16   1  7
D2V6, multiclass
     clus
vv    AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  M0                           33                            90
  M1                            6                            16
  M1A                           1                             1
  MX                            6                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q32.2) MUTATED   22 26
  AMP PEAK  2(1Q32.2) WILD-TYPE 52 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.2) MUTATED     22   26
  AMP PEAK  2(1Q32.2) WILD-TYPE   52   62
        clus
vv       AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  FEMALE                          22                            52
  MALE                            26                            62
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.2) MUTATED    41   4
  AMP PEAK  2(1Q32.2) WILD-TYPE 102   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.2) MUTATED     41    4
  AMP PEAK  2(1Q32.2) WILD-TYPE  102    9
                                clus
vv                               AMP PEAK  2(1Q32.2) MUTATED
  RECTAL ADENOCARCINOMA                                   41
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               AMP PEAK  2(1Q32.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    102
  RECTAL MUCINOUS ADENOCARCINOMA                             9
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.2) MUTATED     3  45
  AMP PEAK  2(1Q32.2) WILD-TYPE   3 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.2) MUTATED      3   45
  AMP PEAK  2(1Q32.2) WILD-TYPE    3  111
     clus
vv    AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  NO                            3                             3
  YES                          45                           111
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  2(1Q32.2) MUTATED   32  1  3  0
  AMP PEAK  2(1Q32.2) WILD-TYPE 89  1  9  3
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  R0                          32                            89
  R1                           1                             1
  R2                           3                             9
  RX                           0                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.2) MUTATED       0                         0    30
  AMP PEAK  2(1Q32.2) WILD-TYPE     1                         3    51
D2V12, multiclass
                           clus
vv                          AMP PEAK  2(1Q32.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              30
                           clus
vv                          AMP PEAK  2(1Q32.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                51
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(5Q22.3) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  3(5Q22.3) MUTATED    19   0
  AMP PEAK  3(5Q22.3) WILD-TYPE 109  22
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           19                           131 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                            0                            22 
$`AMP PEAK  3(5Q22.3) MUTATED`
TCGA-AF-6655 TCGA-AG-3609 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A014 
       20.02        19.99         1.02         1.02        25.97        15.95 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       12.00        31.00        38.04         0.49         0.69         0.72 
TCGA-DC-6683 TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6465 
       10.06        20.55        16.31        11.51        11.97        37.51 
TCGA-F5-6811 
        1.02 

$`AMP PEAK  3(5Q22.3) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03        14.04        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
       13.94         6.02        23.01        37.02        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 
        1.94        38.96        61.97        41.00         1.45         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        13.05         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       15.85        17.69        16.34        16.41         8.61        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       13.64        17.46         8.45         9.96        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                         0.49                          0.39 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                        38.04                        129.27 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                         12.0                          14.5 
[1] "0.5 - 38.0 (12.0)"  "0.4 - 129.3 (14.5)"
[1] "hr="     "7.9e+07"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  3(5Q22.3) MUTATED         2        0         5         0         1
  AMP PEAK  3(5Q22.3) WILD-TYPE      28        8        33         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  3(5Q22.3) MUTATED           0          1          4          2
  AMP PEAK  3(5Q22.3) WILD-TYPE         5          8         19         12
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK  3(5Q22.3) MUTATED          3         0
  AMP PEAK  3(5Q22.3) WILD-TYPE       15         9
D3V3, multiclass
            clus
vv           AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  STAGE I                              2                            28
  STAGE II                             0                             8
  STAGE IIA                            5                            33
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            0                             5
  STAGE IIIA                           1                             8
  STAGE IIIB                           4                            19
  STAGE IIIC                           2                            12
  STAGE IV                             3                            15
  STAGE IVA                            0                             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  3(5Q22.3) MUTATED    0  4 15  1
  AMP PEAK  3(5Q22.3) WILD-TYPE  9 25 94 13
D3V4, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  T1                           0                             9
  T2                           4                            25
  T3                          15                            94
  T4                           1                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK  3(5Q22.3) MUTATED    9  6  4
  AMP PEAK  3(5Q22.3) WILD-TYPE 74 39 28
D3V5, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  N0                           9                            74
  N1                           6                            39
  N2                           4                            28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK  3(5Q22.3) MUTATED    15   4   0   1
  AMP PEAK  3(5Q22.3) WILD-TYPE 108  18   2  12
D3V6, multiclass
     clus
vv    AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  M0                           15                           108
  M1                            4                            18
  M1A                           0                             2
  MX                            1                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(5Q22.3) MUTATED    8 12
  AMP PEAK  3(5Q22.3) WILD-TYPE 66 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED      8   12
  AMP PEAK  3(5Q22.3) WILD-TYPE   66   76
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  FEMALE                           8                            66
  MALE                            12                            76
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    20   0
  AMP PEAK  3(5Q22.3) WILD-TYPE 123  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     20    0
  AMP PEAK  3(5Q22.3) WILD-TYPE  123   13
                                clus
vv                               AMP PEAK  3(5Q22.3) MUTATED
  RECTAL ADENOCARCINOMA                                   20
  RECTAL MUCINOUS ADENOCARCINOMA                           0
                                clus
vv                               AMP PEAK  3(5Q22.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    123
  RECTAL MUCINOUS ADENOCARCINOMA                            13
[1] 2 2
[1] FALSE
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED     0  20
  AMP PEAK  3(5Q22.3) WILD-TYPE   6 136
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED      0   20
  AMP PEAK  3(5Q22.3) WILD-TYPE    6  136
     clus
vv    AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  NO                            0                             6
  YES                          20                           136
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  AMP PEAK  3(5Q22.3) MUTATED    15   0   2   0
  AMP PEAK  3(5Q22.3) WILD-TYPE 106   2  10   3
D3V10, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  R0                          15                           106
  R1                           0                             2
  R2                           2                            10
  RX                           0                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(5Q22.3) MUTATED       0                         0    11
  AMP PEAK  3(5Q22.3) WILD-TYPE     1                         3    70
D3V12, multiclass
                           clus
vv                          AMP PEAK  3(5Q22.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              11
                           clus
vv                          AMP PEAK  3(5Q22.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(6P21.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(6P21.1) MUTATED   38  7
  AMP PEAK  4(6P21.1) WILD-TYPE 90 15
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           45                           105 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                            7                            15 
$`AMP PEAK  4(6P21.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       24.13        43.04        19.10        37.74        10.39        14.50 
TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3600 TCGA-AG-3609 
       15.39         1.02        24.00        46.03         6.05        19.99 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 
       19.99        29.98         1.02         1.02        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AH-6644 
        0.99        36.03         9.07        12.00        31.00         0.72 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 
       10.19         6.05         9.37        10.98        12.99        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       15.02        36.00        13.05       129.27        24.13        51.48 
TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 
       20.55        15.85        17.69        37.51        14.86         0.39 
TCGA-F5-6812 TCGA-G5-6233 TCGA-G5-6641 
        0.66        18.28        26.43 

$`AMP PEAK  4(6P21.1) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6655 
       17.95        17.23        13.55        12.72         8.45        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        2.01         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        0.99        15.95         7.99         0.99         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       36.03        17.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       23.01        37.02        15.95         1.02        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       41.00        38.04         0.49         1.45         0.69         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        1.81         6.05         6.97         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 
        7.99        11.01        15.02        13.97         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       18.28        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       31.30         1.02         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.46        55.76        47.08 

  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                         0.39                          0.46 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                       129.27                        126.44 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                        15.02                         13.97 
[1] "0.4 - 129.3 (15.0)" "0.5 - 126.4 (14.0)"
[1] "hr=" "1.3"
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  4(6P21.1) MUTATED         8        1         9         0         1
  AMP PEAK  4(6P21.1) WILD-TYPE      22        7        29         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  4(6P21.1) MUTATED           2          1         10          6
  AMP PEAK  4(6P21.1) WILD-TYPE         3          8         13          8
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK  4(6P21.1) MUTATED          9         5
  AMP PEAK  4(6P21.1) WILD-TYPE        9         4
D4V3, multiclass
            clus
vv           AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  STAGE I                              8                            22
  STAGE II                             1                             7
  STAGE IIA                            9                            29
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            2                             3
  STAGE IIIA                           1                             8
  STAGE IIIB                          10                            13
  STAGE IIIC                           6                             8
  STAGE IV                             9                             9
  STAGE IVA                            5                             4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK  4(6P21.1) MUTATED    4  6 38  5
  AMP PEAK  4(6P21.1) WILD-TYPE  5 23 71  9
D4V4, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  T1                           4                             5
  T2                           6                            23
  T3                          38                            71
  T4                           5                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK  4(6P21.1) MUTATED   19 17 16
  AMP PEAK  4(6P21.1) WILD-TYPE 64 28 16
D4V5, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  N0                          19                            64
  N1                          17                            28
  N2                          16                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK  4(6P21.1) MUTATED   32 12   1  7
  AMP PEAK  4(6P21.1) WILD-TYPE 91 10   1  6
D4V6, multiclass
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  M0                           32                            91
  M1                           12                            10
  M1A                           1                             1
  MX                            7                             6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                             0  1
  AMP PEAK  4(6P21.1) MUTATED   21 32
  AMP PEAK  4(6P21.1) WILD-TYPE 53 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     21   32
  AMP PEAK  4(6P21.1) WILD-TYPE   53   56
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  FEMALE                          21                            53
  MALE                            32                            56
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                             0  1
  AMP PEAK  4(6P21.1) MUTATED   50  1
  AMP PEAK  4(6P21.1) WILD-TYPE 93 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     50    1
  AMP PEAK  4(6P21.1) WILD-TYPE   93   12
                                clus
vv                               AMP PEAK  4(6P21.1) MUTATED
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK  4(6P21.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     93
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
D4V9, binary
                               cls
clus                              0   1
  AMP PEAK  4(6P21.1) MUTATED     4  49
  AMP PEAK  4(6P21.1) WILD-TYPE   2 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED      4   49
  AMP PEAK  4(6P21.1) WILD-TYPE    2  107
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  NO                            4                             2
  YES                          49                           107
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  4(6P21.1) MUTATED   36  0  7  0
  AMP PEAK  4(6P21.1) WILD-TYPE 85  2  5  3
D4V10, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  R0                          36                            85
  R1                           0                             2
  R2                           7                             5
  RX                           0                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(6P21.1) MUTATED       0                         3    27
  AMP PEAK  4(6P21.1) WILD-TYPE     1                         0    54
D4V12, multiclass
                           clus
vv                          AMP PEAK  4(6P21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              27
                           clus
vv                          AMP PEAK  4(6P21.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(8P11.23) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  5(8P11.23) MUTATED   36 13
  AMP PEAK  5(8P11.23) WILD-TYPE 92  9
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            49                            101 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            13                              9 
$`AMP PEAK  5(8P11.23) MUTATED`
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 
       37.74        20.02        10.39        36.03         1.02        24.00 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        2.01         0.99        36.95        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A01N 
       32.02        36.03         1.02         0.99        15.95        31.00 
TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 
       51.98        38.04         0.49         0.69         0.72         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6157 
        9.37         4.73        60.03         7.99        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        7.10        13.05        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
        0.49        17.00        15.85        16.31        11.51        10.78 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 
       37.51        14.86         1.02         0.69         0.46        18.28 
TCGA-G5-6572 
       47.08 

$`AMP PEAK  5(8P11.23) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AG-3575 
       12.72        10.39        14.50         8.45        15.39        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       32.02         8.02         7.07         2.01         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
       34.03        50.04        12.03         6.05        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        17.03        13.02 
TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       14.01        19.99        28.04        14.04        17.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        37.02        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       49.97         1.94        38.96        61.97        41.00         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
        4.60         1.81        10.19         6.05         6.97        13.97 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE 
       30.05        12.95        10.06         5.29       126.44       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       17.69        16.34        16.41         8.61        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       11.97         8.45         9.96        31.30         0.39         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6641 
        0.53         1.12         0.76        55.76        26.43 

  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                          0.46                           0.39 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                         60.03                         129.27 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                         15.85                          13.97 
[1] "0.5 - 60.0 (15.8)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "2.6"
D5V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  5(8P11.23) MUTATED         6        2        13         1         2
  AMP PEAK  5(8P11.23) WILD-TYPE      24        6        25         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  5(8P11.23) MUTATED           0          2          5          7
  AMP PEAK  5(8P11.23) WILD-TYPE         5          7         18          7
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  5(8P11.23) MUTATED          8         3
  AMP PEAK  5(8P11.23) WILD-TYPE       10         6
D5V3, multiclass
            clus
vv           AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  STAGE I                               6                             24
  STAGE II                              2                              6
  STAGE IIA                            13                             25
  STAGE IIB                             1                              1
  STAGE IIC                             2                              0
  STAGE III                             0                              5
  STAGE IIIA                            2                              7
  STAGE IIIB                            5                             18
  STAGE IIIC                            7                              7
  STAGE IV                              8                             10
  STAGE IVA                             3                              6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  5(8P11.23) MUTATED    1  7 36  7
  AMP PEAK  5(8P11.23) WILD-TYPE  8 22 73  7
D5V4, multiclass
    clus
vv   AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  T1                            1                              8
  T2                            7                             22
  T3                           36                             73
  T4                            7                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK  5(8P11.23) MUTATED   24 13 13
  AMP PEAK  5(8P11.23) WILD-TYPE 59 32 19
D5V5, multiclass
    clus
vv   AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  N0                           24                             59
  N1                           13                             32
  N2                           13                             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK  5(8P11.23) MUTATED   35 10   1  5
  AMP PEAK  5(8P11.23) WILD-TYPE 88 12   1  8
D5V6, multiclass
     clus
vv    AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  M0                            35                             88
  M1                            10                             12
  M1A                            1                              1
  MX                             5                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.23) MUTATED   18 34
  AMP PEAK  5(8P11.23) WILD-TYPE 56 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED     18   34
  AMP PEAK  5(8P11.23) WILD-TYPE   56   54
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  FEMALE                           18                             56
  MALE                             34                             54
[1] 2 2
[1] FALSE
D5V8, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.23) MUTATED   50  2
  AMP PEAK  5(8P11.23) WILD-TYPE 93 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED     50    2
  AMP PEAK  5(8P11.23) WILD-TYPE   93   11
                                clus
vv                               AMP PEAK  5(8P11.23) MUTATED
  RECTAL ADENOCARCINOMA                                    50
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK  5(8P11.23) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      93
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
D5V9, binary
                                cls
clus                               0   1
  AMP PEAK  5(8P11.23) MUTATED     2  50
  AMP PEAK  5(8P11.23) WILD-TYPE   4 106
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED      2   50
  AMP PEAK  5(8P11.23) WILD-TYPE    4  106
     clus
vv    AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  NO                             2                              4
  YES                           50                            106
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  5(8P11.23) MUTATED   30  0  7  2
  AMP PEAK  5(8P11.23) WILD-TYPE 91  2  5  1
D5V10, multiclass
    clus
vv   AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  R0                           30                             91
  R1                            0                              2
  R2                            7                              5
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(8P11.23) MUTATED       0                         1    31
  AMP PEAK  5(8P11.23) WILD-TYPE     1                         2    50
D5V12, multiclass
                           clus
vv                          AMP PEAK  5(8P11.23) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               31
                           clus
vv                          AMP PEAK  5(8P11.23) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  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"

Clustering(6) Variable = AMP PEAK  6(8P11.21) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(8P11.21) MUTATED   50 14
  AMP PEAK  6(8P11.21) WILD-TYPE 78  8
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            64                             86 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            14                              8 
$`AMP PEAK  6(8P11.21) MUTATED`
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       20.02        10.39        36.03         1.02        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
        2.01         0.99        32.98         1.02        36.95         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       48.03        32.02        28.04        14.04         1.02         0.99 
TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y 
       23.01        15.95         9.07         1.02        31.00        64.01 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       51.98         1.94        38.96        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        0.69         0.72         6.05         9.37         4.73        60.03 
TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
        7.99        13.97        15.02        36.00         7.10        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
        0.49        17.00        15.85        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
       13.64        37.51        14.86         1.02         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`AMP PEAK  6(8P11.21) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 
       12.00        32.02         8.02         7.07         2.01        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 
       34.03        50.04        12.03         6.05        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       19.99         7.99         0.99        29.98         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        17.03        13.02        35.01        14.01 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       19.99        36.03        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 
       25.97        37.02        36.03        12.00        70.03        10.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       49.97        61.97        41.00         4.60         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        6.05         6.97        13.97        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DG 
       12.99        12.00        30.05        12.95         5.29        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 
       17.69        16.34        16.41         8.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
        8.45         9.96        31.30         0.39         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 
        0.53         1.12 

  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                          0.46                           0.39 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                        129.27                          70.03 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                        14.450                         14.255 
[1] "0.5 - 129.3 (14.4)" "0.4 - 70.0 (14.3)" 
[1] "hr=" "1.8"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  6(8P11.21) MUTATED         8        4        18         1         2
  AMP PEAK  6(8P11.21) WILD-TYPE      22        4        20         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  6(8P11.21) MUTATED           1          4          7          6
  AMP PEAK  6(8P11.21) WILD-TYPE         4          5         16          8
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  6(8P11.21) MUTATED         12         2
  AMP PEAK  6(8P11.21) WILD-TYPE        6         7
D6V3, multiclass
            clus
vv           AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  STAGE I                               8                             22
  STAGE II                              4                              4
  STAGE IIA                            18                             20
  STAGE IIB                             1                              1
  STAGE IIC                             2                              0
  STAGE III                             1                              4
  STAGE IIIA                            4                              5
  STAGE IIIB                            7                             16
  STAGE IIIC                            6                              8
  STAGE IV                             12                              6
  STAGE IVA                             2                              7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  6(8P11.21) MUTATED    2 11 47  8
  AMP PEAK  6(8P11.21) WILD-TYPE  7 18 62  6
D6V4, multiclass
    clus
vv   AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  T1                            2                              7
  T2                           11                             18
  T3                           47                             62
  T4                            8                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK  6(8P11.21) MUTATED   34 18 15
  AMP PEAK  6(8P11.21) WILD-TYPE 49 27 17
D6V5, multiclass
    clus
vv   AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  N0                           34                             49
  N1                           18                             27
  N2                           15                             17
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK  6(8P11.21) MUTATED   47 13   1  7
  AMP PEAK  6(8P11.21) WILD-TYPE 76  9   1  6
D6V6, multiclass
     clus
vv    AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  M0                            47                             76
  M1                            13                              9
  M1A                            1                              1
  MX                             7                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                                cls
clus                              0  1
  AMP PEAK  6(8P11.21) MUTATED   30 39
  AMP PEAK  6(8P11.21) WILD-TYPE 44 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED     30   39
  AMP PEAK  6(8P11.21) WILD-TYPE   44   49
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  FEMALE                           30                             44
  MALE                             39                             49
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                              0  1
  AMP PEAK  6(8P11.21) MUTATED   64  3
  AMP PEAK  6(8P11.21) WILD-TYPE 79 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED     64    3
  AMP PEAK  6(8P11.21) WILD-TYPE   79   10
                                clus
vv                               AMP PEAK  6(8P11.21) MUTATED
  RECTAL ADENOCARCINOMA                                    64
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK  6(8P11.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      79
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                              0  1
  AMP PEAK  6(8P11.21) MUTATED    1 68
  AMP PEAK  6(8P11.21) WILD-TYPE  5 88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED      1   68
  AMP PEAK  6(8P11.21) WILD-TYPE    5   88
     clus
vv    AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  NO                             1                              5
  YES                           68                             88
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  6(8P11.21) MUTATED   41  2  9  2
  AMP PEAK  6(8P11.21) WILD-TYPE 80  0  3  1
D6V10, multiclass
    clus
vv   AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  R0                           41                             80
  R1                            2                              0
  R2                            9                              3
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(8P11.21) MUTATED       0                         1    37
  AMP PEAK  6(8P11.21) WILD-TYPE     1                         2    44
D6V12, multiclass
                           clus
vv                          AMP PEAK  6(8P11.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               37
                           clus
vv                          AMP PEAK  6(8P11.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(8Q24.21) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  7(8Q24.21) MUTATED   81 19
  AMP PEAK  7(8Q24.21) WILD-TYPE 47  3
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                           100                             50 
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                            19                              3 
$`AMP PEAK  7(8Q24.21) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       24.13        17.95        17.23        43.04        13.55        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       37.74        10.39         8.45        20.02        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       32.02         1.02        24.00         1.02        46.03         2.01 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       50.04         6.05         0.99        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        1.02        32.98         0.99         1.02        36.95        17.03 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A00Y 
       14.04         1.02        17.03         0.99        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W 
       37.02        15.95         9.07         1.02        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       64.01        51.98         1.94        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6619 
        0.49         1.45         0.69         0.72        10.19         6.05 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37         4.73        60.03         7.99        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       13.05        10.06       126.44        41.36        57.24        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
       32.61         0.49         2.40        17.00        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 
       16.31        11.51        10.78        13.64         9.96        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
       14.86         0.39         1.02         0.53         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`AMP PEAK  7(8Q24.21) WILD-TYPE`
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       19.10        14.50        15.39        12.00         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3728 
        2.01        34.03        12.03        15.95        19.99        29.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-A002 
        0.99        19.99        13.02        35.01        14.01        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 
       13.94         6.02        36.03        12.00        10.98        49.97 
TCGA-AG-A02G TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 
       38.96         4.60         1.81         6.05         6.97        13.97 
TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG 
       15.02        30.05        12.95         5.29       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 
       20.55        19.96        20.91        18.28        17.69        16.41 
TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 
        8.61        17.46        11.97         8.45        31.30         0.66 
TCGA-F5-6813 TCGA-F5-6861 
        0.69         1.12 

  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                          0.39                           0.66 
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                        126.44                         129.27 
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                        14.450                         14.255 
[1] "0.4 - 126.4 (14.4)" "0.7 - 129.3 (14.3)"
[1] "hr=" "2.4"
D7V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  7(8Q24.21) MUTATED        16        6        28         1         2
  AMP PEAK  7(8Q24.21) WILD-TYPE      14        2        10         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  7(8Q24.21) MUTATED           3          5         13         11
  AMP PEAK  7(8Q24.21) WILD-TYPE         2          4         10          3
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  7(8Q24.21) MUTATED         15         3
  AMP PEAK  7(8Q24.21) WILD-TYPE        3         6
D7V3, multiclass
            clus
vv           AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  STAGE I                              16                             14
  STAGE II                              6                              2
  STAGE IIA                            28                             10
  STAGE IIB                             1                              1
  STAGE IIC                             2                              0
  STAGE III                             3                              2
  STAGE IIIA                            5                              4
  STAGE IIIB                           13                             10
  STAGE IIIC                           11                              3
  STAGE IV                             15                              3
  STAGE IVA                             3                              6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  7(8Q24.21) MUTATED    4 18 74 10
  AMP PEAK  7(8Q24.21) WILD-TYPE  5 11 35  4
D7V4, multiclass
    clus
vv   AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  T1                            4                              5
  T2                           18                             11
  T3                           74                             35
  T4                           10                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK  7(8Q24.21) MUTATED   54 28 23
  AMP PEAK  7(8Q24.21) WILD-TYPE 29 17  9
D7V5, multiclass
    clus
vv   AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  N0                           54                             29
  N1                           28                             17
  N2                           23                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK  7(8Q24.21) MUTATED   78 17   1  9
  AMP PEAK  7(8Q24.21) WILD-TYPE 45  5   1  4
D7V6, multiclass
     clus
vv    AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  M0                            78                             45
  M1                            17                              5
  M1A                            1                              1
  MX                             9                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q24.21) MUTATED   48 59
  AMP PEAK  7(8Q24.21) WILD-TYPE 26 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.21) MUTATED     48   59
  AMP PEAK  7(8Q24.21) WILD-TYPE   26   29
        clus
vv       AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  FEMALE                           48                             26
  MALE                             59                             29
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q24.21) MUTATED   99  5
  AMP PEAK  7(8Q24.21) WILD-TYPE 44  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.21) MUTATED     99    5
  AMP PEAK  7(8Q24.21) WILD-TYPE   44    8
                                clus
vv                               AMP PEAK  7(8Q24.21) MUTATED
  RECTAL ADENOCARCINOMA                                    99
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK  7(8Q24.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      44
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q24.21) MUTATED     5 102
  AMP PEAK  7(8Q24.21) WILD-TYPE   1  54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.21) MUTATED      5  102
  AMP PEAK  7(8Q24.21) WILD-TYPE    1   54
     clus
vv    AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  NO                             5                              1
  YES                          102                             54
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  7(8Q24.21) MUTATED   76  2 10  2
  AMP PEAK  7(8Q24.21) WILD-TYPE 45  0  2  1
D7V10, multiclass
    clus
vv   AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  R0                           76                             45
  R1                            2                              0
  R2                           10                              2
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8Q24.21) MUTATED       0                         3    55
  AMP PEAK  7(8Q24.21) WILD-TYPE     1                         0    26
D7V12, multiclass
                           clus
vv                          AMP PEAK  7(8Q24.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               55
                           clus
vv                          AMP PEAK  7(8Q24.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(10Q22.2) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  8(10Q22.2) MUTATED     9   1
  AMP PEAK  8(10Q22.2) WILD-TYPE 119  21
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                            10                            140 
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                             1                             21 
$`AMP PEAK  8(10Q22.2) MUTATED`
TCGA-AF-2689 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3999 TCGA-AG-A014 TCGA-AG-A01W 
       17.95        46.03        50.04        28.04        15.95        70.03 
TCGA-AG-A020 TCGA-BM-6198 TCGA-CI-6619 TCGA-DC-4745 
       10.98        10.19         6.05        10.98 

$`AMP PEAK  8(10Q22.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
        1.02         2.01        24.00         1.02        34.03         2.01 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        37.02        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 
        9.07         1.02        12.00        31.00        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        0.49         1.45         0.69         0.72         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
        7.99        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        36.00         7.10        30.05        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                          6.05                           0.39 
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                         70.03                         129.27 
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                        16.950                         14.025 
[1] "6.0 - 70.0 (16.9)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "2.3"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  8(10Q22.2) MUTATED         2        1         2         0         0
  AMP PEAK  8(10Q22.2) WILD-TYPE      28        7        36         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  8(10Q22.2) MUTATED           1          0          2          1
  AMP PEAK  8(10Q22.2) WILD-TYPE         4          9         21         13
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  8(10Q22.2) MUTATED          2         0
  AMP PEAK  8(10Q22.2) WILD-TYPE       16         9
D8V3, multiclass
            clus
vv           AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  STAGE I                               2                             28
  STAGE II                              1                              7
  STAGE IIA                             2                             36
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            2                             21
  STAGE IIIC                            1                             13
  STAGE IV                              2                             16
  STAGE IVA                             0                              9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  8(10Q22.2) MUTATED     0   2   9   0
  AMP PEAK  8(10Q22.2) WILD-TYPE   9  27 100  14
D8V4, multiclass
    clus
vv   AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  T1                            0                              9
  T2                            2                             27
  T3                            9                            100
  T4                            0                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK  8(10Q22.2) MUTATED    5  4  2
  AMP PEAK  8(10Q22.2) WILD-TYPE 78 41 30
D8V5, multiclass
    clus
vv   AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  N0                            5                             78
  N1                            4                             41
  N2                            2                             30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK  8(10Q22.2) MUTATED     8   2   0   0
  AMP PEAK  8(10Q22.2) WILD-TYPE 115  20   2  13
D8V6, multiclass
     clus
vv    AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  M0                             8                            115
  M1                             2                             20
  M1A                            0                              2
  MX                             0                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(10Q22.2) MUTATED    6  5
  AMP PEAK  8(10Q22.2) WILD-TYPE 68 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(10Q22.2) MUTATED      6    5
  AMP PEAK  8(10Q22.2) WILD-TYPE   68   83
        clus
vv       AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  FEMALE                            6                             68
  MALE                              5                             83
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                               0   1
  AMP PEAK  8(10Q22.2) MUTATED     9   1
  AMP PEAK  8(10Q22.2) WILD-TYPE 134  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(10Q22.2) MUTATED      9    1
  AMP PEAK  8(10Q22.2) WILD-TYPE  134   12
                                clus
vv                               AMP PEAK  8(10Q22.2) MUTATED
  RECTAL ADENOCARCINOMA                                     9
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK  8(10Q22.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     134
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
D8V9, binary
                                cls
clus                               0   1
  AMP PEAK  8(10Q22.2) MUTATED     1  10
  AMP PEAK  8(10Q22.2) WILD-TYPE   5 146
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(10Q22.2) MUTATED      1   10
  AMP PEAK  8(10Q22.2) WILD-TYPE    5  146
     clus
vv    AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  NO                             1                              5
  YES                           10                            146
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  8(10Q22.2) MUTATED     9   0   0   0
  AMP PEAK  8(10Q22.2) WILD-TYPE 112   2  12   3
D8V10, multiclass
    clus
vv   AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  R0                            9                            112
  R1                            0                              2
  R2                            0                             12
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(10Q22.2) MUTATED       0                         0     4
  AMP PEAK  8(10Q22.2) WILD-TYPE     1                         3    77
D8V12, multiclass
                           clus
vv                          AMP PEAK  8(10Q22.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                4
                           clus
vv                          AMP PEAK  8(10Q22.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 77
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(11P15.5) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(11P15.5) MUTATED   33  7
  AMP PEAK  9(11P15.5) WILD-TYPE 95 15
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            40                            110 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                             7                             15 
$`AMP PEAK  9(11P15.5) MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       17.95        17.23        13.55        10.39         8.45        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3587 
       10.39        36.03        12.00         8.02         2.01        46.03 
TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3894 TCGA-AG-4001 
       34.03        19.99        19.99         0.99        14.01        36.03 
TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 
        1.02        25.97        31.00         4.60        10.19         9.37 
TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       13.97        11.01        15.02        12.99        12.00        36.00 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 
       30.05       126.44         0.49         2.40        20.55        16.31 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6861 TCGA-G5-6233 
        0.39         1.02         1.12        18.28 

$`AMP PEAK  9(11P15.5) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       24.13        43.04        19.10        12.72        37.74        14.50 
TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       15.39        32.02         7.07         1.02        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       17.03         0.99        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       38.96        61.97        41.00        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72         1.81         6.05         6.05         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6156 
        4.73        60.03         7.99        10.98        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
        7.10        12.95        13.05        10.06         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6507 
       57.24       129.27        24.13        51.48        32.61        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.69         0.53         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                          0.39                           0.46 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                        126.44                         129.27 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                         13.76                          14.94 
[1] "0.4 - 126.4 (13.8)" "0.5 - 129.3 (14.9)"
[1] "hr=" "1.8"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  9(11P15.5) MUTATED         9        2        14         1         1
  AMP PEAK  9(11P15.5) WILD-TYPE      21        6        24         1         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  9(11P15.5) MUTATED           2          3          3          2
  AMP PEAK  9(11P15.5) WILD-TYPE         3          6         20         12
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  9(11P15.5) MUTATED          6         1
  AMP PEAK  9(11P15.5) WILD-TYPE       12         8
D9V3, multiclass
            clus
vv           AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  STAGE I                               9                             21
  STAGE II                              2                              6
  STAGE IIA                            14                             24
  STAGE IIB                             1                              1
  STAGE IIC                             1                              1
  STAGE III                             2                              3
  STAGE IIIA                            3                              6
  STAGE IIIB                            3                             20
  STAGE IIIC                            2                             12
  STAGE IV                              6                             12
  STAGE IVA                             1                              8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK  9(11P15.5) MUTATED    3  8 29  4
  AMP PEAK  9(11P15.5) WILD-TYPE  6 21 80 10
D9V4, multiclass
    clus
vv   AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  T1                            3                              6
  T2                            8                             21
  T3                           29                             80
  T4                            4                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK  9(11P15.5) MUTATED   28  8  8
  AMP PEAK  9(11P15.5) WILD-TYPE 55 37 24
D9V5, multiclass
    clus
vv   AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  N0                           28                             55
  N1                            8                             37
  N2                            8                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK  9(11P15.5) MUTATED   35  6   0  2
  AMP PEAK  9(11P15.5) WILD-TYPE 88 16   2 11
D9V6, multiclass
     clus
vv    AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  M0                            35                             88
  M1                             6                             16
  M1A                            0                              2
  MX                             2                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                                cls
clus                              0  1
  AMP PEAK  9(11P15.5) MUTATED   20 24
  AMP PEAK  9(11P15.5) WILD-TYPE 54 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED     20   24
  AMP PEAK  9(11P15.5) WILD-TYPE   54   64
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  FEMALE                           20                             54
  MALE                             24                             64
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                               0   1
  AMP PEAK  9(11P15.5) MUTATED    42   1
  AMP PEAK  9(11P15.5) WILD-TYPE 101  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED     42    1
  AMP PEAK  9(11P15.5) WILD-TYPE  101   12
                                clus
vv                               AMP PEAK  9(11P15.5) MUTATED
  RECTAL ADENOCARCINOMA                                    42
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK  9(11P15.5) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     101
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
D9V9, binary
                                cls
clus                               0   1
  AMP PEAK  9(11P15.5) MUTATED     2  42
  AMP PEAK  9(11P15.5) WILD-TYPE   4 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED      2   42
  AMP PEAK  9(11P15.5) WILD-TYPE    4  114
     clus
vv    AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  NO                             2                              4
  YES                           42                            114
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  9(11P15.5) MUTATED   35  0  3  0
  AMP PEAK  9(11P15.5) WILD-TYPE 86  2  9  3
D9V10, multiclass
    clus
vv   AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  R0                           35                             86
  R1                            0                              2
  R2                            3                              9
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(11P15.5) MUTATED       0                         3    23
  AMP PEAK  9(11P15.5) WILD-TYPE     1                         0    58
D9V12, multiclass
                           clus
vv                          AMP PEAK  9(11P15.5) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               23
                           clus
vv                          AMP PEAK  9(11P15.5) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(11Q13.3) MUTATION ANALYSIS
D10V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 10(11Q13.3) MUTATED    22   3
  AMP PEAK 10(11Q13.3) WILD-TYPE 106  19
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            25                            125 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                             3                             19 
$`AMP PEAK 10(11Q13.3) MUTATED`
TCGA-AF-2690 TCGA-AF-3913 TCGA-AG-3575 TCGA-AG-3612 TCGA-AG-3883 TCGA-AG-4001 
       17.23        10.39        12.00        19.99         1.02        36.03 
TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A01Y TCGA-AH-6897 TCGA-CI-6623 
        1.02        25.97        31.00        64.01         4.60         9.37 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
        4.73        11.01        12.99        12.00        15.02        36.00 
TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-EI-6514 TCGA-EI-6885 TCGA-F5-6810 
        7.10         5.29       129.27        16.31        13.64         0.39 
TCGA-F5-6811 
        1.02 

$`AMP PEAK 10(11Q13.3) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        32.02         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
        1.02        48.03        32.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       17.03         0.99        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72         1.81        10.19         6.05         6.05         6.97 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 
       13.97        60.03         7.99        10.98        15.02        13.97 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05        10.06       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
       57.24        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       14.86         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                          0.39                           0.46 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                        129.27                         126.44 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                         12.00                          15.02 
[1] "0.4 - 129.3 (12.0)" "0.5 - 126.4 (15.0)"
[1] "hr=" "1.2"
D10V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 10(11Q13.3) MUTATED         7        3         7         0         0
  AMP PEAK 10(11Q13.3) WILD-TYPE      23        5        31         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 10(11Q13.3) MUTATED           1          0          2          1
  AMP PEAK 10(11Q13.3) WILD-TYPE         4          9         21         13
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 10(11Q13.3) MUTATED          4         2
  AMP PEAK 10(11Q13.3) WILD-TYPE       14         7
D10V3, multiclass
            clus
vv           AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  STAGE I                               7                             23
  STAGE II                              3                              5
  STAGE IIA                             7                             31
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            2                             21
  STAGE IIIC                            1                             13
  STAGE IV                              4                             14
  STAGE IVA                             2                              7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 10(11Q13.3) MUTATED    1  7 16  3
  AMP PEAK 10(11Q13.3) WILD-TYPE  8 22 93 11
D10V4, multiclass
    clus
vv   AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  T1                            1                              8
  T2                            7                             22
  T3                           16                             93
  T4                            3                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK 10(11Q13.3) MUTATED   18  5  4
  AMP PEAK 10(11Q13.3) WILD-TYPE 65 40 28
D10V5, multiclass
    clus
vv   AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  N0                           18                             65
  N1                            5                             40
  N2                            4                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 10(11Q13.3) MUTATED    20   5   1   1
  AMP PEAK 10(11Q13.3) WILD-TYPE 103  17   1  12
D10V6, multiclass
     clus
vv    AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  M0                            20                            103
  M1                             5                             17
  M1A                            1                              1
  MX                             1                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                                cls
clus                              0  1
  AMP PEAK 10(11Q13.3) MUTATED   12 15
  AMP PEAK 10(11Q13.3) WILD-TYPE 62 73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED     12   15
  AMP PEAK 10(11Q13.3) WILD-TYPE   62   73
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  FEMALE                           12                             62
  MALE                             15                             73
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                               0   1
  AMP PEAK 10(11Q13.3) MUTATED    26   1
  AMP PEAK 10(11Q13.3) WILD-TYPE 117  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED     26    1
  AMP PEAK 10(11Q13.3) WILD-TYPE  117   12
                                clus
vv                               AMP PEAK 10(11Q13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    26
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 10(11Q13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     117
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(11Q13.3) MUTATED     0  27
  AMP PEAK 10(11Q13.3) WILD-TYPE   6 129
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED      0   27
  AMP PEAK 10(11Q13.3) WILD-TYPE    6  129
     clus
vv    AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  NO                             0                              6
  YES                           27                            129
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(11Q13.3) MUTATED    19   0   2   1
  AMP PEAK 10(11Q13.3) WILD-TYPE 102   2  10   2
D10V10, multiclass
    clus
vv   AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  R0                           19                            102
  R1                            0                              2
  R2                            2                             10
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(11Q13.3) MUTATED       1                         3    14
  AMP PEAK 10(11Q13.3) WILD-TYPE     0                         0    67
D10V12, multiclass
                           clus
vv                          AMP PEAK 10(11Q13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               14
                           clus
vv                          AMP PEAK 10(11Q13.3) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(12P13.33) MUTATION ANALYSIS
D11V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 11(12P13.33) MUTATED   31  7
  AMP PEAK 11(12P13.33) WILD-TYPE 97 15
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             38                             112 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                              7                              15 
$`AMP PEAK 11(12P13.33) MUTATED`
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 
       19.10        12.72        37.74        14.50         8.45        10.39 
TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 
       36.03        46.03         2.01         6.05        19.99         7.99 
TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4022 
        1.02         1.02        36.95         1.02        36.03         0.99 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6624 TCGA-CL-5917 
       15.95        36.03        38.96        61.97         4.73        60.03 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1H8 
       13.05        10.06         5.29       126.44        57.24        32.61 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6812 
       19.96        18.28        17.69        13.64        11.97         0.66 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`AMP PEAK 11(12P13.33) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3913 
       24.13        17.95        17.23        43.04        13.55        10.39 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       15.39        20.02        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3598 
        1.02         2.01        24.00         1.02        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       12.03         0.99        15.95        19.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 
       32.98         0.99         0.99        19.99        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01        48.03        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        23.01        37.02         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        6.97         9.37        13.97         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF 
        7.10        30.05        12.95        41.36       129.27        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       14.86         0.39         1.02         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.76         0.46        55.76        47.08 

  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                           0.66                            0.39 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                         126.44                          129.27 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                          16.82                           13.99 
[1] "0.7 - 126.4 (16.8)" "0.4 - 129.3 (14.0)"
[1] "hr=" "1"  
D11V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 11(12P13.33) MUTATED         9        4        10         0
  AMP PEAK 11(12P13.33) WILD-TYPE      21        4        28         2
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 11(12P13.33) MUTATED           1         0          2          4
  AMP PEAK 11(12P13.33) WILD-TYPE         1         5          7         19
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 11(12P13.33) MUTATED            4        5         2
  AMP PEAK 11(12P13.33) WILD-TYPE         10       13         7
D11V3, multiclass
            clus
vv           AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  STAGE I                                9                              21
  STAGE II                               4                               4
  STAGE IIA                             10                              28
  STAGE IIB                              0                               2
  STAGE IIC                              1                               1
  STAGE III                              0                               5
  STAGE IIIA                             2                               7
  STAGE IIIB                             4                              19
  STAGE IIIC                             4                              10
  STAGE IV                               5                              13
  STAGE IVA                              2                               7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 11(12P13.33) MUTATED    2 11 25  3
  AMP PEAK 11(12P13.33) WILD-TYPE  7 18 84 11
D11V4, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  T1                             2                               7
  T2                            11                              18
  T3                            25                              84
  T4                             3                              11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  AMP PEAK 11(12P13.33) MUTATED   24  9  8
  AMP PEAK 11(12P13.33) WILD-TYPE 59 36 24
D11V5, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  N0                            24                              59
  N1                             9                              36
  N2                             8                              24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  AMP PEAK 11(12P13.33) MUTATED   30  4   0  7
  AMP PEAK 11(12P13.33) WILD-TYPE 93 18   2  6
D11V6, multiclass
     clus
vv    AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  M0                             30                              93
  M1                              4                              18
  M1A                             0                               2
  MX                              7                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                                 cls
clus                               0  1
  AMP PEAK 11(12P13.33) MUTATED   17 24
  AMP PEAK 11(12P13.33) WILD-TYPE 57 64
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     17   24
  AMP PEAK 11(12P13.33) WILD-TYPE   57   64
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  FEMALE                            17                              57
  MALE                              24                              64
[1] 2 2
[1] FALSE
D11V8, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED    33   5
  AMP PEAK 11(12P13.33) WILD-TYPE 110   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     33    5
  AMP PEAK 11(12P13.33) WILD-TYPE  110    8
                                clus
vv                               AMP PEAK 11(12P13.33) MUTATED
  RECTAL ADENOCARCINOMA                                     33
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 11(12P13.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      110
  RECTAL MUCINOUS ADENOCARCINOMA                               8
[1] 2 2
[1] FALSE
D11V9, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED     3  38
  AMP PEAK 11(12P13.33) WILD-TYPE   3 118
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED      3   38
  AMP PEAK 11(12P13.33) WILD-TYPE    3  118
     clus
vv    AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  NO                              3                               3
  YES                            38                             118
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 11(12P13.33) MUTATED   28  0  3  2
  AMP PEAK 11(12P13.33) WILD-TYPE 93  2  9  1
D11V10, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  R0                            28                              93
  R1                             0                               2
  R2                             3                               9
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(12P13.33) MUTATED       1                         0    21
  AMP PEAK 11(12P13.33) WILD-TYPE     0                         3    60
D11V12, multiclass
                           clus
vv                          AMP PEAK 11(12P13.33) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                21
                           clus
vv                          AMP PEAK 11(12P13.33) WILD-TYPE
  ASIAN                                                   0
  BLACK OR AFRICAN AMERICAN                               3
  WHITE                                                  60
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(12P12.1) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(12P12.1) MUTATED   30  6
  AMP PEAK 12(12P12.1) WILD-TYPE 98 16
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                            36                            114 
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                             6                             16 
$`AMP PEAK 12(12P12.1) MUTATED`
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 
       19.10        12.72        37.74        14.50         8.45        10.39 
TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 
       36.03        46.03         2.01         6.05        19.99         7.99 
TCGA-AG-3731 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
        1.02         1.02        36.95         1.02        28.04        36.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6620 TCGA-CI-6624 
       15.95        36.03        38.96        61.97         6.05         4.73 
TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 
       60.03        13.05        10.06         5.29        32.61        19.96 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-G5-6233 TCGA-G5-6641 
       18.28        17.69        13.64        11.97        18.28        26.43 

$`AMP PEAK 12(12P12.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3913 
       24.13        17.95        17.23        43.04        13.55        10.39 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       15.39        20.02        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3598 
        1.02         2.01        24.00         1.02        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       12.03         0.99        15.95        19.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 
       32.98         0.99         0.99        19.99        17.03        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 
       35.01        14.01        48.03        32.02        19.99        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         0.99        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       25.97        23.01        37.02         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 
        0.72         4.60         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        9.37        13.97         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       30.05        12.95       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        17.46         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76         0.46        55.76        47.08 

  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                          1.02                           0.39 
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                         61.97                         129.27 
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                         16.82                          13.99 
[1] "1.0 - 62.0 (16.8)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.1"
D12V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 12(12P12.1) MUTATED         9        3         8         0         1
  AMP PEAK 12(12P12.1) WILD-TYPE      21        5        30         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 12(12P12.1) MUTATED           0          2          3          5
  AMP PEAK 12(12P12.1) WILD-TYPE         5          7         20          9
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 12(12P12.1) MUTATED          6         3
  AMP PEAK 12(12P12.1) WILD-TYPE       12         6
D12V3, multiclass
            clus
vv           AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  STAGE I                               9                             21
  STAGE II                              3                              5
  STAGE IIA                             8                             30
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             0                              5
  STAGE IIIA                            2                              7
  STAGE IIIB                            3                             20
  STAGE IIIC                            5                              9
  STAGE IV                              6                             12
  STAGE IVA                             3                              6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 12(12P12.1) MUTATED    2 11 24  3
  AMP PEAK 12(12P12.1) WILD-TYPE  7 18 85 11
D12V4, multiclass
    clus
vv   AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  T1                            2                              7
  T2                           11                             18
  T3                           24                             85
  T4                            3                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK 12(12P12.1) MUTATED   21  9 10
  AMP PEAK 12(12P12.1) WILD-TYPE 62 36 22
D12V5, multiclass
    clus
vv   AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  N0                           21                             62
  N1                            9                             36
  N2                           10                             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 12(12P12.1) MUTATED   27  6   0  7
  AMP PEAK 12(12P12.1) WILD-TYPE 96 16   2  6
D12V6, multiclass
     clus
vv    AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  M0                            27                             96
  M1                             6                             16
  M1A                            0                              2
  MX                             7                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                cls
clus                              0  1
  AMP PEAK 12(12P12.1) MUTATED   17 23
  AMP PEAK 12(12P12.1) WILD-TYPE 57 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12P12.1) MUTATED     17   23
  AMP PEAK 12(12P12.1) WILD-TYPE   57   65
        clus
vv       AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  FEMALE                           17                             57
  MALE                             23                             65
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                               0   1
  AMP PEAK 12(12P12.1) MUTATED    32   5
  AMP PEAK 12(12P12.1) WILD-TYPE 111   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12P12.1) MUTATED     32    5
  AMP PEAK 12(12P12.1) WILD-TYPE  111    8
                                clus
vv                               AMP PEAK 12(12P12.1) MUTATED
  RECTAL ADENOCARCINOMA                                    32
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 12(12P12.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     111
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
D12V9, binary
                                cls
clus                               0   1
  AMP PEAK 12(12P12.1) MUTATED     3  37
  AMP PEAK 12(12P12.1) WILD-TYPE   3 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12P12.1) MUTATED      3   37
  AMP PEAK 12(12P12.1) WILD-TYPE    3  119
     clus
vv    AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  NO                             3                              3
  YES                           37                            119
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 12(12P12.1) MUTATED   27  0  4  2
  AMP PEAK 12(12P12.1) WILD-TYPE 94  2  8  1
D12V10, multiclass
    clus
vv   AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  R0                           27                             94
  R1                            0                              2
  R2                            4                              8
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(12P12.1) MUTATED       1                         0    19
  AMP PEAK 12(12P12.1) WILD-TYPE     0                         3    62
D12V12, multiclass
                           clus
vv                          AMP PEAK 12(12P12.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               19
                           clus
vv                          AMP PEAK 12(12P12.1) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(13Q12.13) MUTATION ANALYSIS
D13V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 13(13Q12.13) MUTATED   93 20
  AMP PEAK 13(13Q12.13) WILD-TYPE 35  2
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            113                              37 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                             20                               2 
$`AMP PEAK 13(13Q12.13) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
       10.39         7.07         1.02         2.01         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 
       34.03         2.01         0.99        19.99        19.99         0.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
       29.98         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C 
       36.03        14.04         1.02        17.03         0.99         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       25.97        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       12.00        51.98        49.97         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 
        0.49         0.69         0.72         4.60         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       10.98        11.01        15.02        12.99        12.00        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       36.00         7.10        30.05        13.05        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       14.86         0.39         1.02         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 13(13Q12.13) WILD-TYPE`
TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3584 
       12.72        36.03        12.00        32.02         8.02        24.00 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 
       50.04        12.03         6.05        15.95         7.99         1.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 TCGA-AG-A008 
       32.98         0.99        13.02        48.03        20.98        13.94 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02N 
        1.02        31.00        70.03        64.01        10.98        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-DC-6155 TCGA-DC-6681 
       41.00         1.45         1.81        10.19        13.97        12.95 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6814 
        5.29        19.96         8.61        13.64        17.46         0.53 
TCGA-F5-6861 
        1.12 

  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                           0.39                            0.53 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                         129.27                           70.03 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                          15.02                           13.02 
[1] "0.4 - 129.3 (15.0)" "0.5 - 70.0 (13.0)" 
[1] "hr=" "3.7"
D13V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(13Q12.13) MUTATED        21        2        28         2
  AMP PEAK 13(13Q12.13) WILD-TYPE       9        6        10         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 13(13Q12.13) MUTATED           2         4          6         20
  AMP PEAK 13(13Q12.13) WILD-TYPE         0         1          3          3
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 13(13Q12.13) MUTATED           13       14         8
  AMP PEAK 13(13Q12.13) WILD-TYPE          1        4         1
D13V3, multiclass
            clus
vv           AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  STAGE I                               21                               9
  STAGE II                               2                               6
  STAGE IIA                             28                              10
  STAGE IIB                              2                               0
  STAGE IIC                              2                               0
  STAGE III                              4                               1
  STAGE IIIA                             6                               3
  STAGE IIIB                            20                               3
  STAGE IIIC                            13                               1
  STAGE IV                              14                               4
  STAGE IVA                              8                               1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 13(13Q12.13) MUTATED    7 19 82 14
  AMP PEAK 13(13Q12.13) WILD-TYPE  2 10 27  0
D13V4, multiclass
    clus
vv   AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  T1                             7                               2
  T2                            19                              10
  T3                            82                              27
  T4                            14                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  AMP PEAK 13(13Q12.13) MUTATED   55 37 29
  AMP PEAK 13(13Q12.13) WILD-TYPE 28  8  3
D13V5, multiclass
    clus
vv   AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  N0                            55                              28
  N1                            37                               8
  N2                            29                               3
[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"
                                 vv
clus                              M0 M1 M1A MX
  AMP PEAK 13(13Q12.13) MUTATED   91 18   1 12
  AMP PEAK 13(13Q12.13) WILD-TYPE 32  4   1  1
D13V6, multiclass
     clus
vv    AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  M0                             91                              32
  M1                             18                               4
  M1A                             1                               1
  MX                             12                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                                 cls
clus                               0  1
  AMP PEAK 13(13Q12.13) MUTATED   55 68
  AMP PEAK 13(13Q12.13) WILD-TYPE 19 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED     55   68
  AMP PEAK 13(13Q12.13) WILD-TYPE   19   20
        clus
vv       AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  FEMALE                            55                              19
  MALE                              68                              20
[1] 2 2
[1] FALSE
D13V8, binary
                                 cls
clus                                0   1
  AMP PEAK 13(13Q12.13) MUTATED   114   5
  AMP PEAK 13(13Q12.13) WILD-TYPE  29   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED    114    5
  AMP PEAK 13(13Q12.13) WILD-TYPE   29    8
                                clus
vv                               AMP PEAK 13(13Q12.13) MUTATED
  RECTAL ADENOCARCINOMA                                    114
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 13(13Q12.13) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       29
  RECTAL MUCINOUS ADENOCARCINOMA                               8
[1] 2 2
[1] FALSE
D13V9, binary
                                 cls
clus                                0   1
  AMP PEAK 13(13Q12.13) MUTATED     4 119
  AMP PEAK 13(13Q12.13) WILD-TYPE   2  37
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED      4  119
  AMP PEAK 13(13Q12.13) WILD-TYPE    2   37
     clus
vv    AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  NO                              4                               2
  YES                           119                              37
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 13(13Q12.13) MUTATED   88  2  9  2
  AMP PEAK 13(13Q12.13) WILD-TYPE 33  0  3  1
D13V10, multiclass
    clus
vv   AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  R0                            88                              33
  R1                             2                               0
  R2                             9                               3
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(13Q12.13) MUTATED       0                         3    69
  AMP PEAK 13(13Q12.13) WILD-TYPE     1                         0    12
D13V12, multiclass
                           clus
vv                          AMP PEAK 13(13Q12.13) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                69
                           clus
vv                          AMP PEAK 13(13Q12.13) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                  12
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(13Q12.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(13Q12.2) MUTATED   93 19
  AMP PEAK 14(13Q12.2) WILD-TYPE 35  3
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           112                             38 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                            19                              3 
$`AMP PEAK 14(13Q12.2) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07         1.02         2.01         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
        2.01         0.99        19.99        19.99         0.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        17.03        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01         1.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03         0.99         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       23.01        37.02        15.95        36.03         9.07        12.00 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       51.98        49.97         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 
        0.49         0.69         0.72         4.60         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       11.01        15.02        12.99        12.00        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
        7.10        30.05        13.05        10.06       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        20.55        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39         1.02         0.66         0.69         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

$`AMP PEAK 14(13Q12.2) WILD-TYPE`
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72         8.45        36.03        12.00        32.02         8.02 
TCGA-AG-3584 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 
       24.00        50.04        12.03         6.05        15.95         7.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 
        1.02        32.98         0.99        13.02        48.03        20.98 
TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       13.94         1.02        31.00        70.03        64.01        10.98 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 
       61.97         1.45         1.81        10.19         6.05        13.97 
TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       12.95         5.29        19.96         8.61        13.64        17.46 
TCGA-F5-6814 TCGA-F5-6861 
        0.53         1.12 

  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                          0.39                           0.53 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                        129.27                          70.03 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                        15.620                         12.835 
[1] "0.4 - 129.3 (15.6)" "0.5 - 70.0 (12.8)" 
[1] "hr=" "2.2"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 14(13Q12.2) MUTATED        21        2        28         2         2
  AMP PEAK 14(13Q12.2) WILD-TYPE       9        6        10         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 14(13Q12.2) MUTATED           4          6         20         13
  AMP PEAK 14(13Q12.2) WILD-TYPE         1          3          3          1
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 14(13Q12.2) MUTATED         14         7
  AMP PEAK 14(13Q12.2) WILD-TYPE        4         2
D14V3, multiclass
            clus
vv           AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  STAGE I                              21                              9
  STAGE II                              2                              6
  STAGE IIA                            28                             10
  STAGE IIB                             2                              0
  STAGE IIC                             2                              0
  STAGE III                             4                              1
  STAGE IIIA                            6                              3
  STAGE IIIB                           20                              3
  STAGE IIIC                           13                              1
  STAGE IV                             14                              4
  STAGE IVA                             7                              2
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 14(13Q12.2) MUTATED    7 19 81 14
  AMP PEAK 14(13Q12.2) WILD-TYPE  2 10 28  0
D14V4, multiclass
    clus
vv   AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  T1                            7                              2
  T2                           19                             10
  T3                           81                             28
  T4                           14                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK 14(13Q12.2) MUTATED   55 36 29
  AMP PEAK 14(13Q12.2) WILD-TYPE 28  9  3
D14V5, multiclass
    clus
vv   AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  N0                           55                             28
  N1                           36                              9
  N2                           29                              3
[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"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 14(13Q12.2) MUTATED   91 17   1 12
  AMP PEAK 14(13Q12.2) WILD-TYPE 32  5   1  1
D14V6, multiclass
     clus
vv    AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  M0                            91                             32
  M1                            17                              5
  M1A                            1                              1
  MX                            12                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                              0  1
  AMP PEAK 14(13Q12.2) MUTATED   53 69
  AMP PEAK 14(13Q12.2) WILD-TYPE 21 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED     53   69
  AMP PEAK 14(13Q12.2) WILD-TYPE   21   19
        clus
vv       AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  FEMALE                           53                             21
  MALE                             69                             19
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q12.2) MUTATED   113   5
  AMP PEAK 14(13Q12.2) WILD-TYPE  30   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED    113    5
  AMP PEAK 14(13Q12.2) WILD-TYPE   30    8
                                clus
vv                               AMP PEAK 14(13Q12.2) MUTATED
  RECTAL ADENOCARCINOMA                                   113
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 14(13Q12.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      30
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q12.2) MUTATED     4 118
  AMP PEAK 14(13Q12.2) WILD-TYPE   2  38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED      4  118
  AMP PEAK 14(13Q12.2) WILD-TYPE    2   38
     clus
vv    AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  NO                             4                              2
  YES                          118                             38
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 14(13Q12.2) MUTATED   88  2  9  2
  AMP PEAK 14(13Q12.2) WILD-TYPE 33  0  3  1
D14V10, multiclass
    clus
vv   AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  R0                           88                             33
  R1                            2                              0
  R2                            9                              3
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(13Q12.2) MUTATED       0                         3    67
  AMP PEAK 14(13Q12.2) WILD-TYPE     1                         0    14
D14V12, multiclass
                           clus
vv                          AMP PEAK 14(13Q12.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               67
                           clus
vv                          AMP PEAK 14(13Q12.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 14
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(13Q22.1) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(13Q22.1) MUTATED   90 18
  AMP PEAK 15(13Q22.1) WILD-TYPE 38  4
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           108                             42 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                            18                              4 
$`AMP PEAK 15(13Q22.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39        14.50        15.39        20.02        10.39 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07         1.02         2.01         1.02        46.03        34.03 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 
        0.99        19.99        19.99         0.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        17.03        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03         0.99         6.02        25.97        23.01 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        12.00        70.03        64.01 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97         1.94        38.96        38.04         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        0.69         0.72         4.60         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.99        12.00        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       57.24       129.27        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.55        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6464 
       16.31        16.41        11.51        10.78        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.76        18.28        55.76        47.08        26.43 

$`AMP PEAK 15(13Q22.1) WILD-TYPE`
TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       12.72         8.45        36.03        12.00        32.02         8.02 
TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
       24.00         2.01        50.04        12.03         6.05        15.95 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3898 
        7.99         1.02        32.98         0.99        13.02        48.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 
       20.98        13.94        37.02         1.02        31.00        10.98 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       61.97        41.00         1.45         1.81        10.19         6.05 
TCGA-DC-6155 TCGA-DC-6681 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 
       13.97        12.95         2.40        19.96        20.91         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       13.64        17.46         8.45         0.53         1.12         0.46 

  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                          0.39                           0.46 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                        129.27                          61.97 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                        15.900                         12.375 
[1] "0.4 - 129.3 (15.9)" "0.5 - 62.0 (12.4)" 
[1] "hr=" "1.3"
D15V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 15(13Q22.1) MUTATED        20        5        25         2         2
  AMP PEAK 15(13Q22.1) WILD-TYPE      10        3        13         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 15(13Q22.1) MUTATED           4          6         19         12
  AMP PEAK 15(13Q22.1) WILD-TYPE         1          3          4          2
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 15(13Q22.1) MUTATED         13         6
  AMP PEAK 15(13Q22.1) WILD-TYPE        5         3
D15V3, multiclass
            clus
vv           AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  STAGE I                              20                             10
  STAGE II                              5                              3
  STAGE IIA                            25                             13
  STAGE IIB                             2                              0
  STAGE IIC                             2                              0
  STAGE III                             4                              1
  STAGE IIIA                            6                              3
  STAGE IIIB                           19                              4
  STAGE IIIC                           12                              2
  STAGE IV                             13                              5
  STAGE IVA                             6                              3
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 15(13Q22.1) MUTATED    7 18 78 13
  AMP PEAK 15(13Q22.1) WILD-TYPE  2 11 31  1
D15V4, multiclass
    clus
vv   AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  T1                            7                              2
  T2                           18                             11
  T3                           78                             31
  T4                           13                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK 15(13Q22.1) MUTATED   54 35 26
  AMP PEAK 15(13Q22.1) WILD-TYPE 29 10  6
D15V5, multiclass
    clus
vv   AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  N0                           54                             29
  N1                           35                             10
  N2                           26                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 15(13Q22.1) MUTATED   87 16   1 12
  AMP PEAK 15(13Q22.1) WILD-TYPE 36  6   1  1
D15V6, multiclass
     clus
vv    AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  M0                            87                             36
  M1                            16                              6
  M1A                            1                              1
  MX                            12                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   51 66
  AMP PEAK 15(13Q22.1) WILD-TYPE 23 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     51   66
  AMP PEAK 15(13Q22.1) WILD-TYPE   23   22
        clus
vv       AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  FEMALE                           51                             23
  MALE                             66                             22
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED   109   4
  AMP PEAK 15(13Q22.1) WILD-TYPE  34   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED    109    4
  AMP PEAK 15(13Q22.1) WILD-TYPE   34    9
                                clus
vv                               AMP PEAK 15(13Q22.1) MUTATED
  RECTAL ADENOCARCINOMA                                   109
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               AMP PEAK 15(13Q22.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      34
  RECTAL MUCINOUS ADENOCARCINOMA                              9
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED     4 113
  AMP PEAK 15(13Q22.1) WILD-TYPE   2  43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED      4  113
  AMP PEAK 15(13Q22.1) WILD-TYPE    2   43
     clus
vv    AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  NO                             4                              2
  YES                          113                             43
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 15(13Q22.1) MUTATED   83  2  8  3
  AMP PEAK 15(13Q22.1) WILD-TYPE 38  0  4  0
D15V10, multiclass
    clus
vv   AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  R0                           83                             38
  R1                            2                              0
  R2                            8                              4
  RX                            3                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(13Q22.1) MUTATED       1                         3    63
  AMP PEAK 15(13Q22.1) WILD-TYPE     0                         0    18
D15V12, multiclass
                           clus
vv                          AMP PEAK 15(13Q22.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               63
                           clus
vv                          AMP PEAK 15(13Q22.1) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(15Q26.1) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 16(15Q26.1) MUTATED    11   2
  AMP PEAK 16(15Q26.1) WILD-TYPE 117  20
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            13                            137 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                             2                             20 
$`AMP PEAK 16(15Q26.1) MUTATED`
TCGA-AF-3400 TCGA-AG-3587 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-A01W TCGA-AH-6643 
       12.72        46.03        19.99        19.99        70.03         0.69 
TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5918 TCGA-DY-A1DC TCGA-EI-7004 TCGA-F5-6464 
       10.19         9.37         7.99        41.36         8.45         9.96 
TCGA-F5-6864 
        0.46 

$`AMP PEAK 16(15Q26.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       10.39        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
        1.02         2.01        24.00         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 
       50.04        12.03         6.05         0.99        15.95         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       36.03        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y 
       36.03         9.07         1.02        12.00        31.00        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04         0.49         1.45         0.72         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        1.81         6.05         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       60.03        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06         5.29       126.44        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       13.64        17.46        11.97        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        18.28        55.76        47.08        26.43 

  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                          0.46                           0.39 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                         70.03                         129.27 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                         10.19                          14.86 
[1] "0.5 - 70.0 (10.2)"  "0.4 - 129.3 (14.9)"
[1] "hr=" "1.1"
D16V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 16(15Q26.1) MUTATED         2        1         3         0         0
  AMP PEAK 16(15Q26.1) WILD-TYPE      28        7        35         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 16(15Q26.1) MUTATED           0          0          2          4
  AMP PEAK 16(15Q26.1) WILD-TYPE         5          9         21         10
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 16(15Q26.1) MUTATED          0         1
  AMP PEAK 16(15Q26.1) WILD-TYPE       18         8
D16V3, multiclass
            clus
vv           AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  STAGE I                               2                             28
  STAGE II                              1                              7
  STAGE IIA                             3                             35
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             0                              5
  STAGE IIIA                            0                              9
  STAGE IIIB                            2                             21
  STAGE IIIC                            4                             10
  STAGE IV                              0                             18
  STAGE IVA                             1                              8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK 16(15Q26.1) MUTATED     1   1   9   2
  AMP PEAK 16(15Q26.1) WILD-TYPE   8  28 100  12
D16V4, multiclass
    clus
vv   AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  T1                            1                              8
  T2                            1                             28
  T3                            9                            100
  T4                            2                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK 16(15Q26.1) MUTATED    6  2  5
  AMP PEAK 16(15Q26.1) WILD-TYPE 77 43 27
D16V5, multiclass
    clus
vv   AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  N0                            6                             77
  N1                            2                             43
  N2                            5                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  AMP PEAK 16(15Q26.1) MUTATED    11   0   0   1
  AMP PEAK 16(15Q26.1) WILD-TYPE 112  22   2  12
D16V6, multiclass
     clus
vv    AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  M0                            11                            112
  M1                             0                             22
  M1A                            0                              2
  MX                             1                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                                cls
clus                              0  1
  AMP PEAK 16(15Q26.1) MUTATED    8  5
  AMP PEAK 16(15Q26.1) WILD-TYPE 66 83
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED      8    5
  AMP PEAK 16(15Q26.1) WILD-TYPE   66   83
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  FEMALE                            8                             66
  MALE                              5                             83
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.1) MUTATED    11   2
  AMP PEAK 16(15Q26.1) WILD-TYPE 132  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED     11    2
  AMP PEAK 16(15Q26.1) WILD-TYPE  132   11
                                clus
vv                               AMP PEAK 16(15Q26.1) MUTATED
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK 16(15Q26.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     132
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.1) MUTATED     2  11
  AMP PEAK 16(15Q26.1) WILD-TYPE   4 145
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED      2   11
  AMP PEAK 16(15Q26.1) WILD-TYPE    4  145
     clus
vv    AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  NO                             2                              4
  YES                           11                            145
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 16(15Q26.1) MUTATED    10   0   0   1
  AMP PEAK 16(15Q26.1) WILD-TYPE 111   2  12   2
D16V10, multiclass
    clus
vv   AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  R0                           10                            111
  R1                            0                              2
  R2                            0                             12
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(15Q26.1) MUTATED       0                         0     9
  AMP PEAK 16(15Q26.1) WILD-TYPE     1                         3    72
D16V12, multiclass
                           clus
vv                          AMP PEAK 16(15Q26.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                9
                           clus
vv                          AMP PEAK 16(15Q26.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(16P11.2) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(16P11.2) MUTATED   33  7
  AMP PEAK 17(16P11.2) WILD-TYPE 95 15
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            40                            110 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                             7                             15 
$`AMP PEAK 17(16P11.2) MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3582 
       17.95        37.74        10.39        15.39        20.02         1.02 
TCGA-AG-3600 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 
        6.05         7.99         1.02        17.03        19.99        36.03 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
        1.02         0.99        15.95        36.03         9.07        12.00 
TCGA-AG-A01N TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6622 
       31.00        38.96        38.04         0.72        10.19         6.97 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 
        9.37        60.03        11.01        12.99        12.00        10.06 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 
       24.13        51.48         0.49        17.69        16.31        37.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
       14.86         0.39         1.02         0.76 

$`AMP PEAK 17(16P11.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       14.50         8.45        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       19.99        19.99         0.99        29.98        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 
       14.01         1.02        48.03        32.02        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       37.02         1.02        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        61.97        41.00         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
        0.69         4.60         1.81         6.05         6.05         4.73 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 
       13.97         7.99        10.98        15.02        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       36.00         7.10        30.05        12.95        13.05         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        57.24       129.27        32.61         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6812 
       17.46        11.97         8.45         9.96        31.30         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                          0.39                           0.46 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                         60.03                         129.27 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                        12.495                         14.760 
[1] "0.4 - 60.0 (12.5)"  "0.5 - 129.3 (14.8)"
[1] "hr=" "1.7"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 17(16P11.2) MUTATED         6        1         7         2         0
  AMP PEAK 17(16P11.2) WILD-TYPE      24        7        31         0         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 17(16P11.2) MUTATED           1          1         11          4
  AMP PEAK 17(16P11.2) WILD-TYPE         4          8         12         10
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 17(16P11.2) MUTATED          8         3
  AMP PEAK 17(16P11.2) WILD-TYPE       10         6
D17V3, multiclass
            clus
vv           AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  STAGE I                               6                             24
  STAGE II                              1                              7
  STAGE IIA                             7                             31
  STAGE IIB                             2                              0
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            1                              8
  STAGE IIIB                           11                             12
  STAGE IIIC                            4                             10
  STAGE IV                              8                             10
  STAGE IVA                             3                              6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 17(16P11.2) MUTATED    2  7 30  6
  AMP PEAK 17(16P11.2) WILD-TYPE  7 22 79  8
D17V4, multiclass
    clus
vv   AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  T1                            2                              7
  T2                            7                             22
  T3                           30                             79
  T4                            6                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK 17(16P11.2) MUTATED   17 18  9
  AMP PEAK 17(16P11.2) WILD-TYPE 66 27 23
D17V5, multiclass
    clus
vv   AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  N0                           17                             66
  N1                           18                             27
  N2                            9                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 17(16P11.2) MUTATED   29 11   0  4
  AMP PEAK 17(16P11.2) WILD-TYPE 94 11   2  9
D17V6, multiclass
     clus
vv    AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  M0                            29                             94
  M1                            11                             11
  M1A                            0                              2
  MX                             4                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                              0  1
  AMP PEAK 17(16P11.2) MUTATED   19 26
  AMP PEAK 17(16P11.2) WILD-TYPE 55 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED     19   26
  AMP PEAK 17(16P11.2) WILD-TYPE   55   62
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  FEMALE                           19                             55
  MALE                             26                             62
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                              0  1
  AMP PEAK 17(16P11.2) MUTATED   45  0
  AMP PEAK 17(16P11.2) WILD-TYPE 98 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED     45    0
  AMP PEAK 17(16P11.2) WILD-TYPE   98   13
                                clus
vv                               AMP PEAK 17(16P11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    45
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 17(16P11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      98
  RECTAL MUCINOUS ADENOCARCINOMA                             13
[1] 2 2
[1] FALSE
D17V9, binary
                                cls
clus                               0   1
  AMP PEAK 17(16P11.2) MUTATED     3  42
  AMP PEAK 17(16P11.2) WILD-TYPE   3 114
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED      3   42
  AMP PEAK 17(16P11.2) WILD-TYPE    3  114
     clus
vv    AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  NO                             3                              3
  YES                           42                            114
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 17(16P11.2) MUTATED   29  0  7  1
  AMP PEAK 17(16P11.2) WILD-TYPE 92  2  5  2
D17V10, multiclass
    clus
vv   AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  R0                           29                             92
  R1                            0                              2
  R2                            7                              5
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(16P11.2) MUTATED       0                         2    22
  AMP PEAK 17(16P11.2) WILD-TYPE     1                         1    59
D17V12, multiclass
                           clus
vv                          AMP PEAK 17(16P11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               22
                           clus
vv                          AMP PEAK 17(16P11.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(17Q12) MUTATION ANALYSIS
D18V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 18(17Q12) MUTATED   36  4
  AMP PEAK 18(17Q12) WILD-TYPE 92 18
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          40                          110 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                           4                           18 
$`AMP PEAK 18(17Q12) MUTATED`
TCGA-AF-2690 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 
       17.23        12.00         7.07         1.02        46.03        34.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       15.95        19.99        19.99         0.99        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 
       48.03        32.02        36.03         1.02        17.03        15.95 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 
        9.07        31.00        64.01        51.98         0.69         4.60 
TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        6.05         9.37        12.00        13.05        10.06         5.29 
TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 
       51.48        17.00        18.28        16.31        11.97         1.02 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        0.69         0.46        55.76        26.43 

$`AMP PEAK 18(17Q12) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3584 
       10.39        36.03        32.02         8.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
        7.99         0.99        29.98         1.02        32.98         0.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       19.99        28.04        14.04         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02        36.03         1.02 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        10.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 
       61.97        41.00        38.04         0.49         1.45         0.72 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
        1.81        10.19         6.05         6.97         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 
        0.49         2.40        20.55        19.96        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       14.86         0.39         0.66         0.53         1.12         0.76 
TCGA-G5-6233 TCGA-G5-6572 
       18.28        47.08 

  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                        0.46                         0.39 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                       64.01                       129.27 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                      15.950                       14.025 
[1] "0.5 - 64.0 (15.9)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.7"
D18V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 18(17Q12) MUTATED         8        3        10         0         0
  AMP PEAK 18(17Q12) WILD-TYPE      22        5        28         2         2
                              vv
clus                           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 18(17Q12) MUTATED           1          1          4          6
  AMP PEAK 18(17Q12) WILD-TYPE         4          8         19          8
                              vv
clus                           STAGE IV STAGE IVA
  AMP PEAK 18(17Q12) MUTATED          7         3
  AMP PEAK 18(17Q12) WILD-TYPE       11         6
D18V3, multiclass
            clus
vv           AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  STAGE I                             8                           22
  STAGE II                            3                            5
  STAGE IIA                          10                           28
  STAGE IIB                           0                            2
  STAGE IIC                           0                            2
  STAGE III                           1                            4
  STAGE IIIA                          1                            8
  STAGE IIIB                          4                           19
  STAGE IIIC                          6                            8
  STAGE IV                            7                           11
  STAGE IVA                           3                            6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T1 T2 T3 T4
  AMP PEAK 18(17Q12) MUTATED    3  8 27  5
  AMP PEAK 18(17Q12) WILD-TYPE  6 21 82  9
D18V4, multiclass
    clus
vv   AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  T1                          3                            6
  T2                          8                           21
  T3                         27                           82
  T4                          5                            9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 18(17Q12) MUTATED   23  9 11
  AMP PEAK 18(17Q12) WILD-TYPE 60 36 21
D18V5, multiclass
    clus
vv   AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  N0                         23                           60
  N1                          9                           36
  N2                         11                           21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 M1A MX
  AMP PEAK 18(17Q12) MUTATED   30  9   0  4
  AMP PEAK 18(17Q12) WILD-TYPE 93 13   2  9
D18V6, multiclass
     clus
vv    AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  M0                          30                           93
  M1                           9                           13
  M1A                          0                            2
  MX                           4                            9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                              cls
clus                            0  1
  AMP PEAK 18(17Q12) MUTATED   16 27
  AMP PEAK 18(17Q12) WILD-TYPE 58 61
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED     16   27
  AMP PEAK 18(17Q12) WILD-TYPE   58   61
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  FEMALE                         16                           58
  MALE                           27                           61
[1] 2 2
[1] FALSE
D18V8, binary
                              cls
clus                             0   1
  AMP PEAK 18(17Q12) MUTATED    41   2
  AMP PEAK 18(17Q12) WILD-TYPE 102  11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED     41    2
  AMP PEAK 18(17Q12) WILD-TYPE  102   11
                                clus
vv                               AMP PEAK 18(17Q12) MUTATED
  RECTAL ADENOCARCINOMA                                  41
  RECTAL MUCINOUS ADENOCARCINOMA                          2
                                clus
vv                               AMP PEAK 18(17Q12) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   102
  RECTAL MUCINOUS ADENOCARCINOMA                           11
[1] 2 2
[1] FALSE
D18V9, binary
                              cls
clus                             0   1
  AMP PEAK 18(17Q12) MUTATED     0  43
  AMP PEAK 18(17Q12) WILD-TYPE   6 113
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED      0   43
  AMP PEAK 18(17Q12) WILD-TYPE    6  113
     clus
vv    AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  NO                           0                            6
  YES                         43                          113
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 18(17Q12) MUTATED   30  1  6  1
  AMP PEAK 18(17Q12) WILD-TYPE 91  1  6  2
D18V10, multiclass
    clus
vv   AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  R0                         30                           91
  R1                          1                            1
  R2                          6                            6
  RX                          1                            2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(17Q12) MUTATED       1                         0    19
  AMP PEAK 18(17Q12) WILD-TYPE     0                         3    62
D18V12, multiclass
                           clus
vv                          AMP PEAK 18(17Q12) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             19
                           clus
vv                          AMP PEAK 18(17Q12) WILD-TYPE
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = AMP PEAK 19(17Q24.1) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 19(17Q24.1) MUTATED   31  4
  AMP PEAK 19(17Q24.1) WILD-TYPE 97 18
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            35                            115 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                             4                             18 
$`AMP PEAK 19(17Q24.1) MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3587 
       17.95        17.23        13.55        12.00         7.07        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3882 
       34.03        50.04        15.95        19.99        19.99        19.99 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01N 
       36.03         1.02        17.03        15.95         9.07        31.00 
TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-DC-6154 TCGA-DC-6682 
       51.98         0.69         4.60         6.05        12.00        13.05 
TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 
       10.06       129.27        51.48         0.49         2.40        18.28 
TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6864 TCGA-G5-6235 
       16.31        11.97         1.02         0.46        55.76 

$`AMP PEAK 19(17Q24.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       24.13        43.04        19.10        12.72        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         1.02         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
        2.01        12.03         6.05         0.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
       29.98         1.02        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4022 
       48.03        32.02        19.99        28.04        14.04         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       36.03         1.02        12.00        70.03        64.01        10.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       49.97         1.94        38.96        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
        0.49         1.45         0.72         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 
       10.98        11.01        15.02        12.99        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       36.00         7.10        30.05        12.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       41.36        57.24        24.13        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       20.91        17.00        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
        8.61        11.51        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
        9.96        37.51        31.30        14.86         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 
        0.69         0.53         1.12         0.76        18.28        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                          0.46                           0.39 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                        129.27                         126.44 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                         15.95                          14.01 
[1] "0.5 - 129.3 (15.9)" "0.4 - 126.4 (14.0)"
[1] "hr=" "1.6"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 19(17Q24.1) MUTATED         5        1        11         1         0
  AMP PEAK 19(17Q24.1) WILD-TYPE      25        7        27         1         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 19(17Q24.1) MUTATED           1          0          4          4
  AMP PEAK 19(17Q24.1) WILD-TYPE         4          9         19         10
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 19(17Q24.1) MUTATED          7         3
  AMP PEAK 19(17Q24.1) WILD-TYPE       11         6
D19V3, multiclass
            clus
vv           AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  STAGE I                               5                             25
  STAGE II                              1                              7
  STAGE IIA                            11                             27
  STAGE IIB                             1                              1
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            4                             19
  STAGE IIIC                            4                             10
  STAGE IV                              7                             11
  STAGE IVA                             3                              6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 19(17Q24.1) MUTATED    0  7 25  5
  AMP PEAK 19(17Q24.1) WILD-TYPE  9 22 84  9
D19V4, multiclass
    clus
vv   AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  T1                            0                              9
  T2                            7                             22
  T3                           25                             84
  T4                            5                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK 19(17Q24.1) MUTATED   20  7 10
  AMP PEAK 19(17Q24.1) WILD-TYPE 63 38 22
D19V5, multiclass
    clus
vv   AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  N0                           20                             63
  N1                            7                             38
  N2                           10                             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 19(17Q24.1) MUTATED   25  9   0  3
  AMP PEAK 19(17Q24.1) WILD-TYPE 98 13   2 10
D19V6, multiclass
     clus
vv    AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  M0                            25                             98
  M1                             9                             13
  M1A                            0                              2
  MX                             3                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                              0  1
  AMP PEAK 19(17Q24.1) MUTATED   17 20
  AMP PEAK 19(17Q24.1) WILD-TYPE 57 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED     17   20
  AMP PEAK 19(17Q24.1) WILD-TYPE   57   68
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  FEMALE                           17                             57
  MALE                             20                             68
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.1) MUTATED    36   0
  AMP PEAK 19(17Q24.1) WILD-TYPE 107  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED     36    0
  AMP PEAK 19(17Q24.1) WILD-TYPE  107   13
                                clus
vv                               AMP PEAK 19(17Q24.1) MUTATED
  RECTAL ADENOCARCINOMA                                    36
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 19(17Q24.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     107
  RECTAL MUCINOUS ADENOCARCINOMA                             13
[1] 2 2
[1] FALSE
D19V9, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.1) MUTATED     0  37
  AMP PEAK 19(17Q24.1) WILD-TYPE   6 119
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED      0   37
  AMP PEAK 19(17Q24.1) WILD-TYPE    6  119
     clus
vv    AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  NO                             0                              6
  YES                           37                            119
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 19(17Q24.1) MUTATED   26  1  5  0
  AMP PEAK 19(17Q24.1) WILD-TYPE 95  1  7  3
D19V10, multiclass
    clus
vv   AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  R0                           26                             95
  R1                            1                              1
  R2                            5                              7
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q24.1) MUTATED       0                         0    20
  AMP PEAK 19(17Q24.1) WILD-TYPE     1                         3    61
D19V12, multiclass
                           clus
vv                          AMP PEAK 19(17Q24.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               20
                           clus
vv                          AMP PEAK 19(17Q24.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = AMP PEAK 20(19P13.2) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  AMP PEAK 20(19P13.2) MUTATED    23   6
  AMP PEAK 20(19P13.2) WILD-TYPE 105  16
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            29                            121 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                             6                             16 
$`AMP PEAK 20(19P13.2) MUTATED`
TCGA-AF-2690 TCGA-AF-3913 TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3878 
       17.23        10.39         1.02         6.05        19.99         0.99 
TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A01L 
        1.02        28.04        36.03         1.02         0.99        12.00 
TCGA-AG-A01N TCGA-AG-A026 TCGA-AG-A032 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-6154 
       31.00         1.94        38.04        10.98        11.01        12.00 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 
       36.00        13.05        57.24        24.13         0.49        20.55 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 TCGA-F5-6863 
       17.69        16.31        11.51        11.97         0.76 

$`AMP PEAK 20(19P13.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.95        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       29.98         1.02        32.98         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       36.95        17.03        13.02        35.01        14.01        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 
       32.02        19.99        14.04        17.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97        38.96        61.97        41.00         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 
        7.99        15.02        12.99        13.97        15.02         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        10.06         5.29       126.44        41.36 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
      129.27        51.48        32.61         2.40        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 
       17.00        18.28        15.85        16.34        16.41         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                          0.49                           0.39 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                         57.24                         129.27 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                         12.00                          15.02 
[1] "0.5 - 57.2 (12.0)"  "0.4 - 129.3 (15.0)"
[1] "hr=" "2.2"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 20(19P13.2) MUTATED         4        2         7         1         1
  AMP PEAK 20(19P13.2) WILD-TYPE      26        6        31         1         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 20(19P13.2) MUTATED           1          0          7          5
  AMP PEAK 20(19P13.2) WILD-TYPE         4          9         16          9
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 20(19P13.2) MUTATED          5         1
  AMP PEAK 20(19P13.2) WILD-TYPE       13         8
D20V3, multiclass
            clus
vv           AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  STAGE I                               4                             26
  STAGE II                              2                              6
  STAGE IIA                             7                             31
  STAGE IIB                             1                              1
  STAGE IIC                             1                              1
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            7                             16
  STAGE IIIC                            5                              9
  STAGE IV                              5                             13
  STAGE IVA                             1                              8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  AMP PEAK 20(19P13.2) MUTATED    0  5 24  5
  AMP PEAK 20(19P13.2) WILD-TYPE  9 24 85  9
D20V4, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  T1                            0                              9
  T2                            5                             24
  T3                           24                             85
  T4                            5                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  AMP PEAK 20(19P13.2) MUTATED   16 10  8
  AMP PEAK 20(19P13.2) WILD-TYPE 67 35 24
D20V5, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  N0                           16                             67
  N1                           10                             35
  N2                            8                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  AMP PEAK 20(19P13.2) MUTATED   27  6   0  1
  AMP PEAK 20(19P13.2) WILD-TYPE 96 16   2 12
D20V6, multiclass
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  M0                            27                             96
  M1                             6                             16
  M1A                            0                              2
  MX                             1                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                              0  1
  AMP PEAK 20(19P13.2) MUTATED   17 17
  AMP PEAK 20(19P13.2) WILD-TYPE 57 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     17   17
  AMP PEAK 20(19P13.2) WILD-TYPE   57   71
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  FEMALE                           17                             57
  MALE                             17                             71
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED    34   0
  AMP PEAK 20(19P13.2) WILD-TYPE 109  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     34    0
  AMP PEAK 20(19P13.2) WILD-TYPE  109   13
                                clus
vv                               AMP PEAK 20(19P13.2) MUTATED
  RECTAL ADENOCARCINOMA                                    34
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 20(19P13.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     109
  RECTAL MUCINOUS ADENOCARCINOMA                             13
[1] 2 2
[1] FALSE
D20V9, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED     0  34
  AMP PEAK 20(19P13.2) WILD-TYPE   6 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED      0   34
  AMP PEAK 20(19P13.2) WILD-TYPE    6  122
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  NO                             0                              6
  YES                           34                            122
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 20(19P13.2) MUTATED   27  1  3  0
  AMP PEAK 20(19P13.2) WILD-TYPE 94  1  9  3
D20V10, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  R0                           27                             94
  R1                            1                              1
  R2                            3                              9
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 20(19P13.2) MUTATED       0                         2    15
  AMP PEAK 20(19P13.2) WILD-TYPE     1                         1    66
D20V12, multiclass
                           clus
vv                          AMP PEAK 20(19P13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               15
                           clus
vv                          AMP PEAK 20(19P13.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = AMP PEAK 21(20Q11.21) MUTATION ANALYSIS
D21V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 21(20Q11.21) MUTATED   112  21
  AMP PEAK 21(20Q11.21) WILD-TYPE  16   1
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            133                              17 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                             21                               1 
$`AMP PEAK 21(20Q11.21) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       24.13        17.95        17.23        43.04        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81        10.19         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
        7.10        30.05        12.95        13.05        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        13.64        11.97         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`AMP PEAK 21(20Q11.21) WILD-TYPE`
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 
       13.55        12.72        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-CI-6620 
       32.98        13.02        20.98        49.97        61.97         6.05 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
        5.29        19.96         8.61        17.46         8.45 

  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                           0.39                            2.01 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                         129.27                           61.97 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                          14.86                           13.02 
[1] "0.4 - 129.3 (14.9)" "2.0 - 62.0 (13.0)" 
[1] "hr=" "2.7"
D21V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(20Q11.21) MUTATED        26        5        31         2
  AMP PEAK 21(20Q11.21) WILD-TYPE       4        3         7         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 21(20Q11.21) MUTATED           2         5          8         23
  AMP PEAK 21(20Q11.21) WILD-TYPE         0         0          1          0
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 21(20Q11.21) MUTATED           13       17         7
  AMP PEAK 21(20Q11.21) WILD-TYPE          1        1         2
D21V3, multiclass
            clus
vv           AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  STAGE I                               26                               4
  STAGE II                               5                               3
  STAGE IIA                             31                               7
  STAGE IIB                              2                               0
  STAGE IIC                              2                               0
  STAGE III                              5                               0
  STAGE IIIA                             8                               1
  STAGE IIIB                            23                               0
  STAGE IIIC                            13                               1
  STAGE IV                              17                               1
  STAGE IVA                              7                               2
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 21(20Q11.21) MUTATED    7 27 95 13
  AMP PEAK 21(20Q11.21) WILD-TYPE  2  2 14  1
D21V4, multiclass
    clus
vv   AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  T1                             7                               2
  T2                            27                               2
  T3                            95                              14
  T4                            13                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  AMP PEAK 21(20Q11.21) MUTATED   69 43 29
  AMP PEAK 21(20Q11.21) WILD-TYPE 14  2  3
D21V5, multiclass
    clus
vv   AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  N0                            69                              14
  N1                            43                               2
  N2                            29                               3
[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"
                                 vv
clus                               M0  M1 M1A  MX
  AMP PEAK 21(20Q11.21) MUTATED   106  20   2  13
  AMP PEAK 21(20Q11.21) WILD-TYPE  17   2   0   0
D21V6, multiclass
     clus
vv    AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  M0                            106                              17
  M1                             20                               2
  M1A                             2                               0
  MX                             13                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                 cls
clus                               0  1
  AMP PEAK 21(20Q11.21) MUTATED   65 78
  AMP PEAK 21(20Q11.21) WILD-TYPE  9 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED     65   78
  AMP PEAK 21(20Q11.21) WILD-TYPE    9   10
        clus
vv       AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  FEMALE                            65                               9
  MALE                              78                              10
[1] 2 2
[1] FALSE
D21V8, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q11.21) MUTATED   132   7
  AMP PEAK 21(20Q11.21) WILD-TYPE  11   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED    132    7
  AMP PEAK 21(20Q11.21) WILD-TYPE   11    6
                                clus
vv                               AMP PEAK 21(20Q11.21) MUTATED
  RECTAL ADENOCARCINOMA                                    132
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 21(20Q11.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       11
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 2 2
[1] FALSE
D21V9, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q11.21) MUTATED     5 138
  AMP PEAK 21(20Q11.21) WILD-TYPE   1  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED      5  138
  AMP PEAK 21(20Q11.21) WILD-TYPE    1   18
     clus
vv    AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  NO                              5                               1
  YES                           138                              18
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 21(20Q11.21) MUTATED   106   2  11   2
  AMP PEAK 21(20Q11.21) WILD-TYPE  15   0   1   1
D21V10, multiclass
    clus
vv   AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  R0                           106                              15
  R1                             2                               0
  R2                            11                               1
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 21(20Q11.21) MUTATED       0                         3    74
  AMP PEAK 21(20Q11.21) WILD-TYPE     1                         0     7
D21V12, multiclass
                           clus
vv                          AMP PEAK 21(20Q11.21) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                74
                           clus
vv                          AMP PEAK 21(20Q11.21) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                   7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = AMP PEAK 22(20Q11.23) MUTATION ANALYSIS
D22V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 22(20Q11.23) MUTATED   113  21
  AMP PEAK 22(20Q11.23) WILD-TYPE  15   1
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                            134                              16 
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                             21                               1 
$`AMP PEAK 22(20Q11.23) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       24.13        17.95        17.23        43.04        19.10        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        11.97         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`AMP PEAK 22(20Q11.23) WILD-TYPE`
TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 
       13.55        12.72        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3892 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-DT-5265 
       32.98        13.02        20.98        49.97        61.97         5.29 
TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       19.96         8.61        17.46         8.45 

  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                           0.39                            2.01 
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                         129.27                           61.97 
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                         14.680                          13.285 
[1] "0.4 - 129.3 (14.7)" "2.0 - 62.0 (13.3)" 
[1] "hr=" "2.6"
D22V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(20Q11.23) MUTATED        26        5        31         2
  AMP PEAK 22(20Q11.23) WILD-TYPE       4        3         7         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 22(20Q11.23) MUTATED           2         5          8         23
  AMP PEAK 22(20Q11.23) WILD-TYPE         0         0          1          0
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 22(20Q11.23) MUTATED           13       17         8
  AMP PEAK 22(20Q11.23) WILD-TYPE          1        1         1
D22V3, multiclass
            clus
vv           AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  STAGE I                               26                               4
  STAGE II                               5                               3
  STAGE IIA                             31                               7
  STAGE IIB                              2                               0
  STAGE IIC                              2                               0
  STAGE III                              5                               0
  STAGE IIIA                             8                               1
  STAGE IIIB                            23                               0
  STAGE IIIC                            13                               1
  STAGE IV                              17                               1
  STAGE IVA                              8                               1
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 22(20Q11.23) MUTATED    7 27 96 13
  AMP PEAK 22(20Q11.23) WILD-TYPE  2  2 13  1
D22V4, multiclass
    clus
vv   AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  T1                             7                               2
  T2                            27                               2
  T3                            96                              13
  T4                            13                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  AMP PEAK 22(20Q11.23) MUTATED   69 44 29
  AMP PEAK 22(20Q11.23) WILD-TYPE 14  1  3
D22V5, multiclass
    clus
vv   AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  N0                            69                              14
  N1                            44                               1
  N2                            29                               3
[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"
                                 vv
clus                               M0  M1 M1A  MX
  AMP PEAK 22(20Q11.23) MUTATED   106  21   2  13
  AMP PEAK 22(20Q11.23) WILD-TYPE  17   1   0   0
D22V6, multiclass
     clus
vv    AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  M0                            106                              17
  M1                             21                               1
  M1A                             2                               0
  MX                             13                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.23) MUTATED   66 78
  AMP PEAK 22(20Q11.23) WILD-TYPE  8 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.23) MUTATED     66   78
  AMP PEAK 22(20Q11.23) WILD-TYPE    8   10
        clus
vv       AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  FEMALE                            66                               8
  MALE                              78                              10
[1] 2 2
[1] FALSE
D22V8, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.23) MUTATED   133   7
  AMP PEAK 22(20Q11.23) WILD-TYPE  10   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.23) MUTATED    133    7
  AMP PEAK 22(20Q11.23) WILD-TYPE   10    6
                                clus
vv                               AMP PEAK 22(20Q11.23) MUTATED
  RECTAL ADENOCARCINOMA                                    133
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 22(20Q11.23) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       10
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 2 2
[1] FALSE
D22V9, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.23) MUTATED     5 139
  AMP PEAK 22(20Q11.23) WILD-TYPE   1  17
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.23) MUTATED      5  139
  AMP PEAK 22(20Q11.23) WILD-TYPE    1   17
     clus
vv    AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  NO                              5                               1
  YES                           139                              17
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 22(20Q11.23) MUTATED   106   2  11   2
  AMP PEAK 22(20Q11.23) WILD-TYPE  15   0   1   1
D22V10, multiclass
    clus
vv   AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  R0                           106                              15
  R1                             2                               0
  R2                            11                               1
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 22(20Q11.23) MUTATED       0                         3    75
  AMP PEAK 22(20Q11.23) WILD-TYPE     1                         0     6
D22V12, multiclass
                           clus
vv                          AMP PEAK 22(20Q11.23) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                75
                           clus
vv                          AMP PEAK 22(20Q11.23) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                   6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = AMP PEAK 23(20Q13.33) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(20Q13.33) MUTATED   113  20
  AMP PEAK 23(20Q13.33) WILD-TYPE  15   2
  AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE 
                            133                              17 
  AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE 
                             20                               2 
$`AMP PEAK 23(20Q13.33) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50         8.45        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       10.39        36.03         8.02         7.07         1.02         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98         1.02         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        17.03        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       10.78        13.64        11.97         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`AMP PEAK 23(20Q13.33) WILD-TYPE`
TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 
       12.72        12.00        32.02         2.01         6.05        32.98 
TCGA-AG-3892 TCGA-AG-3999 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-DT-5265 
       13.02        28.04        20.98        49.97        61.97         5.29 
TCGA-DY-A1DG TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       51.48        19.96         8.61        17.46         8.45 

  AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE 
                           0.39                            2.01 
  AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE 
                         129.27                           61.97 
  AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE 
                          14.04                           17.46 
[1] "0.4 - 129.3 (14.0)" "2.0 - 62.0 (17.5)" 
[1] "hr=" "1.6"
D23V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20Q13.33) MUTATED        26        5        32         2
  AMP PEAK 23(20Q13.33) WILD-TYPE       4        3         6         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20Q13.33) MUTATED           2         5          8         23
  AMP PEAK 23(20Q13.33) WILD-TYPE         0         0          1          0
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(20Q13.33) MUTATED           12       17         7
  AMP PEAK 23(20Q13.33) WILD-TYPE          2        1         2
D23V3, multiclass
            clus
vv           AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE
  STAGE I                               26                               4
  STAGE II                               5                               3
  STAGE IIA                             32                               6
  STAGE IIB                              2                               0
  STAGE IIC                              2                               0
  STAGE III                              5                               0
  STAGE IIIA                             8                               1
  STAGE IIIB                            23                               0
  STAGE IIIC                            12                               2
  STAGE IV                              17                               1
  STAGE IVA                              7                               2
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  AMP PEAK 23(20Q13.33) MUTATED    7 27 95 13
  AMP PEAK 23(20Q13.33) WILD-TYPE  2  2 14  1
D23V4, multiclass
    clus
vv   AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE
  T1                             7                               2
  T2                            27                               2
  T3                            95                              14
  T4                            13                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  AMP PEAK 23(20Q13.33) MUTATED   70 43 28
  AMP PEAK 23(20Q13.33) WILD-TYPE 13  2  4
D23V5, multiclass
    clus
vv   AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE
  N0                            70                              13
  N1                            43                               2
  N2                            28                               4
[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"
                                 vv
clus                               M0  M1 M1A  MX
  AMP PEAK 23(20Q13.33) MUTATED   106  20   2  13
  AMP PEAK 23(20Q13.33) WILD-TYPE  17   2   0   0
D23V6, multiclass
     clus
vv    AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE
  M0                            106                              17
  M1                             20                               2
  M1A                             2                               0
  MX                             13                               0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                 cls
clus                               0  1
  AMP PEAK 23(20Q13.33) MUTATED   66 77
  AMP PEAK 23(20Q13.33) WILD-TYPE  8 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.33) MUTATED     66   77
  AMP PEAK 23(20Q13.33) WILD-TYPE    8   11
        clus
vv       AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE
  FEMALE                            66                               8
  MALE                              77                              11
[1] 2 2
[1] FALSE
D23V8, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q13.33) MUTATED   131   7
  AMP PEAK 23(20Q13.33) WILD-TYPE  12   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.33) MUTATED    131    7
  AMP PEAK 23(20Q13.33) WILD-TYPE   12    6
                                clus
vv                               AMP PEAK 23(20Q13.33) MUTATED
  RECTAL ADENOCARCINOMA                                    131
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 23(20Q13.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       12
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 2 2
[1] FALSE
D23V9, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q13.33) MUTATED     5 138
  AMP PEAK 23(20Q13.33) WILD-TYPE   1  18
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.33) MUTATED      5  138
  AMP PEAK 23(20Q13.33) WILD-TYPE    1   18
     clus
vv    AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE
  NO                              5                               1
  YES                           138                              18
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(20Q13.33) MUTATED   106   2  11   2
  AMP PEAK 23(20Q13.33) WILD-TYPE  15   0   1   1
D23V10, multiclass
    clus
vv   AMP PEAK 23(20Q13.33) MUTATED AMP PEAK 23(20Q13.33) WILD-TYPE
  R0                           106                              15
  R1                             2                               0
  R2                            11                               1
  RX                             2                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 23(20Q13.33) MUTATED       0                         3    75
  AMP PEAK 23(20Q13.33) WILD-TYPE     1                         0     6
D23V12, multiclass
                           clus
vv                          AMP PEAK 23(20Q13.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                75
                           clus
vv                          AMP PEAK 23(20Q13.33) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                   6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = AMP PEAK 24(XP22.2) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 24(XP22.2) MUTATED    23   4
  AMP PEAK 24(XP22.2) WILD-TYPE 105  18
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                           27                           123 
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                            4                            18 
$`AMP PEAK 24(XP22.2) MUTATED`
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3609 TCGA-AG-3612 
       10.39         8.45        20.02        36.03        19.99        19.99 
TCGA-AG-3999 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N 
       28.04         0.99        15.95        36.03         9.07        31.00 
TCGA-AG-A01Y TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6644 TCGA-AH-6897 TCGA-DC-4745 
       64.01        61.97        38.04         0.72         4.60        10.98 
TCGA-DC-6154 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
       12.00         5.29        32.61        18.28        17.69        13.64 
TCGA-EI-7002 TCGA-F5-6863 TCGA-G5-6235 
       11.97         0.76        55.76 

$`AMP PEAK 24(XP22.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 
       12.72        37.74        14.50        15.39        10.39        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       32.02         8.02         7.07         1.02         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        15.95         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
        1.02        32.98         0.99         0.99        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 
       37.02         1.02        12.00        70.03        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        38.96        41.00         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.73        13.97        60.03         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02        12.99        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       30.05        12.95        13.05        10.06       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 
       20.55        19.96        20.91        17.00        15.85        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        37.51        31.30        14.86         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
        1.02         0.66         0.69         0.53         1.12         0.46 
TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       18.28        47.08        26.43 

  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                         0.72                          0.39 
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                        64.01                        129.27 
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                        17.69                         14.01 
[1] "0.7 - 64.0 (17.7)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.2"
D24V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 24(XP22.2) MUTATED         4        5         2         0         0
  AMP PEAK 24(XP22.2) WILD-TYPE      26        3        36         2         2
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 24(XP22.2) MUTATED           0          2          7          2
  AMP PEAK 24(XP22.2) WILD-TYPE         5          7         16         12
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK 24(XP22.2) MUTATED          6         2
  AMP PEAK 24(XP22.2) WILD-TYPE       12         7
D24V3, multiclass
            clus
vv           AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  STAGE I                              4                            26
  STAGE II                             5                             3
  STAGE IIA                            2                            36
  STAGE IIB                            0                             2
  STAGE IIC                            0                             2
  STAGE III                            0                             5
  STAGE IIIA                           2                             7
  STAGE IIIB                           7                            16
  STAGE IIIC                           2                            12
  STAGE IV                             6                            12
  STAGE IVA                            2                             7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK 24(XP22.2) MUTATED    1  7 20  3
  AMP PEAK 24(XP22.2) WILD-TYPE  8 22 89 11
D24V4, multiclass
    clus
vv   AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  T1                           1                             8
  T2                           7                            22
  T3                          20                            89
  T4                           3                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK 24(XP22.2) MUTATED   13 11  6
  AMP PEAK 24(XP22.2) WILD-TYPE 70 34 26
D24V5, multiclass
    clus
vv   AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  N0                          13                            70
  N1                          11                            34
  N2                           6                            26
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  AMP PEAK 24(XP22.2) MUTATED    21   7   0   3
  AMP PEAK 24(XP22.2) WILD-TYPE 102  15   2  10
D24V6, multiclass
     clus
vv    AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  M0                           21                           102
  M1                            7                            15
  M1A                           0                             2
  MX                            3                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                               cls
clus                             0  1
  AMP PEAK 24(XP22.2) MUTATED   18 13
  AMP PEAK 24(XP22.2) WILD-TYPE 56 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP22.2) MUTATED     18   13
  AMP PEAK 24(XP22.2) WILD-TYPE   56   75
        clus
vv       AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  FEMALE                          18                            56
  MALE                            13                            75
[1] 2 2
[1] FALSE
D24V8, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP22.2) MUTATED    30   1
  AMP PEAK 24(XP22.2) WILD-TYPE 113  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP22.2) MUTATED     30    1
  AMP PEAK 24(XP22.2) WILD-TYPE  113   12
                                clus
vv                               AMP PEAK 24(XP22.2) MUTATED
  RECTAL ADENOCARCINOMA                                   30
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK 24(XP22.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    113
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
D24V9, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP22.2) MUTATED     0  31
  AMP PEAK 24(XP22.2) WILD-TYPE   6 125
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP22.2) MUTATED      0   31
  AMP PEAK 24(XP22.2) WILD-TYPE    6  125
     clus
vv    AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  NO                            0                             6
  YES                          31                           125
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 24(XP22.2) MUTATED   23  1  4  1
  AMP PEAK 24(XP22.2) WILD-TYPE 98  1  8  2
D24V10, multiclass
    clus
vv   AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  R0                          23                            98
  R1                           1                             1
  R2                           4                             8
  RX                           1                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(XP22.2) MUTATED       1                         1    13
  AMP PEAK 24(XP22.2) WILD-TYPE     0                         2    68
D24V12, multiclass
                           clus
vv                          AMP PEAK 24(XP22.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              13
                           clus
vv                          AMP PEAK 24(XP22.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = AMP PEAK 25(XQ27.3) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 25(XQ27.3) MUTATED    27   6
  AMP PEAK 25(XQ27.3) WILD-TYPE 101  16
  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                           33                           117 
  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                            6                            16 
$`AMP PEAK 25(XQ27.3) MUTATED`
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AG-3575 TCGA-AG-3584 
       13.55        19.10        10.39         8.45        12.00        24.00 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3893 
       46.03         2.01        19.99        19.99         7.99        35.01 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       28.04         1.02         0.99        15.95        36.03         9.07 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 
       41.00        38.04         0.72         9.37        60.03        10.98 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EI-6885 TCGA-F5-6464 
       12.00        15.02        57.24       129.27        13.64         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 
       37.51         0.39         0.76 

$`AMP PEAK 25(XQ27.3) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 
       24.13        17.95        17.23        43.04        12.72        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 
       14.50        15.39        20.02        10.39        36.03        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 
        8.02         7.07         1.02         2.01         1.02        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3727 
       50.04        12.03         6.05         0.99        15.95         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        17.03        13.02        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       48.03        32.02        19.99        36.03        14.04        17.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 
       51.98        49.97         1.94        38.96        61.97         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
        6.05         6.97         4.73        13.97         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       15.02        12.99        13.97        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       17.46        11.97         8.45        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                         0.39                          0.46 
  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                       129.27                        126.44 
  AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE 
                        13.64                         14.50 
[1] "0.4 - 129.3 (13.6)" "0.5 - 126.4 (14.5)"
[1] "hr=" "1.1"
D25V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 25(XQ27.3) MUTATED         8        2         6         0         0
  AMP PEAK 25(XQ27.3) WILD-TYPE      22        6        32         2         2
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 25(XQ27.3) MUTATED           0          0          8          4
  AMP PEAK 25(XQ27.3) WILD-TYPE         5          9         15         10
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK 25(XQ27.3) MUTATED          5         2
  AMP PEAK 25(XQ27.3) WILD-TYPE       13         7
D25V3, multiclass
            clus
vv           AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  STAGE I                              8                            22
  STAGE II                             2                             6
  STAGE IIA                            6                            32
  STAGE IIB                            0                             2
  STAGE IIC                            0                             2
  STAGE III                            0                             5
  STAGE IIIA                           0                             9
  STAGE IIIB                           8                            15
  STAGE IIIC                           4                            10
  STAGE IV                             5                            13
  STAGE IVA                            2                             7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  AMP PEAK 25(XQ27.3) MUTATED    2  6 22  6
  AMP PEAK 25(XQ27.3) WILD-TYPE  7 23 87  8
D25V4, multiclass
    clus
vv   AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  T1                           2                             7
  T2                           6                            23
  T3                          22                            87
  T4                           6                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK 25(XQ27.3) MUTATED   16 10  9
  AMP PEAK 25(XQ27.3) WILD-TYPE 67 35 23
D25V5, multiclass
    clus
vv   AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  N0                          16                            67
  N1                          10                            35
  N2                           9                            23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  AMP PEAK 25(XQ27.3) MUTATED   26  6   1  3
  AMP PEAK 25(XQ27.3) WILD-TYPE 97 16   1 10
D25V6, multiclass
     clus
vv    AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  M0                           26                            97
  M1                            6                            16
  M1A                           1                             1
  MX                            3                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                               cls
clus                             0  1
  AMP PEAK 25(XQ27.3) MUTATED   19 17
  AMP PEAK 25(XQ27.3) WILD-TYPE 55 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ27.3) MUTATED     19   17
  AMP PEAK 25(XQ27.3) WILD-TYPE   55   71
        clus
vv       AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  FEMALE                          19                            55
  MALE                            17                            71
[1] 2 2
[1] FALSE
D25V8, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ27.3) MUTATED    32   1
  AMP PEAK 25(XQ27.3) WILD-TYPE 111  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ27.3) MUTATED     32    1
  AMP PEAK 25(XQ27.3) WILD-TYPE  111   12
                                clus
vv                               AMP PEAK 25(XQ27.3) MUTATED
  RECTAL ADENOCARCINOMA                                   32
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK 25(XQ27.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    111
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
D25V9, binary
                               cls
clus                              0   1
  AMP PEAK 25(XQ27.3) MUTATED     0  36
  AMP PEAK 25(XQ27.3) WILD-TYPE   6 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 25(XQ27.3) MUTATED      0   36
  AMP PEAK 25(XQ27.3) WILD-TYPE    6  120
     clus
vv    AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  NO                            0                             6
  YES                          36                           120
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 25(XQ27.3) MUTATED   25  0  4  1
  AMP PEAK 25(XQ27.3) WILD-TYPE 96  2  8  2
D25V10, multiclass
    clus
vv   AMP PEAK 25(XQ27.3) MUTATED AMP PEAK 25(XQ27.3) WILD-TYPE
  R0                          25                            96
  R1                           0                             2
  R2                           4                             8
  RX                           1                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 25(XQ27.3) MUTATED       0                         1    16
  AMP PEAK 25(XQ27.3) WILD-TYPE     1                         2    65
D25V12, multiclass
                           clus
vv                          AMP PEAK 25(XQ27.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              16
                           clus
vv                          AMP PEAK 25(XQ27.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.11) MUTATED   56 11
  DEL PEAK  1(1P36.11) WILD-TYPE 72 11
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            67                             83 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            11                             11 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 
       24.13        17.23        43.04        13.55        19.10        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       14.50        15.39        32.02         1.02         2.01        24.00 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 
       46.03        34.03         6.05        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 
        1.02        19.99         1.02        36.95        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H 
       48.03        19.99        28.04        36.03        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
       23.01        12.00        70.03        64.01        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6622 
       38.96        38.04         0.49         0.69        10.19         6.97 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
        4.73        11.01        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DE 
       36.00        30.05        12.95        10.06       126.44       129.27 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 
       32.61         0.49         2.40        20.55        15.85        11.97 
TCGA-EI-7004 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 
        8.45        14.86         1.02         0.69         0.46        47.08 
TCGA-G5-6641 
       26.43 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       17.95        12.72        37.74         8.45        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 
       36.03        12.00         8.02         7.07         1.02         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        19.99         7.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       32.98         0.99         0.99        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       32.02        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 
       31.00        10.98        49.97        61.97        41.00         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 
        0.72         4.60         1.81         6.05         6.05         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6158 
       13.97        60.03         7.99        10.98        15.02         7.10 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       13.05         5.29        41.36        57.24        24.13        51.48 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       17.46         9.96        37.51        31.30         0.39         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76        18.28        55.76 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.46                           0.39 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        129.27                          61.97 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         15.39                          13.64 
[1] "0.5 - 129.3 (15.4)" "0.4 - 62.0 (13.6)" 
[1] "hr=" "1"  
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  1(1P36.11) MUTATED        12        3        15         2         0
  DEL PEAK  1(1P36.11) WILD-TYPE      18        5        23         0         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  1(1P36.11) MUTATED           2          3         11          8
  DEL PEAK  1(1P36.11) WILD-TYPE         3          6         12          6
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK  1(1P36.11) MUTATED          8         6
  DEL PEAK  1(1P36.11) WILD-TYPE       10         3
D26V3, multiclass
            clus
vv           DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  STAGE I                              12                             18
  STAGE II                              3                              5
  STAGE IIA                            15                             23
  STAGE IIB                             2                              0
  STAGE IIC                             0                              2
  STAGE III                             2                              3
  STAGE IIIA                            3                              6
  STAGE IIIB                           11                             12
  STAGE IIIC                            8                              6
  STAGE IV                              8                             10
  STAGE IVA                             6                              3
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK  1(1P36.11) MUTATED    2 14 45 10
  DEL PEAK  1(1P36.11) WILD-TYPE  7 15 64  4
D26V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            2                              7
  T2                           14                             15
  T3                           45                             64
  T4                           10                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK  1(1P36.11) MUTATED   32 22 17
  DEL PEAK  1(1P36.11) WILD-TYPE 51 23 15
D26V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           32                             51
  N1                           22                             23
  N2                           17                             15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK  1(1P36.11) MUTATED   52 11   2  5
  DEL PEAK  1(1P36.11) WILD-TYPE 71 11   0  8
D26V6, multiclass
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  M0                            52                             71
  M1                            11                             11
  M1A                            2                              0
  MX                             5                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   32 40
  DEL PEAK  1(1P36.11) WILD-TYPE 42 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     32   40
  DEL PEAK  1(1P36.11) WILD-TYPE   42   48
        clus
vv       DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  FEMALE                           32                             42
  MALE                             40                             48
[1] 2 2
[1] FALSE
D26V8, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   61  7
  DEL PEAK  1(1P36.11) WILD-TYPE 82  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     61    7
  DEL PEAK  1(1P36.11) WILD-TYPE   82    6
                                clus
vv                               DEL PEAK  1(1P36.11) MUTATED
  RECTAL ADENOCARCINOMA                                    61
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK  1(1P36.11) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      82
  RECTAL MUCINOUS ADENOCARCINOMA                              6
[1] 2 2
[1] FALSE
D26V9, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED    3 69
  DEL PEAK  1(1P36.11) WILD-TYPE  3 87
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED      3   69
  DEL PEAK  1(1P36.11) WILD-TYPE    3   87
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                             3                              3
  YES                           69                             87
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  1(1P36.11) MUTATED   52  1  7  0
  DEL PEAK  1(1P36.11) WILD-TYPE 69  1  5  3
D26V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           52                             69
  R1                            1                              1
  R2                            7                              5
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       0                         3    35
  DEL PEAK  1(1P36.11) WILD-TYPE     1                         0    46
D26V12, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               35
                           clus
vv                          DEL PEAK  1(1P36.11) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D27V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  2(1P33) MUTATED   40  7
  DEL PEAK  2(1P33) WILD-TYPE 88 15
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         47                         103 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                          7                          15 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3578 
       24.13        17.23        13.55        14.50        15.39        32.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 
        1.02        24.00        34.03        29.98         1.02        19.99 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H 
        1.02        48.03        19.99        28.04        36.03        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       23.01        12.00        70.03         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        0.49         0.69        10.19         9.37         4.73        13.97 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 
       10.98        11.01        12.99        13.97        36.00        30.05 
TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6885 
      126.44       129.27         0.49        20.55        15.85        13.64 
TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
       11.97        14.86         1.02         0.69        47.08 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.95        43.04        19.10        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
        8.45        20.02        10.39        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        7.07         2.01         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99        32.98         0.99         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
       36.95        17.03        13.02        35.01        14.01        32.02 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       31.00        64.01        10.98        51.98        49.97        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       41.00         1.45         0.72         4.60         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
        6.05         6.97        60.03         7.99        15.02        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02         7.10        12.95        13.05        10.06         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       41.36        57.24        24.13        51.48        32.61         2.40 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 
       16.31        16.41         8.61        11.51        10.78        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
        8.45         9.96        37.51        31.30         0.39         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6641 
       26.43 

  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                       0.49                        0.39 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                     129.27                       64.01 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      15.39                       13.94 
[1] "0.5 - 129.3 (15.4)" "0.4 - 64.0 (13.9)" 
[1] "hr=" "1.1"
D27V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  2(1P33) MUTATED         7        2        13         1         0
  DEL PEAK  2(1P33) WILD-TYPE      23        6        25         1         2
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  2(1P33) MUTATED           1          2          9          5
  DEL PEAK  2(1P33) WILD-TYPE         4          7         14          9
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  2(1P33) MUTATED          6         2
  DEL PEAK  2(1P33) WILD-TYPE       12         7
D27V3, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                            7                          23
  STAGE II                           2                           6
  STAGE IIA                         13                          25
  STAGE IIB                          1                           1
  STAGE IIC                          0                           2
  STAGE III                          1                           4
  STAGE IIIA                         2                           7
  STAGE IIIB                         9                          14
  STAGE IIIC                         5                           9
  STAGE IV                           6                          12
  STAGE IVA                          2                           7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK  2(1P33) MUTATED    1  8 36  4
  DEL PEAK  2(1P33) WILD-TYPE  8 21 73 10
D27V4, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         1                           8
  T2                         8                          21
  T3                        36                          73
  T4                         4                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK  2(1P33) MUTATED   23 18  8
  DEL PEAK  2(1P33) WILD-TYPE 60 27 24
D27V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        23                          60
  N1                        18                          27
  N2                         8                          24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 M1A MX
  DEL PEAK  2(1P33) MUTATED   37  8   0  3
  DEL PEAK  2(1P33) WILD-TYPE 86 14   2 10
D27V6, multiclass
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  M0                         37                          86
  M1                          8                          14
  M1A                         0                           2
  MX                          3                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                             cls
clus                           0  1
  DEL PEAK  2(1P33) MUTATED   23 27
  DEL PEAK  2(1P33) WILD-TYPE 51 61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     23   27
  DEL PEAK  2(1P33) WILD-TYPE   51   61
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        23                          51
  MALE                          27                          61
[1] 2 2
[1] FALSE
D27V8, binary
                             cls
clus                           0  1
  DEL PEAK  2(1P33) MUTATED   46  1
  DEL PEAK  2(1P33) WILD-TYPE 97 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     46    1
  DEL PEAK  2(1P33) WILD-TYPE   97   12
                                clus
vv                               DEL PEAK  2(1P33) MUTATED
  RECTAL ADENOCARCINOMA                                 46
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  2(1P33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   97
  RECTAL MUCINOUS ADENOCARCINOMA                          12
[1] 2 2
[1] FALSE
D27V9, binary
                             cls
clus                            0   1
  DEL PEAK  2(1P33) MUTATED     3  47
  DEL PEAK  2(1P33) WILD-TYPE   3 109
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED      3   47
  DEL PEAK  2(1P33) WILD-TYPE    3  109
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                          3                           3
  YES                        47                         109
[1] 2 2
[1] FALSE
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  2(1P33) MUTATED   34  1  4  0
  DEL PEAK  2(1P33) WILD-TYPE 87  1  8  3
D27V10, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                        34                          87
  R1                         1                           1
  R2                         4                           8
  RX                         0                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P33) MUTATED       0                         2    26
  DEL PEAK  2(1P33) WILD-TYPE     1                         1    55
D27V12, multiclass
                           clus
vv                          DEL PEAK  2(1P33) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            26
                           clus
vv                          DEL PEAK  2(1P33) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = DEL PEAK  3(1P13.2) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(1P13.2) MUTATED   40  9
  DEL PEAK  3(1P13.2) WILD-TYPE 88 13
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           49                           101 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                            9                            13 
$`DEL PEAK  3(1P13.2) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3578 
       24.13        17.23        13.55        14.50        15.39        32.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3728 TCGA-AG-3731 
        1.02        24.00        34.03         2.01        29.98         1.02 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H 
       19.99         1.02        19.99        28.04        36.03        25.97 
TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 
       23.01        12.00        70.03         1.94        38.04         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
        0.69        10.19         9.37        11.01        12.99        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5830 
       36.00        30.05       126.44        41.36       129.27         0.49 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 
       20.55        17.00        15.85        11.51        13.64        11.97 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 
       14.86         1.02         0.66         0.69         0.76        18.28 
TCGA-G5-6572 
       47.08 

$`DEL PEAK  3(1P13.2) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       17.95        43.04        19.10        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
        8.45        20.02        10.39        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3599 
        7.07         2.01         1.02        46.03        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.99        32.98         0.99         0.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
       31.00        64.01        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       61.97        41.00         1.45         0.72         4.60         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.05         6.97         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
        7.99        10.98        15.02        12.00        15.02         7.10 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF 
       12.95        13.05        10.06         5.29        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       51.48        32.61         2.40        19.96        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 
       17.69        16.34        16.31        16.41         8.61        10.78 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        0.53         1.12         0.46        55.76        26.43 

  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                         0.49                          0.39 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                       129.27                         64.01 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                        15.39                         13.97 
[1] "0.5 - 129.3 (15.4)" "0.4 - 64.0 (14.0)" 
[1] "hr=" "1.4"
D28V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  3(1P13.2) MUTATED         6        2        15         1         2
  DEL PEAK  3(1P13.2) WILD-TYPE      24        6        23         1         0
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  3(1P13.2) MUTATED           0          1          9          6
  DEL PEAK  3(1P13.2) WILD-TYPE         5          8         14          8
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  3(1P13.2) MUTATED          6         2
  DEL PEAK  3(1P13.2) WILD-TYPE       12         7
D28V3, multiclass
            clus
vv           DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  STAGE I                              6                            24
  STAGE II                             2                             6
  STAGE IIA                           15                            23
  STAGE IIB                            1                             1
  STAGE IIC                            2                             0
  STAGE III                            0                             5
  STAGE IIIA                           1                             8
  STAGE IIIB                           9                            14
  STAGE IIIC                           6                             8
  STAGE IV                             6                            12
  STAGE IVA                            2                             7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  3(1P13.2) MUTATED    1  6 39  5
  DEL PEAK  3(1P13.2) WILD-TYPE  8 23 70  9
D28V4, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  T1                           1                             8
  T2                           6                            23
  T3                          39                            70
  T4                           5                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  3(1P13.2) MUTATED   25 15 11
  DEL PEAK  3(1P13.2) WILD-TYPE 58 30 21
D28V5, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  N0                          25                            58
  N1                          15                            30
  N2                          11                            21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  3(1P13.2) MUTATED   40  8   0  2
  DEL PEAK  3(1P13.2) WILD-TYPE 83 14   2 11
D28V6, multiclass
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  M0                           40                            83
  M1                            8                            14
  M1A                           0                             2
  MX                            2                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P13.2) MUTATED   23 29
  DEL PEAK  3(1P13.2) WILD-TYPE 51 59
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     23   29
  DEL PEAK  3(1P13.2) WILD-TYPE   51   59
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  FEMALE                          23                            51
  MALE                            29                            59
[1] 2 2
[1] FALSE
D28V8, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P13.2) MUTATED   47  2
  DEL PEAK  3(1P13.2) WILD-TYPE 96 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     47    2
  DEL PEAK  3(1P13.2) WILD-TYPE   96   11
                                clus
vv                               DEL PEAK  3(1P13.2) MUTATED
  RECTAL ADENOCARCINOMA                                   47
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK  3(1P13.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     96
  RECTAL MUCINOUS ADENOCARCINOMA                            11
[1] 2 2
[1] FALSE
D28V9, binary
                               cls
clus                              0   1
  DEL PEAK  3(1P13.2) MUTATED     3  49
  DEL PEAK  3(1P13.2) WILD-TYPE   3 107
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED      3   49
  DEL PEAK  3(1P13.2) WILD-TYPE    3  107
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  NO                            3                             3
  YES                          49                           107
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  3(1P13.2) MUTATED   38  1  4  0
  DEL PEAK  3(1P13.2) WILD-TYPE 83  1  8  3
D28V10, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  R0                          38                            83
  R1                           1                             1
  R2                           4                             8
  RX                           0                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P13.2) MUTATED       0                         2    29
  DEL PEAK  3(1P13.2) WILD-TYPE     1                         1    52
D28V12, multiclass
                           clus
vv                          DEL PEAK  3(1P13.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              29
                           clus
vv                          DEL PEAK  3(1P13.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK  4(2P12) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2P12) MUTATED    14   1
  DEL PEAK  4(2P12) WILD-TYPE 114  21
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         15                         135 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                          1                          21 
$`DEL PEAK  4(2P12) MUTATED`
TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3896 
       15.39        32.02         1.02         6.05        19.99         1.02 
TCGA-AG-3999 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A02X TCGA-DC-6156 TCGA-DC-6682 
       28.04        17.03        25.97        41.00        15.02        13.05 
TCGA-EF-5831 TCGA-EI-6508 TCGA-F5-6571 
        2.40        20.91        31.30 

$`DEL PEAK  4(2P12) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       12.72        37.74        10.39        14.50         8.45        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       10.39        36.03        12.00         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72         4.60         1.81        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        13.97        60.03         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       10.98        11.01        15.02        12.99        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 
       32.61         0.49        20.55        19.96        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                       1.02                        0.39 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      41.00                      129.27 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      17.03                       13.97 
[1] "1.0 - 41.0 (17.0)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.8"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  4(2P12) MUTATED         2        0         9         0         0
  DEL PEAK  4(2P12) WILD-TYPE      28        8        29         2         2
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  4(2P12) MUTATED           0          0          2          3
  DEL PEAK  4(2P12) WILD-TYPE         5          9         21         11
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  4(2P12) MUTATED          1         1
  DEL PEAK  4(2P12) WILD-TYPE       17         8
D29V3, multiclass
            clus
vv           DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  STAGE I                            2                          28
  STAGE II                           0                           8
  STAGE IIA                          9                          29
  STAGE IIB                          0                           2
  STAGE IIC                          0                           2
  STAGE III                          0                           5
  STAGE IIIA                         0                           9
  STAGE IIIB                         2                          21
  STAGE IIIC                         3                          11
  STAGE IV                           1                          17
  STAGE IVA                          1                           8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK  4(2P12) MUTATED    0  2 15  1
  DEL PEAK  4(2P12) WILD-TYPE  9 27 94 13
D29V4, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  T1                         0                           9
  T2                         2                          27
  T3                        15                          94
  T4                         1                          13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK  4(2P12) MUTATED   11  3  4
  DEL PEAK  4(2P12) WILD-TYPE 72 42 28
D29V5, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  N0                        11                          72
  N1                         3                          42
  N2                         4                          28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  DEL PEAK  4(2P12) MUTATED    15   1   1   1
  DEL PEAK  4(2P12) WILD-TYPE 108  21   1  12
D29V6, multiclass
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  M0                         15                         108
  M1                          1                          21
  M1A                         1                           1
  MX                          1                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                             cls
clus                           0  1
  DEL PEAK  4(2P12) MUTATED    8 10
  DEL PEAK  4(2P12) WILD-TYPE 66 78
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      8   10
  DEL PEAK  4(2P12) WILD-TYPE   66   78
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  FEMALE                         8                          66
  MALE                          10                          78
[1] 2 2
[1] FALSE
D29V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    16   1
  DEL PEAK  4(2P12) WILD-TYPE 127  12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     16    1
  DEL PEAK  4(2P12) WILD-TYPE  127   12
                                clus
vv                               DEL PEAK  4(2P12) MUTATED
  RECTAL ADENOCARCINOMA                                 16
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  4(2P12) WILD-TYPE
  RECTAL ADENOCARCINOMA                                  127
  RECTAL MUCINOUS ADENOCARCINOMA                          12
[1] 2 2
[1] FALSE
D29V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     1  17
  DEL PEAK  4(2P12) WILD-TYPE   5 139
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      1   17
  DEL PEAK  4(2P12) WILD-TYPE    5  139
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  NO                          1                           5
  YES                        17                         139
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(2P12) MUTATED    15   0   1   0
  DEL PEAK  4(2P12) WILD-TYPE 106   2  11   3
D29V10, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  R0                        15                         106
  R1                         0                           2
  R2                         1                          11
  RX                         0                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2P12) MUTATED       0                         0     6
  DEL PEAK  4(2P12) WILD-TYPE     1                         3    75
D29V12, multiclass
                           clus
vv                          DEL PEAK  4(2P12) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             6
                           clus
vv                          DEL PEAK  4(2P12) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              75
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = DEL PEAK  5(3P14.2) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P14.2) MUTATED    21   5
  DEL PEAK  5(3P14.2) WILD-TYPE 107  17
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           26                           124 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                            5                            17 
$`DEL PEAK  5(3P14.2) MUTATED`
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3580 TCGA-AG-3581 
       43.04        19.10        12.72        14.50         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-4007 
        2.01        24.00         1.02        32.98        19.99         1.02 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A02G TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 
       17.03         6.02        38.96         0.49        10.19         6.05 
TCGA-CI-6623 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6508 
        9.37        15.02         7.10        13.05         5.29        20.91 
TCGA-F5-6810 TCGA-G5-6233 
        0.39        18.28 

$`DEL PEAK  5(3P14.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        13.55        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
        8.45        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       32.02         1.02         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        29.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       14.04         0.99        20.98        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.97        41.00        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        0.72         4.60         1.81         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
       13.97        60.03         7.99        10.98        11.01        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       12.00        13.97        15.02        36.00        30.05        12.95 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        1.02         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                         0.39                          0.46 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                        43.04                        129.27 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                       11.455                        15.205 
[1] "0.4 - 43.0 (11.5)"  "0.5 - 129.3 (15.2)"
[1] "hr=" "2.7"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  5(3P14.2) MUTATED         9        1         6         0         1
  DEL PEAK  5(3P14.2) WILD-TYPE      21        7        32         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  5(3P14.2) MUTATED           0          0          4          0
  DEL PEAK  5(3P14.2) WILD-TYPE         5          9         19         14
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  5(3P14.2) MUTATED          6         1
  DEL PEAK  5(3P14.2) WILD-TYPE       12         8
D30V3, multiclass
            clus
vv           DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  STAGE I                              9                            21
  STAGE II                             1                             7
  STAGE IIA                            6                            32
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            0                             5
  STAGE IIIA                           0                             9
  STAGE IIIB                           4                            19
  STAGE IIIC                           0                            14
  STAGE IV                             6                            12
  STAGE IVA                            1                             8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  5(3P14.2) MUTATED    4  6 17  2
  DEL PEAK  5(3P14.2) WILD-TYPE  5 23 92 12
D30V4, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  T1                           4                             5
  T2                           6                            23
  T3                          17                            92
  T4                           2                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  5(3P14.2) MUTATED   16  8  5
  DEL PEAK  5(3P14.2) WILD-TYPE 67 37 27
D30V5, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  N0                          16                            67
  N1                           8                            37
  N2                           5                            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK  5(3P14.2) MUTATED    19   7   0   2
  DEL PEAK  5(3P14.2) WILD-TYPE 104  15   2  11
D30V6, multiclass
     clus
vv    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  M0                           19                           104
  M1                            7                            15
  M1A                           0                             2
  MX                            2                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED    7 22
  DEL PEAK  5(3P14.2) WILD-TYPE 67 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED      7   22
  DEL PEAK  5(3P14.2) WILD-TYPE   67   66
        clus
vv       DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  FEMALE                           7                            67
  MALE                            22                            66
[1] 2 2
[1] FALSE
D30V8, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P14.2) MUTATED    23   3
  DEL PEAK  5(3P14.2) WILD-TYPE 120  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     23    3
  DEL PEAK  5(3P14.2) WILD-TYPE  120   10
                                clus
vv                               DEL PEAK  5(3P14.2) MUTATED
  RECTAL ADENOCARCINOMA                                   23
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  5(3P14.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    120
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 2 2
[1] FALSE
D30V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P14.2) MUTATED     2  27
  DEL PEAK  5(3P14.2) WILD-TYPE   4 129
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED      2   27
  DEL PEAK  5(3P14.2) WILD-TYPE    4  129
     clus
vv    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  NO                            2                             4
  YES                          27                           129
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(3P14.2) MUTATED    18   0   5   1
  DEL PEAK  5(3P14.2) WILD-TYPE 103   2   7   2
D30V10, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  R0                          18                           103
  R1                           0                             2
  R2                           5                             7
  RX                           1                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P14.2) MUTATED       1                         0    14
  DEL PEAK  5(3P14.2) WILD-TYPE     0                         3    67
D30V12, multiclass
                           clus
vv                          DEL PEAK  5(3P14.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              14
                           clus
vv                          DEL PEAK  5(3P14.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = DEL PEAK  6(3Q26.31) MUTATION ANALYSIS
D31V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  6(3Q26.31) MUTATED    12   4
  DEL PEAK  6(3Q26.31) WILD-TYPE 116  18
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            16                            134 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                             4                             18 
$`DEL PEAK  6(3Q26.31) MUTATED`
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3728 TCGA-AG-3894 
       12.72        14.50        32.02         2.01        29.98        14.01 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A026 TCGA-AG-A02G TCGA-CI-6619 TCGA-DC-6682 
       36.03         1.02         1.94        38.96         6.05        13.05 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-7002 TCGA-G5-6233 
        5.29        19.96        11.97        18.28 

$`DEL PEAK  6(3Q26.31) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        10.39         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       36.03        12.00         8.02         7.07         1.02        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        6.05         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99         1.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 
        1.02        36.95        17.03        13.02        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       48.03        32.02        19.99        28.04        14.04        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04         0.49         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 
        0.72         4.60         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA 
       36.00         7.10        30.05        12.95        10.06       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.69         0.53         1.12         0.76         0.46        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                          1.02                           0.39 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                         38.96                         129.27 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                         13.53                          14.94 
[1] "1.0 - 39.0 (13.5)"  "0.4 - 129.3 (14.9)"
[1] "hr=" "2.9"
D31V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  6(3Q26.31) MUTATED         0        2         6         0         1
  DEL PEAK  6(3Q26.31) WILD-TYPE      30        6        32         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  6(3Q26.31) MUTATED           0          0          1          0
  DEL PEAK  6(3Q26.31) WILD-TYPE         5          9         22         14
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK  6(3Q26.31) MUTATED          5         1
  DEL PEAK  6(3Q26.31) WILD-TYPE       13         8
D31V3, multiclass
            clus
vv           DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  STAGE I                               0                             30
  STAGE II                              2                              6
  STAGE IIA                             6                             32
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             0                              5
  STAGE IIIA                            0                              9
  STAGE IIIB                            1                             22
  STAGE IIIC                            0                             14
  STAGE IV                              5                             13
  STAGE IVA                             1                              8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK  6(3Q26.31) MUTATED    0  1 12  3
  DEL PEAK  6(3Q26.31) WILD-TYPE  9 28 97 11
D31V4, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  T1                            0                              9
  T2                            1                             28
  T3                           12                             97
  T4                            3                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK  6(3Q26.31) MUTATED    8  3  5
  DEL PEAK  6(3Q26.31) WILD-TYPE 75 42 27
D31V5, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  N0                            8                             75
  N1                            3                             42
  N2                            5                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK  6(3Q26.31) MUTATED    10   5   0   1
  DEL PEAK  6(3Q26.31) WILD-TYPE 113  17   2  12
D31V6, multiclass
     clus
vv    DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  M0                            10                            113
  M1                             5                             17
  M1A                            0                              2
  MX                             1                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                                cls
clus                              0  1
  DEL PEAK  6(3Q26.31) MUTATED    2 14
  DEL PEAK  6(3Q26.31) WILD-TYPE 72 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED      2   14
  DEL PEAK  6(3Q26.31) WILD-TYPE   72   74
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  FEMALE                            2                             72
  MALE                             14                             74
[1] 2 2
[1] FALSE
D31V8, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q26.31) MUTATED    11   4
  DEL PEAK  6(3Q26.31) WILD-TYPE 132   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED     11    4
  DEL PEAK  6(3Q26.31) WILD-TYPE  132    9
                                clus
vv                               DEL PEAK  6(3Q26.31) MUTATED
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               DEL PEAK  6(3Q26.31) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     132
  RECTAL MUCINOUS ADENOCARCINOMA                              9
[1] 2 2
[1] FALSE
D31V9, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q26.31) MUTATED     1  15
  DEL PEAK  6(3Q26.31) WILD-TYPE   5 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED      1   15
  DEL PEAK  6(3Q26.31) WILD-TYPE    5  141
     clus
vv    DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  NO                             1                              5
  YES                           15                            141
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  6(3Q26.31) MUTATED    10   1   3   1
  DEL PEAK  6(3Q26.31) WILD-TYPE 111   1   9   2
D31V10, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  R0                           10                            111
  R1                            1                              1
  R2                            3                              9
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3Q26.31) MUTATED       1                         0     7
  DEL PEAK  6(3Q26.31) WILD-TYPE     0                         3    74
D31V12, multiclass
                           clus
vv                          DEL PEAK  6(3Q26.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                7
                           clus
vv                          DEL PEAK  6(3Q26.31) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 74
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK  7(4P13) MUTATION ANALYSIS
D32V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  7(4P13) MUTATED   47  6
  DEL PEAK  7(4P13) WILD-TYPE 81 16
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         53                          97 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                          6                          16 
$`DEL PEAK  7(4P13) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       24.13        17.23        43.04        12.72        37.74        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3612 TCGA-AG-3728 
       15.39        10.39         1.02        34.03        19.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
        1.02        32.98         1.02        17.03        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G 
       13.94        25.97        23.01        12.00        70.03        38.96 
TCGA-AG-A02X TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-DC-5869 
       41.00         0.69        10.19         6.05         6.05        12.99 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
       15.02        36.00         7.10        30.05       126.44       129.27 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 
       32.61         2.40        15.85        16.34        16.41        11.97 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-G5-6641 
       31.30        14.86         0.39         0.69        26.43 

$`DEL PEAK  7(4P13) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 
       17.95        13.55        19.10        10.39         8.45        20.02 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       36.03        12.00        32.02         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        46.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        0.99         0.99        19.99        36.95        13.02        14.01 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 
        1.02        17.03         0.99        20.98         6.02        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y 
       15.95        36.03         9.07         1.02        31.00        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 
       10.98        51.98        49.97         1.94        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 
        0.49         1.45         0.72         4.60         1.81         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 
       11.01        15.02        12.00        13.97        12.95        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         5.29        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 
       17.46         8.45         9.96        37.51         1.02         0.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                       0.39                        0.46 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                     129.27                       64.01 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                      17.03                       12.95 
[1] "0.4 - 129.3 (17.0)" "0.5 - 64.0 (12.9)" 
[1] "hr=" "1.7"
D32V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  7(4P13) MUTATED        10        1        16         0         0
  DEL PEAK  7(4P13) WILD-TYPE      20        7        22         2         2
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  7(4P13) MUTATED           1          3         11          6
  DEL PEAK  7(4P13) WILD-TYPE         4          6         12          8
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  7(4P13) MUTATED          7         4
  DEL PEAK  7(4P13) WILD-TYPE       11         5
D32V3, multiclass
            clus
vv           DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  STAGE I                           10                          20
  STAGE II                           1                           7
  STAGE IIA                         16                          22
  STAGE IIB                          0                           2
  STAGE IIC                          0                           2
  STAGE III                          1                           4
  STAGE IIIA                         3                           6
  STAGE IIIB                        11                          12
  STAGE IIIC                         6                           8
  STAGE IV                           7                          11
  STAGE IVA                          4                           5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK  7(4P13) MUTATED    2 11 42  4
  DEL PEAK  7(4P13) WILD-TYPE  7 18 67 10
D32V4, multiclass
    clus
vv   DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  T1                         2                           7
  T2                        11                          18
  T3                        42                          67
  T4                         4                          10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK  7(4P13) MUTATED   27 20 12
  DEL PEAK  7(4P13) WILD-TYPE 56 25 20
D32V5, multiclass
    clus
vv   DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  N0                        27                          56
  N1                        20                          25
  N2                        12                          20
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          M0 M1 M1A MX
  DEL PEAK  7(4P13) MUTATED   44  8   1  5
  DEL PEAK  7(4P13) WILD-TYPE 79 14   1  8
D32V6, multiclass
     clus
vv    DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  M0                         44                          79
  M1                          8                          14
  M1A                         1                           1
  MX                          5                           8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V7, binary
                             cls
clus                           0  1
  DEL PEAK  7(4P13) MUTATED   22 37
  DEL PEAK  7(4P13) WILD-TYPE 52 51
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED     22   37
  DEL PEAK  7(4P13) WILD-TYPE   52   51
        clus
vv       DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  FEMALE                        22                          52
  MALE                          37                          51
[1] 2 2
[1] FALSE
D32V8, binary
                             cls
clus                           0  1
  DEL PEAK  7(4P13) MUTATED   54  3
  DEL PEAK  7(4P13) WILD-TYPE 89 10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED     54    3
  DEL PEAK  7(4P13) WILD-TYPE   89   10
                                clus
vv                               DEL PEAK  7(4P13) MUTATED
  RECTAL ADENOCARCINOMA                                 54
  RECTAL MUCINOUS ADENOCARCINOMA                         3
                                clus
vv                               DEL PEAK  7(4P13) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   89
  RECTAL MUCINOUS ADENOCARCINOMA                          10
[1] 2 2
[1] FALSE
D32V9, binary
                             cls
clus                            0   1
  DEL PEAK  7(4P13) MUTATED     6  53
  DEL PEAK  7(4P13) WILD-TYPE   0 103
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED      6   53
  DEL PEAK  7(4P13) WILD-TYPE    0  103
     clus
vv    DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  NO                          6                           0
  YES                        53                         103
[1] 2 2
[1] FALSE
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  7(4P13) MUTATED   47  0  3  0
  DEL PEAK  7(4P13) WILD-TYPE 74  2  9  3
D32V10, multiclass
    clus
vv   DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  R0                        47                          74
  R1                         0                           2
  R2                         3                           9
  RX                         0                           3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D32V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4P13) MUTATED       0                         2    28
  DEL PEAK  7(4P13) WILD-TYPE     1                         1    53
D32V12, multiclass
                           clus
vv                          DEL PEAK  7(4P13) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            28
                           clus
vv                          DEL PEAK  7(4P13) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              53
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK  8(4Q22.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(4Q22.1) MUTATED   58  6
  DEL PEAK  8(4Q22.1) WILD-TYPE 70 16
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           64                            86 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                            6                            16 
$`DEL PEAK  8(4Q22.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3593 TCGA-AG-3600 
       37.74        14.50        15.39         1.02        34.03         6.05 
TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3898 
       19.99        29.98        32.98         1.02         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
       13.94         6.02        25.97        23.01        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       64.01         1.94        41.00         0.49         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 
        6.05         6.05         4.73        11.01        12.99        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE 
       36.00         7.10        30.05        13.05       126.44       129.27 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
        2.40        20.91        17.00        15.85        16.34        16.41 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97         8.45        31.30        14.86         0.39         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.69        18.28        26.43 

$`DEL PEAK  8(4Q22.1) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       17.95        10.39         8.45        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         8.02         7.07         2.01        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        1.02        46.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       15.95        19.99         7.99         0.99         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 
       14.01        32.02         0.99        20.98        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 
       36.03         9.07         1.02        31.00        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
       49.97        38.96        61.97        38.04         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 
        4.60         1.81         6.97         9.37        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 
        7.99        10.98        15.02        12.00        13.97        12.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       10.06         5.29        41.36        57.24        24.13        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 
       32.61         0.49        20.55        19.96        18.28        17.69 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31         8.61        11.51        10.78        13.64        17.46 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        9.96        37.51         0.53         1.12         0.76         0.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                         0.39                          0.46 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                       129.27                         61.97 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                       15.205                        13.805 
[1] "0.4 - 129.3 (15.2)" "0.5 - 62.0 (13.8)" 
[1] "hr=" "2"  
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  8(4Q22.1) MUTATED        12        3        20         0         1
  DEL PEAK  8(4Q22.1) WILD-TYPE      18        5        18         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  8(4Q22.1) MUTATED           2          2         13          8
  DEL PEAK  8(4Q22.1) WILD-TYPE         3          7         10          6
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  8(4Q22.1) MUTATED          5         5
  DEL PEAK  8(4Q22.1) WILD-TYPE       13         4
D33V3, multiclass
            clus
vv           DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  STAGE I                             12                            18
  STAGE II                             3                             5
  STAGE IIA                           20                            18
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            2                             3
  STAGE IIIA                           2                             7
  STAGE IIIB                          13                            10
  STAGE IIIC                           8                             6
  STAGE IV                             5                            13
  STAGE IVA                            5                             4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  8(4Q22.1) MUTATED    2 11 52  7
  DEL PEAK  8(4Q22.1) WILD-TYPE  7 18 57  7
D33V4, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  T1                           2                             7
  T2                          11                            18
  T3                          52                            57
  T4                           7                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  8(4Q22.1) MUTATED   35 21 16
  DEL PEAK  8(4Q22.1) WILD-TYPE 48 24 16
D33V5, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  N0                          35                            48
  N1                          21                            24
  N2                          16                            16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  8(4Q22.1) MUTATED   56  8   1  6
  DEL PEAK  8(4Q22.1) WILD-TYPE 67 14   1  7
D33V6, multiclass
     clus
vv    DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  M0                           56                            67
  M1                            8                            14
  M1A                           1                             1
  MX                            6                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   28 44
  DEL PEAK  8(4Q22.1) WILD-TYPE 46 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     28   44
  DEL PEAK  8(4Q22.1) WILD-TYPE   46   44
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  FEMALE                          28                            46
  MALE                            44                            44
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   64  4
  DEL PEAK  8(4Q22.1) WILD-TYPE 79  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     64    4
  DEL PEAK  8(4Q22.1) WILD-TYPE   79    9
                                clus
vv                               DEL PEAK  8(4Q22.1) MUTATED
  RECTAL ADENOCARCINOMA                                   64
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK  8(4Q22.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     79
  RECTAL MUCINOUS ADENOCARCINOMA                             9
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED    5 67
  DEL PEAK  8(4Q22.1) WILD-TYPE  1 89
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED      5   67
  DEL PEAK  8(4Q22.1) WILD-TYPE    1   89
     clus
vv    DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  NO                            5                             1
  YES                          67                            89
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  8(4Q22.1) MUTATED   56  1  3  0
  DEL PEAK  8(4Q22.1) WILD-TYPE 65  1  9  3
D33V10, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  R0                          56                            65
  R1                           1                             1
  R2                           3                             9
  RX                           0                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D33V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q22.1) MUTATED       0                         2    39
  DEL PEAK  8(4Q22.1) WILD-TYPE     1                         1    42
D33V12, multiclass
                           clus
vv                          DEL PEAK  8(4Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              39
                           clus
vv                          DEL PEAK  8(4Q22.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK  9(4Q35.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(4Q35.1) MUTATED   54  8
  DEL PEAK  9(4Q35.1) WILD-TYPE 74 14
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           62                            88 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                            8                            14 
$`DEL PEAK  9(4Q35.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3582 TCGA-AG-3587 
       37.74        10.39        14.50        15.39         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       34.03         6.05        19.99        29.98        32.98         0.99 
TCGA-AG-3883 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       13.94        25.97        23.01        12.00        70.03        64.01 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
       41.00         0.49         0.69        10.19         6.05         6.05 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        4.73        11.01        12.99        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 
       30.05       126.44       129.27        24.13         2.40        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6571 
       15.85        16.34        16.41        11.97         9.96        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6864 
       14.86         0.39         1.02         0.66         0.53         0.46 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
       17.95         8.45        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        7.99         0.99         1.02         0.99        19.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       17.03        13.02        35.01        14.01         1.02        32.02 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 
        1.02        17.03         0.99        20.98         6.02        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 
       15.95        36.03         9.07         1.02        31.00        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
       51.98        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 
        1.45         0.72         4.60         1.81         6.97         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       13.97        60.03         7.99        10.98        15.02        12.00 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       13.97        12.95        13.05        10.06         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 
       57.24        51.48        32.61         0.49        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       20.91        18.28        17.69        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6813 
       10.78        13.64        17.46         8.45        37.51         0.69 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        55.76        47.08 

  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                         0.39                          0.49 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                       129.27                         61.97 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                       15.620                        13.345 
[1] "0.4 - 129.3 (15.6)" "0.5 - 62.0 (13.3)" 
[1] "hr=" "1.4"
D34V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  9(4Q35.1) MUTATED        13        2        19         0         1
  DEL PEAK  9(4Q35.1) WILD-TYPE      17        6        19         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  9(4Q35.1) MUTATED           2          2         11         10
  DEL PEAK  9(4Q35.1) WILD-TYPE         3          7         12          4
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  9(4Q35.1) MUTATED          6         4
  DEL PEAK  9(4Q35.1) WILD-TYPE       12         5
D34V3, multiclass
            clus
vv           DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  STAGE I                             13                            17
  STAGE II                             2                             6
  STAGE IIA                           19                            19
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            2                             3
  STAGE IIIA                           2                             7
  STAGE IIIB                          11                            12
  STAGE IIIC                          10                             4
  STAGE IV                             6                            12
  STAGE IVA                            4                             5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK  9(4Q35.1) MUTATED    3 12 52  4
  DEL PEAK  9(4Q35.1) WILD-TYPE  6 17 57 10
D34V4, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  T1                           3                             6
  T2                          12                            17
  T3                          52                            57
  T4                           4                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  9(4Q35.1) MUTATED   34 20 17
  DEL PEAK  9(4Q35.1) WILD-TYPE 49 25 15
D34V5, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  N0                          34                            49
  N1                          20                            25
  N2                          17                            15
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK  9(4Q35.1) MUTATED   54  9   1  6
  DEL PEAK  9(4Q35.1) WILD-TYPE 69 13   1  7
D34V6, multiclass
     clus
vv    DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  M0                           54                            69
  M1                            9                            13
  M1A                           1                             1
  MX                            6                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   29 42
  DEL PEAK  9(4Q35.1) WILD-TYPE 45 46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     29   42
  DEL PEAK  9(4Q35.1) WILD-TYPE   45   46
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          29                            45
  MALE                            42                            46
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   64  3
  DEL PEAK  9(4Q35.1) WILD-TYPE 79 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     64    3
  DEL PEAK  9(4Q35.1) WILD-TYPE   79   10
                                clus
vv                               DEL PEAK  9(4Q35.1) MUTATED
  RECTAL ADENOCARCINOMA                                   64
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  9(4Q35.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     79
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 2 2
[1] FALSE
D34V9, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED    5 66
  DEL PEAK  9(4Q35.1) WILD-TYPE  1 90
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED      5   66
  DEL PEAK  9(4Q35.1) WILD-TYPE    1   90
     clus
vv    DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  NO                            5                             1
  YES                          66                            90
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  9(4Q35.1) MUTATED   55  0  3  0
  DEL PEAK  9(4Q35.1) WILD-TYPE 66  2  9  3
D34V10, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  R0                          55                            66
  R1                           0                             2
  R2                           3                             9
  RX                           0                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q35.1) MUTATED       0                         3    39
  DEL PEAK  9(4Q35.1) WILD-TYPE     1                         0    42
D34V12, multiclass
                           clus
vv                          DEL PEAK  9(4Q35.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              39
                           clus
vv                          DEL PEAK  9(4Q35.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK 10(5Q11.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(5Q11.2) MUTATED   36  9
  DEL PEAK 10(5Q11.2) WILD-TYPE 92 13
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                           45                           105 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                            9                            13 
$`DEL PEAK 10(5Q11.2) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 
       24.13        17.23        43.04        37.74        10.39        15.39 
TCGA-AF-6672 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3882 TCGA-AG-3890 
       10.39        29.98         1.02        32.98        19.99        17.03 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-A00Y 
        1.02        48.03        28.04        36.03        17.03        23.01 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-BM-6198 
       70.03        64.01         1.94        38.96        41.00        10.19 
TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
        6.05         7.99        12.99        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 
        7.10       126.44        57.24       129.27        51.48        20.55 
TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6702 
       16.41        13.64        11.97         8.45        37.51        14.86 
TCGA-F5-6811 TCGA-G5-6233 TCGA-G5-6641 
        1.02        18.28        26.43 

$`DEL PEAK 10(5Q11.2) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       17.95        13.55        19.10        12.72        14.50         8.45 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       20.02        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
        2.01        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
       19.99        19.99         7.99         0.99         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
        1.02        36.95        13.02        35.01        14.01        32.02 
TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       19.99        14.04         1.02         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        31.00        10.98        51.98        49.97 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        4.60         1.81         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       13.97        60.03        10.98        11.01        15.02        12.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       30.05        12.95        13.05        10.06         5.29        41.36 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49         2.40        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6571 
        8.61        11.51        10.78        17.46         9.96        31.30 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.46        55.76        47.08 

  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                         1.02                          0.39 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                       129.27                         61.97 
  DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE 
                        18.28                         12.95 
[1] "1.0 - 129.3 (18.3)" "0.4 - 62.0 (12.9)" 
[1] "hr=" "1.1"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 10(5Q11.2) MUTATED         8        3        14         0         1
  DEL PEAK 10(5Q11.2) WILD-TYPE      22        5        24         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 10(5Q11.2) MUTATED           1          3          5          4
  DEL PEAK 10(5Q11.2) WILD-TYPE         4          6         18         10
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 10(5Q11.2) MUTATED          7         5
  DEL PEAK 10(5Q11.2) WILD-TYPE       11         4
D35V3, multiclass
            clus
vv           DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  STAGE I                              8                            22
  STAGE II                             3                             5
  STAGE IIA                           14                            24
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           3                             6
  STAGE IIIB                           5                            18
  STAGE IIIC                           4                            10
  STAGE IV                             7                            11
  STAGE IVA                            5                             4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 10(5Q11.2) MUTATED    2  9 36  4
  DEL PEAK 10(5Q11.2) WILD-TYPE  7 20 73 10
D35V4, multiclass
    clus
vv   DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  T1                           2                             7
  T2                           9                            20
  T3                          36                            73
  T4                           4                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 10(5Q11.2) MUTATED   25 15 11
  DEL PEAK 10(5Q11.2) WILD-TYPE 58 30 21
D35V5, multiclass
    clus
vv   DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  N0                          25                            58
  N1                          15                            30
  N2                          11                            21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 10(5Q11.2) MUTATED   35  9   1  5
  DEL PEAK 10(5Q11.2) WILD-TYPE 88 13   1  8
D35V6, multiclass
     clus
vv    DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  M0                           35                            88
  M1                            9                            13
  M1A                           1                             1
  MX                            5                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q11.2) MUTATED   27 24
  DEL PEAK 10(5Q11.2) WILD-TYPE 47 64
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q11.2) MUTATED     27   24
  DEL PEAK 10(5Q11.2) WILD-TYPE   47   64
        clus
vv       DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  FEMALE                          27                            47
  MALE                            24                            64
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q11.2) MUTATED   48  2
  DEL PEAK 10(5Q11.2) WILD-TYPE 95 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q11.2) MUTATED     48    2
  DEL PEAK 10(5Q11.2) WILD-TYPE   95   11
                                clus
vv                               DEL PEAK 10(5Q11.2) MUTATED
  RECTAL ADENOCARCINOMA                                   48
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 10(5Q11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     95
  RECTAL MUCINOUS ADENOCARCINOMA                            11
[1] 2 2
[1] FALSE
D35V9, binary
                               cls
clus                              0   1
  DEL PEAK 10(5Q11.2) MUTATED     5  46
  DEL PEAK 10(5Q11.2) WILD-TYPE   1 110
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q11.2) MUTATED      5   46
  DEL PEAK 10(5Q11.2) WILD-TYPE    1  110
     clus
vv    DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  NO                            5                             1
  YES                          46                           110
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 10(5Q11.2) MUTATED   36  1  3  1
  DEL PEAK 10(5Q11.2) WILD-TYPE 85  1  9  2
D35V10, multiclass
    clus
vv   DEL PEAK 10(5Q11.2) MUTATED DEL PEAK 10(5Q11.2) WILD-TYPE
  R0                          36                            85
  R1                           1                             1
  R2                           3                             9
  RX                           1                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(5Q11.2) MUTATED       0                         3    26
  DEL PEAK 10(5Q11.2) WILD-TYPE     1                         0    55
D35V12, multiclass
                           clus
vv                          DEL PEAK 10(5Q11.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              26
                           clus
vv                          DEL PEAK 10(5Q11.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK 11(5Q22.2) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(5Q22.2) MUTATED   39 11
  DEL PEAK 11(5Q22.2) WILD-TYPE 89 11
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           50                           100 
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           11                            11 
$`DEL PEAK 11(5Q22.2) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 
       24.13        17.23        43.04        37.74        10.39        15.39 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       10.39        32.02        19.99        29.98         1.02        32.98 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 
       19.99        17.03         1.02        48.03        28.04        36.03 
TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       17.03         6.02        23.01        12.00        70.03        64.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
        1.94        38.96        41.00         1.81        10.19         6.05 
TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        7.99        12.99        13.97        15.02        36.00         7.10 
TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 
       13.05       126.44        41.36        57.24        51.48        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6881 TCGA-F5-6464 TCGA-F5-6702 
       19.96        18.28        16.34        16.41         9.96        14.86 
TCGA-F5-6864 TCGA-G5-6233 
        0.46        18.28 

$`DEL PEAK 11(5Q22.2) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       17.95        13.55        19.10        12.72        14.50         8.45 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       20.02        36.03        12.00         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        7.99         0.99         0.99         0.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 
       13.02        35.01        14.01        32.02        19.99        14.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 
        1.02         0.99        20.98        13.94        25.97        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 
       15.95        36.03         9.07         1.02        31.00        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       51.98        49.97        61.97        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 
        0.69         0.72         4.60         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03        10.98        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DE 
       12.00        30.05        12.95        10.06         5.29       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 
       24.13        32.61         0.49         2.40        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         8.45        37.51        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        55.76        47.08        26.43 

  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                         0.46                          0.39 
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                       126.44                        129.27 
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                       17.755                        12.835 
[1] "0.5 - 126.4 (17.8)" "0.4 - 129.3 (12.8)"
[1] "hr=" "1.3"
D36V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 11(5Q22.2) MUTATED         8        3        15         0         1
  DEL PEAK 11(5Q22.2) WILD-TYPE      22        5        23         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 11(5Q22.2) MUTATED           1          2         11          6
  DEL PEAK 11(5Q22.2) WILD-TYPE         4          7         12          8
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 11(5Q22.2) MUTATED          5         5
  DEL PEAK 11(5Q22.2) WILD-TYPE       13         4
D36V3, multiclass
            clus
vv           DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  STAGE I                              8                            22
  STAGE II                             3                             5
  STAGE IIA                           15                            23
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           2                             7
  STAGE IIIB                          11                            12
  STAGE IIIC                           6                             8
  STAGE IV                             5                            13
  STAGE IVA                            5                             4
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 11(5Q22.2) MUTATED    1 10 41  5
  DEL PEAK 11(5Q22.2) WILD-TYPE  8 19 68  9
D36V4, multiclass
    clus
vv   DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  T1                           1                             8
  T2                          10                            19
  T3                          41                            68
  T4                           5                             9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 11(5Q22.2) MUTATED   27 19 11
  DEL PEAK 11(5Q22.2) WILD-TYPE 56 26 21
D36V5, multiclass
    clus
vv   DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  N0                          27                            56
  N1                          19                            26
  N2                          11                            21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 11(5Q22.2) MUTATED   43  7   1  5
  DEL PEAK 11(5Q22.2) WILD-TYPE 80 15   1  8
D36V6, multiclass
     clus
vv    DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  M0                           43                            80
  M1                            7                            15
  M1A                           1                             1
  MX                            5                             8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q22.2) MUTATED   29 28
  DEL PEAK 11(5Q22.2) WILD-TYPE 45 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED     29   28
  DEL PEAK 11(5Q22.2) WILD-TYPE   45   60
        clus
vv       DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  FEMALE                          29                            45
  MALE                            28                            60
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q22.2) MUTATED   54  2
  DEL PEAK 11(5Q22.2) WILD-TYPE 89 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED     54    2
  DEL PEAK 11(5Q22.2) WILD-TYPE   89   11
                                clus
vv                               DEL PEAK 11(5Q22.2) MUTATED
  RECTAL ADENOCARCINOMA                                   54
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 11(5Q22.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     89
  RECTAL MUCINOUS ADENOCARCINOMA                            11
[1] 2 2
[1] FALSE
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK 11(5Q22.2) MUTATED     5  52
  DEL PEAK 11(5Q22.2) WILD-TYPE   1 104
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED      5   52
  DEL PEAK 11(5Q22.2) WILD-TYPE    1  104
     clus
vv    DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  NO                            5                             1
  YES                          52                           104
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 11(5Q22.2) MUTATED   42  1  4  1
  DEL PEAK 11(5Q22.2) WILD-TYPE 79  1  8  2
D36V10, multiclass
    clus
vv   DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  R0                          42                            79
  R1                           1                             1
  R2                           4                             8
  RX                           1                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(5Q22.2) MUTATED       0                         3    27
  DEL PEAK 11(5Q22.2) WILD-TYPE     1                         0    54
D36V12, multiclass
                           clus
vv                          DEL PEAK 11(5Q22.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              27
                           clus
vv                          DEL PEAK 11(5Q22.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK 12(6P25.3) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6P25.3) MUTATED    15   3
  DEL PEAK 12(6P25.3) WILD-TYPE 113  19
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           18                           132 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                            3                            19 
$`DEL PEAK 12(6P25.3) MUTATED`
TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3584 
       17.23        13.55        19.10        12.72        14.50        24.00 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A011 TCGA-BM-6198 
       34.03        50.04        36.03        13.94        37.02        10.19 
TCGA-DC-4745 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6511 TCGA-EI-6883 
       10.98        13.05         5.29        24.13        15.85        11.51 

$`DEL PEAK 12(6P25.3) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       24.13        17.95        43.04        37.74        10.39         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       15.39        20.02        10.39        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07         1.02         2.01         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        14.04         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       20.98         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       41.00        38.04         0.49         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        13.97        60.03         7.99        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       12.99        12.00        13.97        15.02        36.00         7.10 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       30.05        12.95        10.06       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        51.48        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41         8.61        10.78        13.64        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        37.51        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                         5.29                          0.39 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                        50.04                        129.27 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                       15.175                        14.025 
[1] "5.3 - 50.0 (15.2)"  "0.4 - 129.3 (14.0)"
[1] "hr=" "1.3"
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 12(6P25.3) MUTATED         2        1        11         0         1
  DEL PEAK 12(6P25.3) WILD-TYPE      28        7        27         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 12(6P25.3) MUTATED           1          0          3          2
  DEL PEAK 12(6P25.3) WILD-TYPE         4          9         20         12
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 12(6P25.3) MUTATED          2         1
  DEL PEAK 12(6P25.3) WILD-TYPE       16         8
D37V3, multiclass
            clus
vv           DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  STAGE I                              2                            28
  STAGE II                             1                             7
  STAGE IIA                           11                            27
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           0                             9
  STAGE IIIB                           3                            20
  STAGE IIIC                           2                            12
  STAGE IV                             2                            16
  STAGE IVA                            1                             8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 12(6P25.3) MUTATED    0  2 21  1
  DEL PEAK 12(6P25.3) WILD-TYPE  9 27 88 13
D37V4, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  T1                           0                             9
  T2                           2                            27
  T3                          21                            88
  T4                           1                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 12(6P25.3) MUTATED   15  4  5
  DEL PEAK 12(6P25.3) WILD-TYPE 68 41 27
D37V5, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  N0                          15                            68
  N1                           4                            41
  N2                           5                            27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 12(6P25.3) MUTATED    18   2   0   3
  DEL PEAK 12(6P25.3) WILD-TYPE 105  20   2  10
D37V6, multiclass
     clus
vv    DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  M0                           18                           105
  M1                            2                            20
  M1A                           0                             2
  MX                            3                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P25.3) MUTATED   10 14
  DEL PEAK 12(6P25.3) WILD-TYPE 64 74
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     10   14
  DEL PEAK 12(6P25.3) WILD-TYPE   64   74
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  FEMALE                          10                            64
  MALE                            14                            74
[1] 2 2
[1] FALSE
D37V8, binary
                               cls
clus                              0   1
  DEL PEAK 12(6P25.3) MUTATED    18   3
  DEL PEAK 12(6P25.3) WILD-TYPE 125  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     18    3
  DEL PEAK 12(6P25.3) WILD-TYPE  125   10
                                clus
vv                               DEL PEAK 12(6P25.3) MUTATED
  RECTAL ADENOCARCINOMA                                   18
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK 12(6P25.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    125
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 2 2
[1] FALSE
D37V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(6P25.3) MUTATED     2  22
  DEL PEAK 12(6P25.3) WILD-TYPE   4 134
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED      2   22
  DEL PEAK 12(6P25.3) WILD-TYPE    4  134
     clus
vv    DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  NO                            2                             4
  YES                          22                           134
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 12(6P25.3) MUTATED    18   0   2   1
  DEL PEAK 12(6P25.3) WILD-TYPE 103   2  10   2
D37V10, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  R0                          18                           103
  R1                           0                             2
  R2                           2                            10
  RX                           1                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(6P25.3) MUTATED       1                         0    12
  DEL PEAK 12(6P25.3) WILD-TYPE     0                         3    69
D37V12, multiclass
                           clus
vv                          DEL PEAK 12(6P25.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              12
                           clus
vv                          DEL PEAK 12(6P25.3) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D38V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(6Q26) MUTATED    22   4
  DEL PEAK 13(6Q26) WILD-TYPE 106  18
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         26                         124 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                          4                          18 
$`DEL PEAK 13(6Q26) MUTATED`
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        12.72        37.74 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       12.00        32.02        24.00        46.03        34.03         2.01 
TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A011 
        6.05        19.99        14.04         1.02        13.94        37.02 
TCGA-AH-6544 TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6863 
        0.49         0.72         9.37        13.05         5.29         0.76 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`DEL PEAK 13(6Q26) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       24.13        17.95        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       20.02        10.39        36.03         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
        2.01         1.02        50.04        12.03         0.99        15.95 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       19.99         7.99         0.99        29.98         1.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       19.99        28.04        36.03        17.03         0.99        20.98 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       38.04         1.45         0.69         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.05         6.97         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       10.06       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       14.86         0.39         1.02         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.46        55.76        47.08 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       0.49                        0.39 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                      46.03                      129.27 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                      13.99                       14.68 
[1] "0.5 - 46.0 (14.0)"  "0.4 - 129.3 (14.7)"
[1] "hr=" "1.4"
D38V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 13(6Q26) MUTATED         5        2         9         0         1
  DEL PEAK 13(6Q26) WILD-TYPE      25        6        29         2         1
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 13(6Q26) MUTATED           0          1          2          5
  DEL PEAK 13(6Q26) WILD-TYPE         5          8         21          9
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK 13(6Q26) MUTATED          3         0
  DEL PEAK 13(6Q26) WILD-TYPE       15         9
D38V3, multiclass
            clus
vv           DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  STAGE I                            5                          25
  STAGE II                           2                           6
  STAGE IIA                          9                          29
  STAGE IIB                          0                           2
  STAGE IIC                          1                           1
  STAGE III                          0                           5
  STAGE IIIA                         1                           8
  STAGE IIIB                         2                          21
  STAGE IIIC                         5                           9
  STAGE IV                           3                          15
  STAGE IVA                          0                           9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          T1 T2 T3 T4
  DEL PEAK 13(6Q26) MUTATED    3  3 21  3
  DEL PEAK 13(6Q26) WILD-TYPE  6 26 88 11
D38V4, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  T1                         3                           6
  T2                         3                          26
  T3                        21                          88
  T4                         3                          11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                          N0 N1 N2
  DEL PEAK 13(6Q26) MUTATED   16  4  9
  DEL PEAK 13(6Q26) WILD-TYPE 67 41 23
D38V5, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  N0                        16                          67
  N1                         4                          41
  N2                         9                          23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1 M1A  MX
  DEL PEAK 13(6Q26) MUTATED    22   4   0   4
  DEL PEAK 13(6Q26) WILD-TYPE 101  18   2   9
D38V6, multiclass
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  M0                         22                         101
  M1                          4                          18
  M1A                         0                           2
  MX                          4                           9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   10 20
  DEL PEAK 13(6Q26) WILD-TYPE 64 68
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     10   20
  DEL PEAK 13(6Q26) WILD-TYPE   64   68
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  FEMALE                        10                          64
  MALE                          20                          68
[1] 2 2
[1] FALSE
D38V8, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    22   6
  DEL PEAK 13(6Q26) WILD-TYPE 121   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     22    6
  DEL PEAK 13(6Q26) WILD-TYPE  121    7
                                clus
vv                               DEL PEAK 13(6Q26) MUTATED
  RECTAL ADENOCARCINOMA                                 22
  RECTAL MUCINOUS ADENOCARCINOMA                         6
                                clus
vv                               DEL PEAK 13(6Q26) WILD-TYPE
  RECTAL ADENOCARCINOMA                                  121
  RECTAL MUCINOUS ADENOCARCINOMA                           7
[1] 2 2
[1] FALSE
D38V9, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED     2  28
  DEL PEAK 13(6Q26) WILD-TYPE   4 128
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED      2   28
  DEL PEAK 13(6Q26) WILD-TYPE    4  128
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                          2                           4
  YES                        28                         128
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK 13(6Q26) MUTATED    21   0   3   1
  DEL PEAK 13(6Q26) WILD-TYPE 100   2   9   2
D38V10, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  R0                        21                         100
  R1                         0                           2
  R2                         3                           9
  RX                         1                           2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q26) MUTATED       1                         0    13
  DEL PEAK 13(6Q26) WILD-TYPE     0                         3    68
D38V12, multiclass
                           clus
vv                          DEL PEAK 13(6Q26) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                            13
                           clus
vv                          DEL PEAK 13(6Q26) WILD-TYPE
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK 14(7Q31.1) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(7Q31.1) MUTATED     3   0
  DEL PEAK 14(7Q31.1) WILD-TYPE 125  22
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            3                           147 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            0                            22 
$`DEL PEAK 14(7Q31.1) MUTATED`
TCGA-AG-3600 TCGA-AG-A008 TCGA-DC-6682 
        6.05        13.94        13.05 

$`DEL PEAK 14(7Q31.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       20.02        10.39        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99         7.99         0.99        29.98         1.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       32.98         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.03        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        20.98         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.94        38.96        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05         6.05         6.97         9.37         4.73        13.97 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       60.03         7.99        10.98        11.01        15.02        12.99 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        15.02        36.00         7.10        30.05 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      129.27        24.13        51.48        32.61         0.49         2.40 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       17.69        16.34        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.69         0.53         1.12         0.76         0.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                         6.05                          0.39 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                        13.94                        129.27 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                        13.05                         14.86 
[1] "6.0 - 13.9 (13.1)"  "0.4 - 129.3 (14.9)"
[1] "hr="     "9200000"
D39V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 14(7Q31.1) MUTATED         1        0         2         0         0
  DEL PEAK 14(7Q31.1) WILD-TYPE      29        8        36         2         2
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 14(7Q31.1) MUTATED           0          0          0          1
  DEL PEAK 14(7Q31.1) WILD-TYPE         5          9         23         13
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 14(7Q31.1) MUTATED          0         0
  DEL PEAK 14(7Q31.1) WILD-TYPE       18         9
D39V3, multiclass
            clus
vv           DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  STAGE I                              1                            29
  STAGE II                             0                             8
  STAGE IIA                            2                            36
  STAGE IIB                            0                             2
  STAGE IIC                            0                             2
  STAGE III                            0                             5
  STAGE IIIA                           0                             9
  STAGE IIIB                           0                            23
  STAGE IIIC                           1                            13
  STAGE IV                             0                            18
  STAGE IVA                            0                             9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(7Q31.1) MUTATED     0   1   3   0
  DEL PEAK 14(7Q31.1) WILD-TYPE   9  28 106  14
D39V4, multiclass
    clus
vv   DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  T1                           0                             9
  T2                           1                            28
  T3                           3                           106
  T4                           0                            14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 14(7Q31.1) MUTATED    3  0  1
  DEL PEAK 14(7Q31.1) WILD-TYPE 80 45 31
D39V5, multiclass
    clus
vv   DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  N0                           3                            80
  N1                           0                            45
  N2                           1                            31
[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"
                               vv
clus                             M0  M1 M1A  MX
  DEL PEAK 14(7Q31.1) MUTATED     4   0   0   0
  DEL PEAK 14(7Q31.1) WILD-TYPE 119  22   2  13
D39V6, multiclass
     clus
vv    DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  M0                            4                           119
  M1                            0                            22
  M1A                           0                             2
  MX                            0                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(7Q31.1) MUTATED    2  2
  DEL PEAK 14(7Q31.1) WILD-TYPE 72 86
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      2    2
  DEL PEAK 14(7Q31.1) WILD-TYPE   72   86
        clus
vv       DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  FEMALE                           2                            72
  MALE                             2                            86
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(7Q31.1) MUTATED     3   1
  DEL PEAK 14(7Q31.1) WILD-TYPE 140  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      3    1
  DEL PEAK 14(7Q31.1) WILD-TYPE  140   12
                                clus
vv                               DEL PEAK 14(7Q31.1) MUTATED
  RECTAL ADENOCARCINOMA                                    3
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 14(7Q31.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    140
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
D39V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(7Q31.1) MUTATED     0   4
  DEL PEAK 14(7Q31.1) WILD-TYPE   6 152
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      0    4
  DEL PEAK 14(7Q31.1) WILD-TYPE    6  152
     clus
vv    DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  NO                            0                             6
  YES                           4                           152
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 14(7Q31.1) MUTATED     4   0   0   0
  DEL PEAK 14(7Q31.1) WILD-TYPE 117   2  12   3
D39V10, multiclass
    clus
vv   DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  R0                           4                           117
  R1                           0                             2
  R2                           0                            12
  RX                           0                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(7Q31.1) MUTATED       0                         0     1
  DEL PEAK 14(7Q31.1) WILD-TYPE     1                         3    80
D39V12, multiclass
[1] "Remove cluster labels:"      "DEL PEAK 14(7Q31.1) MUTATED"
clus
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            1                            84 
                   TCGA-AF-2687                    TCGA-AF-2689 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-2690                    TCGA-AF-2691 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-2692                    TCGA-AF-2693 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-3400                    TCGA-AF-3911 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-3913                    TCGA-AF-4110 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-5654                    TCGA-AF-6136 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-6655                    TCGA-AF-6672 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6544                    TCGA-AH-6547 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6643                    TCGA-AH-6644 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6897                    TCGA-AH-6903 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-BM-6198                    TCGA-CI-6619 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6620                    TCGA-CI-6621 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6622                    TCGA-CI-6623 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6624                    TCGA-CL-5917 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CL-5918                    TCGA-DC-4745 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-4749                    TCGA-DC-5337 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-5869                    TCGA-DC-6154 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6155                    TCGA-DC-6156 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6157                    TCGA-DC-6158 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6160                    TCGA-DC-6681 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6683                    TCGA-DT-5265 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A0XA                    TCGA-DY-A1DC 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DD                    TCGA-DY-A1DE 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DF                    TCGA-DY-A1DG 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1H8                    TCGA-EF-5830 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EF-5831                    TCGA-EI-6506 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6507                    TCGA-EI-6508 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6509                    TCGA-EI-6510 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6511                    TCGA-EI-6512 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6513                    TCGA-EI-6514 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6881                    TCGA-EI-6882 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6883                    TCGA-EI-6884 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6885                    TCGA-EI-6917 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-7002                    TCGA-EI-7004 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6464                    TCGA-F5-6465 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6571                    TCGA-F5-6702 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6810                    TCGA-F5-6811 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6812                    TCGA-F5-6813 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6814                    TCGA-F5-6861 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6863                    TCGA-F5-6864 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-G5-6233                    TCGA-G5-6235 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-G5-6572                    TCGA-G5-6641 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 

Clustering(40) Variable = DEL PEAK 15(8P23.2) MUTATION ANALYSIS
D40V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(8P23.2) MUTATED   76 15
  DEL PEAK 15(8P23.2) WILD-TYPE 52  7
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           91                            59 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           15                             7 
$`DEL PEAK 15(8P23.2) MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3578 
       37.74        10.39        15.39        20.02        10.39        32.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        1.02        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        19.99         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       32.98         0.99         1.02        17.03        35.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 
       17.03        20.98        25.97        23.01        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        1.02        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
       51.98         1.94        38.96        41.00         1.45         0.72 
TCGA-BM-6198 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
       10.19         4.73        13.97        60.03        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       12.99        13.97        15.02        36.00         7.10        13.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       10.06         5.29       126.44        41.36        57.24       129.27 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6884 
        0.49         2.40        15.85        16.34        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 
       13.64        11.97         8.45         9.96        31.30        14.86 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 
        0.39         0.66         0.69         0.76         0.46        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 15(8P23.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       24.13        14.50         8.45        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 
        7.07         2.01        50.04        12.03        15.95        19.99 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        1.02         0.99        19.99        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A015 
       48.03         0.99        13.94         6.02        37.02        36.03 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 
       49.97        61.97        38.04         0.49         0.69         4.60 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 
        1.81         6.05         6.05         6.97         9.37         7.99 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG 
       15.02        12.00        30.05        12.95        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 
       17.69        16.31        16.41         8.61        17.46        37.51 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6572 
        1.02         0.53         1.12        55.76        47.08 

  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                         0.39                          0.49 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                       129.27                         61.97 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                        13.97                         15.02 
[1] "0.4 - 129.3 (14.0)" "0.5 - 62.0 (15.0)" 
[1] "hr=" "1.3"
D40V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 15(8P23.2) MUTATED        16        4        24         1         2
  DEL PEAK 15(8P23.2) WILD-TYPE      14        4        14         1         0
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 15(8P23.2) MUTATED           4          5         15          8
  DEL PEAK 15(8P23.2) WILD-TYPE         1          4          8          6
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 15(8P23.2) MUTATED         15         3
  DEL PEAK 15(8P23.2) WILD-TYPE        3         6
D40V3, multiclass
            clus
vv           DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  STAGE I                             16                            14
  STAGE II                             4                             4
  STAGE IIA                           24                            14
  STAGE IIB                            1                             1
  STAGE IIC                            2                             0
  STAGE III                            4                             1
  STAGE IIIA                           5                             4
  STAGE IIIB                          15                             8
  STAGE IIIC                           8                             6
  STAGE IV                            15                             3
  STAGE IVA                            3                             6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            T1 T2 T3 T4
  DEL PEAK 15(8P23.2) MUTATED    3 18 67 11
  DEL PEAK 15(8P23.2) WILD-TYPE  6 11 42  3
D40V4, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  T1                           3                             6
  T2                          18                            11
  T3                          67                            42
  T4                          11                             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 15(8P23.2) MUTATED   48 29 21
  DEL PEAK 15(8P23.2) WILD-TYPE 35 16 11
D40V5, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  N0                          48                            35
  N1                          29                            16
  N2                          21                            11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 M1A MX
  DEL PEAK 15(8P23.2) MUTATED   73 15   1  9
  DEL PEAK 15(8P23.2) WILD-TYPE 50  7   1  4
D40V6, multiclass
     clus
vv    DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  M0                           73                            50
  M1                           15                             7
  M1A                           1                             1
  MX                            9                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED   45 54
  DEL PEAK 15(8P23.2) WILD-TYPE 29 34
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     45   54
  DEL PEAK 15(8P23.2) WILD-TYPE   29   34
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  FEMALE                          45                            29
  MALE                            54                            34
[1] 2 2
[1] FALSE
D40V8, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED   88  7
  DEL PEAK 15(8P23.2) WILD-TYPE 55  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     88    7
  DEL PEAK 15(8P23.2) WILD-TYPE   55    6
                                clus
vv                               DEL PEAK 15(8P23.2) MUTATED
  RECTAL ADENOCARCINOMA                                   88
  RECTAL MUCINOUS ADENOCARCINOMA                           7
                                clus
vv                               DEL PEAK 15(8P23.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     55
  RECTAL MUCINOUS ADENOCARCINOMA                             6
[1] 2 2
[1] FALSE
D40V9, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED    5 94
  DEL PEAK 15(8P23.2) WILD-TYPE  1 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED      5   94
  DEL PEAK 15(8P23.2) WILD-TYPE    1   62
     clus
vv    DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  NO                            5                             1
  YES                          94                            62
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 15(8P23.2) MUTATED   72  1 10  2
  DEL PEAK 15(8P23.2) WILD-TYPE 49  1  2  1
D40V10, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  R0                          72                            49
  R1                           1                             1
  R2                          10                             2
  RX                           2                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P23.2) MUTATED       1                         3    46
  DEL PEAK 15(8P23.2) WILD-TYPE     0                         0    35
D40V12, multiclass
                           clus
vv                          DEL PEAK 15(8P23.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              46
                           clus
vv                          DEL PEAK 15(8P23.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             0
  WHITE                                                35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 16(8P11.21) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(8P11.21) MUTATED    16   4
  DEL PEAK 16(8P11.21) WILD-TYPE 112  18
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            20                            130 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                             4                             18 
$`DEL PEAK 16(8P11.21) MUTATED`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3726 
       17.95        13.55        12.72        32.02         1.02         7.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A011 TCGA-AG-A01L 
       29.98         0.99        17.03        17.03        37.02        12.00 
TCGA-AG-A01W TCGA-AG-A02G TCGA-BM-6198 TCGA-DC-5869 TCGA-DC-6156 TCGA-DY-A1DG 
       70.03        38.96        10.19        12.99        15.02        51.48 
TCGA-EI-7002 TCGA-F5-6810 
       11.97         0.39 

$`DEL PEAK 16(8P11.21) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       14.50         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02         7.07         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99        19.99         0.99         1.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       35.01        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       28.04        36.03        14.04         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        9.07         1.02        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        61.97        41.00        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        1.45         0.69         0.72         4.60         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 
        7.99        10.98        11.01        15.02        12.00        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       36.00         7.10        30.05        12.95        13.05        10.06 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.29       126.44        41.36        57.24       129.27        24.13 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.41         8.61        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        8.45         9.96        37.51        31.30        14.86         1.02 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.66         0.69         0.53         1.12         0.76         0.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        47.08        26.43 

  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                          0.39                           0.46 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                         70.03                         129.27 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                        14.285                         14.270 
[1] "0.4 - 70.0 (14.3)"  "0.5 - 129.3 (14.3)"
[1] "hr=" "1.4"
D41V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 16(8P11.21) MUTATED         3        1         8         0         0
  DEL PEAK 16(8P11.21) WILD-TYPE      27        7        30         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 16(8P11.21) MUTATED           1          0          4          0
  DEL PEAK 16(8P11.21) WILD-TYPE         4          9         19         14
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 16(8P11.21) MUTATED          5         2
  DEL PEAK 16(8P11.21) WILD-TYPE       13         7
D41V3, multiclass
            clus
vv           DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  STAGE I                               3                             27
  STAGE II                              1                              7
  STAGE IIA                             8                             30
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            4                             19
  STAGE IIIC                            0                             14
  STAGE IV                              5                             13
  STAGE IVA                             2                              7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 16(8P11.21) MUTATED    1  3 19  1
  DEL PEAK 16(8P11.21) WILD-TYPE  8 26 90 13
D41V4, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  T1                            1                              8
  T2                            3                             26
  T3                           19                             90
  T4                            1                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 16(8P11.21) MUTATED   12  8  4
  DEL PEAK 16(8P11.21) WILD-TYPE 71 37 28
D41V5, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  N0                           12                             71
  N1                            8                             37
  N2                            4                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 16(8P11.21) MUTATED    15   6   1   1
  DEL PEAK 16(8P11.21) WILD-TYPE 108  16   1  12
D41V6, multiclass
     clus
vv    DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  M0                            15                            108
  M1                             6                             16
  M1A                            1                              1
  MX                             1                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                                cls
clus                              0  1
  DEL PEAK 16(8P11.21) MUTATED    9 15
  DEL PEAK 16(8P11.21) WILD-TYPE 65 73
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED      9   15
  DEL PEAK 16(8P11.21) WILD-TYPE   65   73
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  FEMALE                            9                             65
  MALE                             15                             73
[1] 2 2
[1] FALSE
D41V8, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED    20   2
  DEL PEAK 16(8P11.21) WILD-TYPE 123  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     20    2
  DEL PEAK 16(8P11.21) WILD-TYPE  123   11
                                clus
vv                               DEL PEAK 16(8P11.21) MUTATED
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 16(8P11.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     123
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
D41V9, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED     2  22
  DEL PEAK 16(8P11.21) WILD-TYPE   4 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED      2   22
  DEL PEAK 16(8P11.21) WILD-TYPE    4  134
     clus
vv    DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  NO                             2                              4
  YES                           22                            134
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 16(8P11.21) MUTATED    18   0   3   0
  DEL PEAK 16(8P11.21) WILD-TYPE 103   2   9   3
D41V10, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  R0                           18                            103
  R1                            0                              2
  R2                            3                              9
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(8P11.21) MUTATED       0                         1     9
  DEL PEAK 16(8P11.21) WILD-TYPE     1                         2    72
D41V12, multiclass
                           clus
vv                          DEL PEAK 16(8P11.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                9
                           clus
vv                          DEL PEAK 16(8P11.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 17(10Q21.1) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(10Q21.1) MUTATED   32  3
  DEL PEAK 17(10Q21.1) WILD-TYPE 96 19
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            35                            115 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                             3                             19 
$`DEL PEAK 17(10Q21.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3587 
       24.13        13.55        12.72        10.39        32.02        46.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
       34.03         6.05        29.98         1.02        36.95         1.02 
TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       19.99        13.94         6.02        25.97        23.01        12.00 
TCGA-AG-A026 TCGA-AG-A02X TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-6155 
        1.94        41.00         6.97         4.73        13.97        13.97 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EI-6509 
       36.00         7.10        13.05        10.06       129.27        17.00 
TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
       16.31        16.41        14.86         0.46        26.43 

$`DEL PEAK 17(10Q21.1) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 
       17.95        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 
       14.50         8.45        15.39        20.02        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99        17.03        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        32.02        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       17.03         0.99        20.98        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        31.00        70.03        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97        38.96        61.97        38.04         0.49 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72         4.60         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.05         6.05         9.37        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
       11.01        15.02        12.99        12.00        15.02        30.05 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       12.95         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 
       20.91        18.28        15.85        17.69        16.34         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        9.96        37.51        31.30         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.69         0.53         1.12         0.76        18.28        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                          0.46                           0.39 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                         13.97                          14.50 
[1] "0.5 - 129.3 (14.0)" "0.4 - 126.4 (14.5)"
[1] "hr=" "1.6"
D42V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 17(10Q21.1) MUTATED         8        1        12         1         0
  DEL PEAK 17(10Q21.1) WILD-TYPE      22        7        26         1         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 17(10Q21.1) MUTATED           0          4          5          4
  DEL PEAK 17(10Q21.1) WILD-TYPE         5          5         18         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 17(10Q21.1) MUTATED          1         1
  DEL PEAK 17(10Q21.1) WILD-TYPE       17         8
D42V3, multiclass
            clus
vv           DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  STAGE I                               8                             22
  STAGE II                              1                              7
  STAGE IIA                            12                             26
  STAGE IIB                             1                              1
  STAGE IIC                             0                              2
  STAGE III                             0                              5
  STAGE IIIA                            4                              5
  STAGE IIIB                            5                             18
  STAGE IIIC                            4                             10
  STAGE IV                              1                             17
  STAGE IVA                             1                              8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 17(10Q21.1) MUTATED    1  9 24  3
  DEL PEAK 17(10Q21.1) WILD-TYPE  8 20 85 11
D42V4, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  T1                            1                              8
  T2                            9                             20
  T3                           24                             85
  T4                            3                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 17(10Q21.1) MUTATED   22 10  5
  DEL PEAK 17(10Q21.1) WILD-TYPE 61 35 27
D42V5, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  N0                           22                             61
  N1                           10                             35
  N2                            5                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 17(10Q21.1) MUTATED   34  1   0  2
  DEL PEAK 17(10Q21.1) WILD-TYPE 89 21   2 11
D42V6, multiclass
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  M0                            34                             89
  M1                             1                             21
  M1A                            0                              2
  MX                             2                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q21.1) MUTATED   15 22
  DEL PEAK 17(10Q21.1) WILD-TYPE 59 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     15   22
  DEL PEAK 17(10Q21.1) WILD-TYPE   59   66
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  FEMALE                           15                             59
  MALE                             22                             66
[1] 2 2
[1] FALSE
D42V8, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED    31   5
  DEL PEAK 17(10Q21.1) WILD-TYPE 112   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     31    5
  DEL PEAK 17(10Q21.1) WILD-TYPE  112    8
                                clus
vv                               DEL PEAK 17(10Q21.1) MUTATED
  RECTAL ADENOCARCINOMA                                    31
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 17(10Q21.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     112
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
D42V9, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED     3  34
  DEL PEAK 17(10Q21.1) WILD-TYPE   3 122
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED      3   34
  DEL PEAK 17(10Q21.1) WILD-TYPE    3  122
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  NO                             3                              3
  YES                           34                            122
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 17(10Q21.1) MUTATED   31  1  0  0
  DEL PEAK 17(10Q21.1) WILD-TYPE 90  1 12  3
D42V10, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  R0                           31                             90
  R1                            1                              1
  R2                            0                             12
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D42V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(10Q21.1) MUTATED       0                         1    17
  DEL PEAK 17(10Q21.1) WILD-TYPE     1                         2    64
D42V12, multiclass
                           clus
vv                          DEL PEAK 17(10Q21.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               17
                           clus
vv                          DEL PEAK 17(10Q21.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 18(10Q25.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(10Q25.2) MUTATED   37  4
  DEL PEAK 18(10Q25.2) WILD-TYPE 91 18
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            41                            109 
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                             4                             18 
$`DEL PEAK 18(10Q25.2) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AG-3578 
       24.13        17.95        13.55        12.72        10.39        32.02 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 
       34.03         6.05        29.98        36.95        17.03         1.02 
TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L 
       19.99        36.03        13.94        25.97        37.02        12.00 
TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6624 
       70.03        10.98        41.00         4.60        10.19         4.73 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
       13.97        36.00        30.05        13.05        10.06       129.27 
TCGA-DY-A1DF TCGA-EF-5831 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 
       24.13         2.40        17.00        16.31        16.41        11.97 
TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       14.86         0.66         0.46        47.08        26.43 

$`DEL PEAK 18(10Q25.2) WILD-TYPE`
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 
       17.23        43.04        19.10        37.74        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
        8.45        15.39        20.02        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07         1.02         2.01        24.00         1.02        46.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99         1.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        0.99        19.99         1.02        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       48.03        32.02        28.04        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 
        0.99        20.98         6.02        23.01        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 
        9.07         1.02        31.00        64.01        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        61.97        38.04         0.49         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.69         0.72         1.81         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       15.02        12.99        12.00        15.02         7.10        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49        20.55        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.34         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       17.46         8.45         9.96        37.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        1.02         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 
       55.76 

  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                          0.46                           0.39 
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                         16.41                          13.97 
[1] "0.5 - 129.3 (16.4)" "0.4 - 126.4 (14.0)"
[1] "hr=" "1.8"
D43V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 18(10Q25.2) MUTATED         8        1        16         0         0
  DEL PEAK 18(10Q25.2) WILD-TYPE      22        7        22         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 18(10Q25.2) MUTATED           1          3          6          6
  DEL PEAK 18(10Q25.2) WILD-TYPE         4          6         17          8
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 18(10Q25.2) MUTATED          4         1
  DEL PEAK 18(10Q25.2) WILD-TYPE       14         8
D43V3, multiclass
            clus
vv           DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  STAGE I                               8                             22
  STAGE II                              1                              7
  STAGE IIA                            16                             22
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            3                              6
  STAGE IIIB                            6                             17
  STAGE IIIC                            6                              8
  STAGE IV                              4                             14
  STAGE IVA                             1                              8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 18(10Q25.2) MUTATED    1  9 35  1
  DEL PEAK 18(10Q25.2) WILD-TYPE  8 20 74 13
D43V4, multiclass
    clus
vv   DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  T1                            1                              8
  T2                            9                             20
  T3                           35                             74
  T4                            1                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 18(10Q25.2) MUTATED   25 11 10
  DEL PEAK 18(10Q25.2) WILD-TYPE 58 34 22
D43V5, multiclass
    clus
vv   DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  N0                           25                             58
  N1                           11                             34
  N2                           10                             22
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 18(10Q25.2) MUTATED   39  4   0  2
  DEL PEAK 18(10Q25.2) WILD-TYPE 84 18   2 11
D43V6, multiclass
     clus
vv    DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  M0                            39                             84
  M1                             4                             18
  M1A                            0                              2
  MX                             2                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(10Q25.2) MUTATED   22 25
  DEL PEAK 18(10Q25.2) WILD-TYPE 52 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED     22   25
  DEL PEAK 18(10Q25.2) WILD-TYPE   52   63
        clus
vv       DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  FEMALE                           22                             52
  MALE                             25                             63
[1] 2 2
[1] FALSE
D43V8, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q25.2) MUTATED    38   7
  DEL PEAK 18(10Q25.2) WILD-TYPE 105   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED     38    7
  DEL PEAK 18(10Q25.2) WILD-TYPE  105    6
                                clus
vv                               DEL PEAK 18(10Q25.2) MUTATED
  RECTAL ADENOCARCINOMA                                    38
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK 18(10Q25.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     105
  RECTAL MUCINOUS ADENOCARCINOMA                              6
[1] 2 2
[1] FALSE
D43V9, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q25.2) MUTATED     4  43
  DEL PEAK 18(10Q25.2) WILD-TYPE   2 113
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED      4   43
  DEL PEAK 18(10Q25.2) WILD-TYPE    2  113
     clus
vv    DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  NO                             4                              2
  YES                           43                            113
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 18(10Q25.2) MUTATED   40  0  1  0
  DEL PEAK 18(10Q25.2) WILD-TYPE 81  2 11  3
D43V10, multiclass
    clus
vv   DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  R0                           40                             81
  R1                            0                              2
  R2                            1                             11
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(10Q25.2) MUTATED       0                         1    24
  DEL PEAK 18(10Q25.2) WILD-TYPE     1                         2    57
D43V12, multiclass
                           clus
vv                          DEL PEAK 18(10Q25.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               24
                           clus
vv                          DEL PEAK 18(10Q25.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK 19(11Q22.3) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 19(11Q22.3) MUTATED   31  3
  DEL PEAK 19(11Q22.3) WILD-TYPE 97 19
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            34                            116 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                             3                             19 
$`DEL PEAK 19(11Q22.3) MUTATED`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       43.04        13.55        19.10        14.50        15.39        10.39 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3727 
       32.02         7.07        46.03         2.01         6.05         0.99 
TCGA-AG-3732 TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       32.98         1.02        13.94        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 
       10.98        41.00         0.49         0.69         0.72        10.19 
TCGA-CL-4957 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF 
       13.97        13.97         7.10        30.05         5.29        24.13 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-7004 
       20.91        17.00        16.41         8.45 

$`DEL PEAK 19(11Q22.3) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 
       24.13        17.95        17.23        12.72        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 
        8.45        20.02        36.03        12.00         8.02         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
        2.01        24.00         1.02        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 
        0.99        15.95        19.99        19.99         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        35.01        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       19.99        28.04        36.03        14.04         1.02        17.03 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        0.99        20.98         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A023 
       15.95        36.03         9.07         1.02        31.00        51.98 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 
       49.97         1.94        38.96        61.97        38.04         1.45 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        4.60         1.81         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
       12.99        12.00        15.02        36.00        12.95        13.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       10.06       126.44        41.36        57.24       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 
       32.61         0.49         2.40        20.55        19.96        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46        11.97         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        14.86         0.39         1.02         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                          0.49                           0.39 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                         70.03                         129.27 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                        13.955                         15.020 
[1] "0.5 - 70.0 (14.0)"  "0.4 - 129.3 (15.0)"
[1] "hr=" "1.7"
D44V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 19(11Q22.3) MUTATED        10        3         6         0         0
  DEL PEAK 19(11Q22.3) WILD-TYPE      20        5        32         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 19(11Q22.3) MUTATED           2          3          5          4
  DEL PEAK 19(11Q22.3) WILD-TYPE         3          6         18         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 19(11Q22.3) MUTATED          1         2
  DEL PEAK 19(11Q22.3) WILD-TYPE       17         7
D44V3, multiclass
            clus
vv           DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  STAGE I                              10                             20
  STAGE II                              3                              5
  STAGE IIA                             6                             32
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             2                              3
  STAGE IIIA                            3                              6
  STAGE IIIB                            5                             18
  STAGE IIIC                            4                             10
  STAGE IV                              1                             17
  STAGE IVA                             2                              7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 19(11Q22.3) MUTATED    1 10 24  3
  DEL PEAK 19(11Q22.3) WILD-TYPE  8 19 85 11
D44V4, multiclass
    clus
vv   DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  T1                            1                              8
  T2                           10                             19
  T3                           24                             85
  T4                            3                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 19(11Q22.3) MUTATED   19 11  7
  DEL PEAK 19(11Q22.3) WILD-TYPE 64 34 25
D44V5, multiclass
    clus
vv   DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  N0                           19                             64
  N1                           11                             34
  N2                            7                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 19(11Q22.3) MUTATED   31  1   0  5
  DEL PEAK 19(11Q22.3) WILD-TYPE 92 21   2  8
D44V6, multiclass
     clus
vv    DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  M0                            31                             92
  M1                             1                             21
  M1A                            0                              2
  MX                             5                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(11Q22.3) MUTATED   19 19
  DEL PEAK 19(11Q22.3) WILD-TYPE 55 69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED     19   19
  DEL PEAK 19(11Q22.3) WILD-TYPE   55   69
        clus
vv       DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  FEMALE                           19                             55
  MALE                             19                             69
[1] 2 2
[1] FALSE
D44V8, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q22.3) MUTATED    28   6
  DEL PEAK 19(11Q22.3) WILD-TYPE 115   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED     28    6
  DEL PEAK 19(11Q22.3) WILD-TYPE  115    7
                                clus
vv                               DEL PEAK 19(11Q22.3) MUTATED
  RECTAL ADENOCARCINOMA                                    28
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 19(11Q22.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     115
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 2 2
[1] FALSE
D44V9, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q22.3) MUTATED     3  35
  DEL PEAK 19(11Q22.3) WILD-TYPE   3 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED      3   35
  DEL PEAK 19(11Q22.3) WILD-TYPE    3  121
     clus
vv    DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  NO                             3                              3
  YES                           35                            121
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 19(11Q22.3) MUTATED   29  0  0  1
  DEL PEAK 19(11Q22.3) WILD-TYPE 92  2 12  2
D44V10, multiclass
    clus
vv   DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  R0                           29                             92
  R1                            0                              2
  R2                            0                             12
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(11Q22.3) MUTATED       1                         0    18
  DEL PEAK 19(11Q22.3) WILD-TYPE     0                         3    63
D44V12, multiclass
                           clus
vv                          DEL PEAK 19(11Q22.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               18
                           clus
vv                          DEL PEAK 19(11Q22.3) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 63
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 20(12P13.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(12P13.1) MUTATED    22   7
  DEL PEAK 20(12P13.1) WILD-TYPE 106  15
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                            29                            121 
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                             7                             15 
$`DEL PEAK 20(12P13.1) MUTATED`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 
       43.04        13.55        19.10        10.39        14.50        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3898 
       20.02        36.03        34.03        29.98         1.02        48.03 
TCGA-AG-A00C TCGA-AG-A01W TCGA-AG-A026 TCGA-AH-6544 TCGA-CI-6620 TCGA-DC-4749 
        6.02        70.03         1.94         0.49         6.05        11.01 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6508 TCGA-EI-6509 
       13.97         7.10        24.13        51.48        20.91        17.00 
TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6641 
       16.31        16.41        14.86         0.66        26.43 

$`DEL PEAK 20(12P13.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       24.13        17.95        17.23        12.72        37.74         8.45 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       10.39        12.00        32.02         8.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00         1.02        46.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 
       12.03         6.05         0.99        15.95        19.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        7.99         0.99        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H 
        1.02        17.03         0.99        20.98        13.94        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       23.01        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       12.00        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.04         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6622 
        0.72         4.60         1.81        10.19         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       15.02        12.99        12.00        15.02        36.00        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       12.95        13.05        10.06         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       57.24       129.27        32.61         0.49         2.40        20.55 
TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 
       19.96        18.28        15.85        17.69        16.34         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
        9.96        37.51        31.30         0.39         1.02         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.53         1.12         0.76         0.46        18.28        55.76 
TCGA-G5-6572 
       47.08 

  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                          0.49                           0.39 
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                         70.03                         129.27 
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                         16.31                          13.94 
[1] "0.5 - 70.0 (16.3)"  "0.4 - 129.3 (13.9)"
[1] "hr=" "1.9"
D45V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 20(12P13.1) MUTATED         4        3         7         0         0
  DEL PEAK 20(12P13.1) WILD-TYPE      26        5        31         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 20(12P13.1) MUTATED           0          4          4          3
  DEL PEAK 20(12P13.1) WILD-TYPE         5          5         19         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 20(12P13.1) MUTATED          3         4
  DEL PEAK 20(12P13.1) WILD-TYPE       15         5
D45V3, multiclass
            clus
vv           DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  STAGE I                               4                             26
  STAGE II                              3                              5
  STAGE IIA                             7                             31
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             0                              5
  STAGE IIIA                            4                              5
  STAGE IIIB                            4                             19
  STAGE IIIC                            3                             11
  STAGE IV                              3                             15
  STAGE IVA                             4                              5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 20(12P13.1) MUTATED    2  5 24  2
  DEL PEAK 20(12P13.1) WILD-TYPE  7 24 85 12
D45V4, multiclass
    clus
vv   DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  T1                            2                              7
  T2                            5                             24
  T3                           24                             85
  T4                            2                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 20(12P13.1) MUTATED   14 14  5
  DEL PEAK 20(12P13.1) WILD-TYPE 69 31 27
D45V5, multiclass
    clus
vv   DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  N0                           14                             69
  N1                           14                             31
  N2                            5                             27
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 20(12P13.1) MUTATED    22   7   0   4
  DEL PEAK 20(12P13.1) WILD-TYPE 101  15   2   9
D45V6, multiclass
     clus
vv    DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  M0                            22                            101
  M1                             7                             15
  M1A                            0                              2
  MX                             4                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(12P13.1) MUTATED   16 17
  DEL PEAK 20(12P13.1) WILD-TYPE 58 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P13.1) MUTATED     16   17
  DEL PEAK 20(12P13.1) WILD-TYPE   58   71
        clus
vv       DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  FEMALE                           16                             58
  MALE                             17                             71
[1] 2 2
[1] FALSE
D45V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P13.1) MUTATED    29   1
  DEL PEAK 20(12P13.1) WILD-TYPE 114  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P13.1) MUTATED     29    1
  DEL PEAK 20(12P13.1) WILD-TYPE  114   12
                                clus
vv                               DEL PEAK 20(12P13.1) MUTATED
  RECTAL ADENOCARCINOMA                                    29
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 20(12P13.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     114
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
D45V9, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P13.1) MUTATED     1  32
  DEL PEAK 20(12P13.1) WILD-TYPE   5 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P13.1) MUTATED      1   32
  DEL PEAK 20(12P13.1) WILD-TYPE    5  124
     clus
vv    DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  NO                             1                              5
  YES                           32                            124
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 20(12P13.1) MUTATED   24  1  2  0
  DEL PEAK 20(12P13.1) WILD-TYPE 97  1 10  3
D45V10, multiclass
    clus
vv   DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  R0                           24                             97
  R1                            1                              1
  R2                            2                             10
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12P13.1) MUTATED       0                         1    20
  DEL PEAK 20(12P13.1) WILD-TYPE     1                         2    61
D45V12, multiclass
                           clus
vv                          DEL PEAK 20(12P13.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               20
                           clus
vv                          DEL PEAK 20(12P13.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 21(12Q22) MUTATION ANALYSIS
D46V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 21(12Q22) MUTATED    19   5
  DEL PEAK 21(12Q22) WILD-TYPE 109  17
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                          24                          126 
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                           5                           17 
$`DEL PEAK 21(12Q22) MUTATED`
TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3574 TCGA-AG-3593 
       43.04        12.72        14.50        15.39        36.03        34.03 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3898 TCGA-AG-4001 TCGA-AG-A014 TCGA-AG-A032 
       29.98        32.98        48.03        36.03        15.95        38.04 
TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6509 
        0.49        13.97         7.10       129.27        24.13        17.00 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-F5-6702 TCGA-F5-6812 TCGA-G5-6233 
       16.31        16.41        11.51        14.86         0.66        18.28 

$`DEL PEAK 21(12Q22) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 
       24.13        17.95        17.23        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 
       10.39         8.45        20.02        10.39        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
        8.02         7.07         1.02         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        19.99         7.99         0.99         1.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99         1.02        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 
       28.04        14.04         1.02        17.03         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       13.94         6.02        25.97        23.01        37.02        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       10.98        51.98        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       41.00         1.45         0.69         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05         6.05         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       13.97        60.03         7.99        10.98        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 
       12.99        12.00        15.02        36.00        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       13.05        10.06         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       51.48        32.61         0.49         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 
       20.91        18.28        15.85        17.69        16.34         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       10.78        13.64        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       37.51        31.30         0.39         1.02         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12         0.76         0.46        55.76        47.08        26.43 

  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                        0.49                         0.39 
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                      129.27                       126.44 
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                      16.705                       13.300 
[1] "0.5 - 129.3 (16.7)" "0.4 - 126.4 (13.3)"
[1] "hr=" "1.3"
D46V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 21(12Q22) MUTATED         4        1         7         0         2
  DEL PEAK 21(12Q22) WILD-TYPE      26        7        31         2         0
                              vv
clus                           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 21(12Q22) MUTATED           0          2          3          2
  DEL PEAK 21(12Q22) WILD-TYPE         5          7         20         12
                              vv
clus                           STAGE IV STAGE IVA
  DEL PEAK 21(12Q22) MUTATED          0         2
  DEL PEAK 21(12Q22) WILD-TYPE       18         7
D46V3, multiclass
            clus
vv           DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  STAGE I                             4                           26
  STAGE II                            1                            7
  STAGE IIA                           7                           31
  STAGE IIB                           0                            2
  STAGE IIC                           2                            0
  STAGE III                           0                            5
  STAGE IIIA                          2                            7
  STAGE IIIB                          3                           20
  STAGE IIIC                          2                           12
  STAGE IV                            0                           18
  STAGE IVA                           2                            7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T1 T2 T3 T4
  DEL PEAK 21(12Q22) MUTATED    1  4 18  1
  DEL PEAK 21(12Q22) WILD-TYPE  8 25 91 13
D46V4, multiclass
    clus
vv   DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  T1                          1                            8
  T2                          4                           25
  T3                         18                           91
  T4                          1                           13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  DEL PEAK 21(12Q22) MUTATED   13  7  4
  DEL PEAK 21(12Q22) WILD-TYPE 70 38 28
D46V5, multiclass
    clus
vv   DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  N0                         13                           70
  N1                          7                           38
  N2                          4                           28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            M0  M1 M1A  MX
  DEL PEAK 21(12Q22) MUTATED    20   2   0   2
  DEL PEAK 21(12Q22) WILD-TYPE 103  20   2  11
D46V6, multiclass
     clus
vv    DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  M0                          20                          103
  M1                           2                           20
  M1A                          0                            2
  MX                           2                           11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V7, binary
                              cls
clus                            0  1
  DEL PEAK 21(12Q22) MUTATED   10 14
  DEL PEAK 21(12Q22) WILD-TYPE 64 74
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(12Q22) MUTATED     10   14
  DEL PEAK 21(12Q22) WILD-TYPE   64   74
        clus
vv       DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  FEMALE                         10                           64
  MALE                           14                           74
[1] 2 2
[1] FALSE
D46V8, binary
                              cls
clus                             0   1
  DEL PEAK 21(12Q22) MUTATED    22   1
  DEL PEAK 21(12Q22) WILD-TYPE 121  12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(12Q22) MUTATED     22    1
  DEL PEAK 21(12Q22) WILD-TYPE  121   12
                                clus
vv                               DEL PEAK 21(12Q22) MUTATED
  RECTAL ADENOCARCINOMA                                  22
  RECTAL MUCINOUS ADENOCARCINOMA                          1
                                clus
vv                               DEL PEAK 21(12Q22) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   121
  RECTAL MUCINOUS ADENOCARCINOMA                           12
[1] 2 2
[1] FALSE
D46V9, binary
                              cls
clus                             0   1
  DEL PEAK 21(12Q22) MUTATED     2  22
  DEL PEAK 21(12Q22) WILD-TYPE   4 134
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(12Q22) MUTATED      2   22
  DEL PEAK 21(12Q22) WILD-TYPE    4  134
     clus
vv    DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  NO                           2                            4
  YES                         22                          134
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 21(12Q22) MUTATED    20   0   0   0
  DEL PEAK 21(12Q22) WILD-TYPE 101   2  12   3
D46V10, multiclass
    clus
vv   DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  R0                         20                          101
  R1                          0                            2
  R2                          0                           12
  RX                          0                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(12Q22) MUTATED       0                         0    16
  DEL PEAK 21(12Q22) WILD-TYPE     1                         3    65
D46V12, multiclass
                           clus
vv                          DEL PEAK 21(12Q22) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             16
                           clus
vv                          DEL PEAK 21(12Q22) WILD-TYPE
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 22(14Q11.2) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(14Q11.2) MUTATED   54  8
  DEL PEAK 22(14Q11.2) WILD-TYPE 74 14
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                            62                             88 
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                             8                             14 
$`DEL PEAK 22(14Q11.2) MUTATED`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-6672 
       17.95        13.55        19.10        12.72        37.74        10.39 
TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 
       36.03         7.07        34.03        50.04         6.05         0.99 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
        0.99        19.99         1.02        17.03        35.01         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H 
       28.04        36.03        14.04        17.03         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 
       23.01         1.94        38.96        38.04         0.49        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        6.05         6.05         9.37         4.73        13.97         7.99 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       11.01        12.99        13.97        36.00         7.10        13.05 
TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6508 
       10.06       129.27        24.13        51.48        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 
       17.00        16.34        16.31        16.41        10.78        11.97 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 
       31.30         0.39         1.02         0.66         0.76        18.28 
TCGA-G5-6235 TCGA-G5-6641 
       55.76        26.43 

$`DEL PEAK 22(14Q11.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       24.13        17.23        43.04        10.39        14.50         8.45 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 
       15.39        20.02        12.00        32.02         8.02         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 
        2.01        24.00         1.02        46.03         2.01        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3728 
        0.99        15.95        19.99        19.99         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        1.02        32.98         0.99        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       48.03        32.02        19.99         1.02         0.99        20.98 
TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       13.94        37.02        15.95        36.03         9.07         1.02 
TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       49.97        61.97        41.00         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 
        4.60         1.81         6.97        60.03        10.98        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       12.00        15.02        30.05        12.95         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 
       41.36        57.24        32.61         0.49         2.40        19.96 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 
       18.28        15.85        17.69         8.61        11.51        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 
       17.46         8.45         9.96        37.51        14.86         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
        0.53         1.12         0.46        47.08 

  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                          0.39                           0.46 
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                        14.005                         14.680 
[1] "0.4 - 129.3 (14.0)" "0.5 - 126.4 (14.7)"
[1] "hr=" "1"  
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 22(14Q11.2) MUTATED        12        2        20         0         1
  DEL PEAK 22(14Q11.2) WILD-TYPE      18        6        18         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 22(14Q11.2) MUTATED           1          5         12          6
  DEL PEAK 22(14Q11.2) WILD-TYPE         4          4         11          8
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 22(14Q11.2) MUTATED          6         2
  DEL PEAK 22(14Q11.2) WILD-TYPE       12         7
D47V3, multiclass
            clus
vv           DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  STAGE I                              12                             18
  STAGE II                              2                              6
  STAGE IIA                            20                             18
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             1                              4
  STAGE IIIA                            5                              4
  STAGE IIIB                           12                             11
  STAGE IIIC                            6                              8
  STAGE IV                              6                             12
  STAGE IVA                             2                              7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 22(14Q11.2) MUTATED    3 12 49  4
  DEL PEAK 22(14Q11.2) WILD-TYPE  6 17 60 10
D47V4, multiclass
    clus
vv   DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  T1                            3                              6
  T2                           12                             17
  T3                           49                             60
  T4                            4                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 22(14Q11.2) MUTATED   34 23 11
  DEL PEAK 22(14Q11.2) WILD-TYPE 49 22 21
D47V5, multiclass
    clus
vv   DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  N0                           34                             49
  N1                           23                             22
  N2                           11                             21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 22(14Q11.2) MUTATED   53  8   0  6
  DEL PEAK 22(14Q11.2) WILD-TYPE 70 14   2  7
D47V6, multiclass
     clus
vv    DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  M0                            53                             70
  M1                             8                             14
  M1A                            0                              2
  MX                             6                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V7, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q11.2) MUTATED   29 39
  DEL PEAK 22(14Q11.2) WILD-TYPE 45 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q11.2) MUTATED     29   39
  DEL PEAK 22(14Q11.2) WILD-TYPE   45   49
        clus
vv       DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  FEMALE                           29                             45
  MALE                             39                             49
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q11.2) MUTATED   64  2
  DEL PEAK 22(14Q11.2) WILD-TYPE 79 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q11.2) MUTATED     64    2
  DEL PEAK 22(14Q11.2) WILD-TYPE   79   11
                                clus
vv                               DEL PEAK 22(14Q11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    64
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 22(14Q11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      79
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
D47V9, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q11.2) MUTATED    4 64
  DEL PEAK 22(14Q11.2) WILD-TYPE  2 92
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q11.2) MUTATED      4   64
  DEL PEAK 22(14Q11.2) WILD-TYPE    2   92
     clus
vv    DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  NO                             4                              2
  YES                           64                             92
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 22(14Q11.2) MUTATED   50  2  2  1
  DEL PEAK 22(14Q11.2) WILD-TYPE 71  0 10  2
D47V10, multiclass
    clus
vv   DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  R0                           50                             71
  R1                            2                              0
  R2                            2                             10
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(14Q11.2) MUTATED       0                         2    37
  DEL PEAK 22(14Q11.2) WILD-TYPE     1                         1    44
D47V12, multiclass
                           clus
vv                          DEL PEAK 22(14Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               37
                           clus
vv                          DEL PEAK 22(14Q11.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(48) Variable = DEL PEAK 23(14Q31.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(14Q31.1) MUTATED   54  9
  DEL PEAK 23(14Q31.1) WILD-TYPE 74 13
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                            63                             87 
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                             9                             13 
$`DEL PEAK 23(14Q31.1) MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AG-3582 TCGA-AG-3587 
       17.95        17.23        13.55        37.74         1.02        46.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3731 
       34.03        50.04        12.03         6.05         0.99         1.02 
TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        0.99         1.02        17.03        35.01         1.02        48.03 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       36.03        14.04        17.03         6.02        25.97        23.01 
TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 
       70.03         1.94        38.96        38.04         0.49        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        6.05         6.05         9.37         4.73        13.97         7.99 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       10.98        11.01        12.99        13.97        36.00         7.10 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 
       13.05        10.06        41.36       129.27        51.48        20.55 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.00        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 
       11.97        31.30         0.39         1.02         0.66         0.76 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       18.28        55.76        26.43 

$`DEL PEAK 23(14Q31.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 
       24.13        43.04        19.10        12.72        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 
        8.45        15.39        20.02        10.39        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         2.01        24.00         1.02 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 
        2.01         0.99        15.95        19.99        19.99         7.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 
       29.98        32.98         0.99        19.99        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4022 
       14.01        32.02        19.99        28.04         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98        13.94        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
        1.02        12.00        31.00        64.01        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       49.97        61.97        41.00         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6154 
        4.60         1.81         6.97        60.03        15.02        12.00 
TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       15.02        30.05        12.95         5.29       126.44        57.24 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 
       24.13        32.61         0.49         2.40        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       18.28        15.85        17.69         8.61        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 
        8.45         9.96        37.51        14.86         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
        1.12         0.46        47.08 

  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                          0.39                           0.46 
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                         13.97                          15.02 
[1] "0.4 - 129.3 (14.0)" "0.5 - 126.4 (15.0)"
[1] "hr=" "1"  
D48V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 23(14Q31.1) MUTATED        11        2        22         0         2
  DEL PEAK 23(14Q31.1) WILD-TYPE      19        6        16         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 23(14Q31.1) MUTATED           1          5         12          5
  DEL PEAK 23(14Q31.1) WILD-TYPE         4          4         11          9
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 23(14Q31.1) MUTATED          7         2
  DEL PEAK 23(14Q31.1) WILD-TYPE       11         7
D48V3, multiclass
            clus
vv           DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  STAGE I                              11                             19
  STAGE II                              2                              6
  STAGE IIA                            22                             16
  STAGE IIB                             0                              2
  STAGE IIC                             2                              0
  STAGE III                             1                              4
  STAGE IIIA                            5                              4
  STAGE IIIB                           12                             11
  STAGE IIIC                            5                              9
  STAGE IV                              7                             11
  STAGE IVA                             2                              7
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 23(14Q31.1) MUTATED    3 11 53  3
  DEL PEAK 23(14Q31.1) WILD-TYPE  6 18 56 11
D48V4, multiclass
    clus
vv   DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  T1                            3                              6
  T2                           11                             18
  T3                           53                             56
  T4                            3                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 23(14Q31.1) MUTATED   36 25  9
  DEL PEAK 23(14Q31.1) WILD-TYPE 47 20 23
D48V5, multiclass
    clus
vv   DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  N0                           36                             47
  N1                           25                             20
  N2                            9                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 23(14Q31.1) MUTATED   55 10   0  4
  DEL PEAK 23(14Q31.1) WILD-TYPE 68 12   2  9
D48V6, multiclass
     clus
vv    DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  M0                            55                             68
  M1                            10                             12
  M1A                            0                              2
  MX                             4                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(14Q31.1) MUTATED   29 41
  DEL PEAK 23(14Q31.1) WILD-TYPE 45 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q31.1) MUTATED     29   41
  DEL PEAK 23(14Q31.1) WILD-TYPE   45   47
        clus
vv       DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  FEMALE                           29                             45
  MALE                             41                             47
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                              0  1
  DEL PEAK 23(14Q31.1) MUTATED   66  1
  DEL PEAK 23(14Q31.1) WILD-TYPE 77 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q31.1) MUTATED     66    1
  DEL PEAK 23(14Q31.1) WILD-TYPE   77   12
                                clus
vv                               DEL PEAK 23(14Q31.1) MUTATED
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 23(14Q31.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      77
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
D48V9, binary
                                cls
clus                              0  1
  DEL PEAK 23(14Q31.1) MUTATED    2 68
  DEL PEAK 23(14Q31.1) WILD-TYPE  4 88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q31.1) MUTATED      2   68
  DEL PEAK 23(14Q31.1) WILD-TYPE    4   88
     clus
vv    DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  NO                             2                              4
  YES                           68                             88
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 23(14Q31.1) MUTATED   51  2  4  1
  DEL PEAK 23(14Q31.1) WILD-TYPE 70  0  8  2
D48V10, multiclass
    clus
vv   DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  R0                           51                             70
  R1                            2                              0
  R2                            4                              8
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D48V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(14Q31.1) MUTATED       0                         2    36
  DEL PEAK 23(14Q31.1) WILD-TYPE     1                         1    45
D48V12, multiclass
                           clus
vv                          DEL PEAK 23(14Q31.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               36
                           clus
vv                          DEL PEAK 23(14Q31.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  WHITE                                                 45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(49) Variable = DEL PEAK 24(15Q22.33) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 24(15Q22.33) MUTATED   59 10
  DEL PEAK 24(15Q22.33) WILD-TYPE 69 12
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             69                              81 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             10                              12 
$`DEL PEAK 24(15Q22.33) MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       24.13        43.04        13.55        12.72        37.74        14.50 
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 
       10.39        32.02         1.02         2.01        24.00        34.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 
        6.05        15.95        19.99        29.98         0.99        19.99 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       17.03        35.01         1.02        19.99        28.04        14.04 
TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       17.03        13.94        25.97        23.01        37.02         1.02 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       12.00        70.03        38.96        41.00        38.04         0.49 
TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 
        0.69        10.19         6.05         9.37         7.99        10.98 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC 
       12.99        13.97        36.00        13.05        10.06        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 
       57.24       129.27        24.13        51.48         0.49         2.40 
TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       15.85        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       11.97        31.30        14.86         1.02         0.66         0.69 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
        0.46        18.28        26.43 

$`DEL PEAK 24(15Q22.33) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       17.95        17.23        19.10        10.39         8.45        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 
       20.02        36.03        12.00         8.02         7.07         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 
       46.03         2.01        50.04        12.03         0.99        19.99 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99         1.02        32.98         0.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 
       36.95        13.02        14.01        48.03        32.02        36.03 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 
        1.02         0.99        20.98         6.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        9.07        31.00        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
        1.94        61.97         1.45         0.72         4.60         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 
        6.05         6.97         4.73        13.97        60.03        11.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       15.02        12.00        15.02         7.10        30.05        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
        5.29       126.44        32.61        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 
       17.00        18.28        17.69        16.34         8.61        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 
        8.45         9.96        37.51         0.39         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.76        55.76        47.08 

  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                           0.46                            0.39 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                         129.27                          126.44 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                          14.86                           13.97 
[1] "0.5 - 129.3 (14.9)" "0.4 - 126.4 (14.0)"
[1] "hr=" "1"  
D49V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(15Q22.33) MUTATED         9        1        23         1
  DEL PEAK 24(15Q22.33) WILD-TYPE      21        7        15         1
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(15Q22.33) MUTATED           2         2          4         13
  DEL PEAK 24(15Q22.33) WILD-TYPE         0         3          5         10
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(15Q22.33) MUTATED            8        9         3
  DEL PEAK 24(15Q22.33) WILD-TYPE          6        9         6
D49V3, multiclass
            clus
vv           DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  STAGE I                                9                              21
  STAGE II                               1                               7
  STAGE IIA                             23                              15
  STAGE IIB                              1                               1
  STAGE IIC                              2                               0
  STAGE III                              2                               3
  STAGE IIIA                             4                               5
  STAGE IIIB                            13                              10
  STAGE IIIC                             8                               6
  STAGE IV                               9                               9
  STAGE IVA                              3                               6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 24(15Q22.33) MUTATED    4  8 60  4
  DEL PEAK 24(15Q22.33) WILD-TYPE  5 21 49 10
D49V4, multiclass
    clus
vv   DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  T1                             4                               5
  T2                             8                              21
  T3                            60                              49
  T4                             4                              10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 24(15Q22.33) MUTATED   35 25 16
  DEL PEAK 24(15Q22.33) WILD-TYPE 48 20 16
D49V5, multiclass
    clus
vv   DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  N0                            35                              48
  N1                            25                              20
  N2                            16                              16
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  DEL PEAK 24(15Q22.33) MUTATED   58 11   0  6
  DEL PEAK 24(15Q22.33) WILD-TYPE 65 11   2  7
D49V6, multiclass
     clus
vv    DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  M0                             58                              65
  M1                             11                              11
  M1A                             0                               2
  MX                              6                               7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V7, binary
                                 cls
clus                               0  1
  DEL PEAK 24(15Q22.33) MUTATED   32 44
  DEL PEAK 24(15Q22.33) WILD-TYPE 42 44
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(15Q22.33) MUTATED     32   44
  DEL PEAK 24(15Q22.33) WILD-TYPE   42   44
        clus
vv       DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  FEMALE                            32                              42
  MALE                              44                              44
[1] 2 2
[1] FALSE
D49V8, binary
                                 cls
clus                               0  1
  DEL PEAK 24(15Q22.33) MUTATED   67  6
  DEL PEAK 24(15Q22.33) WILD-TYPE 76  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(15Q22.33) MUTATED     67    6
  DEL PEAK 24(15Q22.33) WILD-TYPE   76    7
                                clus
vv                               DEL PEAK 24(15Q22.33) MUTATED
  RECTAL ADENOCARCINOMA                                     67
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 24(15Q22.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       76
  RECTAL MUCINOUS ADENOCARCINOMA                               7
[1] 2 2
[1] FALSE
D49V9, binary
                                 cls
clus                               0  1
  DEL PEAK 24(15Q22.33) MUTATED    5 71
  DEL PEAK 24(15Q22.33) WILD-TYPE  1 85
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(15Q22.33) MUTATED      5   71
  DEL PEAK 24(15Q22.33) WILD-TYPE    1   85
     clus
vv    DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  NO                              5                               1
  YES                            71                              85
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 24(15Q22.33) MUTATED   58  0  4  1
  DEL PEAK 24(15Q22.33) WILD-TYPE 63  2  8  2
D49V10, multiclass
    clus
vv   DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  R0                            58                              63
  R1                             0                               2
  R2                             4                               8
  RX                             1                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D49V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(15Q22.33) MUTATED       0                         2    40
  DEL PEAK 24(15Q22.33) WILD-TYPE     1                         1    41
D49V12, multiclass
                           clus
vv                          DEL PEAK 24(15Q22.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                40
                           clus
vv                          DEL PEAK 24(15Q22.33) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               1
  WHITE                                                  41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(50) Variable = DEL PEAK 25(16P13.3) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(16P13.3) MUTATED     9   2
  DEL PEAK 25(16P13.3) WILD-TYPE 119  20
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                            11                            139 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                             2                             20 
$`DEL PEAK 25(16P13.3) MUTATED`
TCGA-AG-3578 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-4005 TCGA-AG-A02G 
       32.02         6.05        19.99         7.99        14.04        38.96 
TCGA-DC-6682 TCGA-EI-6882 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
       13.05         8.61         1.02         0.53        18.28 

$`DEL PEAK 25(16P13.3) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       20.02        10.39        36.03        12.00         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        1.02         2.01        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98         1.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99         1.02        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03         1.02        17.03         0.99        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
        6.02        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X 
       10.98        51.98        49.97         1.94        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        12.95        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       41.36        57.24       129.27        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       11.51        10.78        13.64        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
        9.96        37.51        31.30        14.86         0.39         0.66 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.12         0.76         0.46        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                          0.53                           0.39 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                         38.96                         129.27 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                         13.05                          14.86 
[1] "0.5 - 39.0 (13.1)"  "0.4 - 129.3 (14.9)"
[1] "hr=" "2.1"
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 25(16P13.3) MUTATED         1        0         7         0         1
  DEL PEAK 25(16P13.3) WILD-TYPE      29        8        31         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 25(16P13.3) MUTATED           0          0          0          2
  DEL PEAK 25(16P13.3) WILD-TYPE         5          9         23         12
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 25(16P13.3) MUTATED          2         0
  DEL PEAK 25(16P13.3) WILD-TYPE       16         9
D50V3, multiclass
            clus
vv           DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  STAGE I                               1                             29
  STAGE II                              0                              8
  STAGE IIA                             7                             31
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             0                              5
  STAGE IIIA                            0                              9
  STAGE IIIB                            0                             23
  STAGE IIIC                            2                             12
  STAGE IV                              2                             16
  STAGE IVA                             0                              9
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 25(16P13.3) MUTATED    0  3 10  0
  DEL PEAK 25(16P13.3) WILD-TYPE  9 26 99 14
D50V4, multiclass
    clus
vv   DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  T1                            0                              9
  T2                            3                             26
  T3                           10                             99
  T4                            0                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 25(16P13.3) MUTATED    8  1  4
  DEL PEAK 25(16P13.3) WILD-TYPE 75 44 28
D50V5, multiclass
    clus
vv   DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  N0                            8                             75
  N1                            1                             44
  N2                            4                             28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 25(16P13.3) MUTATED    11   2   0   0
  DEL PEAK 25(16P13.3) WILD-TYPE 112  20   2  13
D50V6, multiclass
     clus
vv    DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  M0                            11                            112
  M1                             2                             20
  M1A                            0                              2
  MX                             0                             13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V7, binary
                                cls
clus                              0  1
  DEL PEAK 25(16P13.3) MUTATED    6  7
  DEL PEAK 25(16P13.3) WILD-TYPE 68 81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16P13.3) MUTATED      6    7
  DEL PEAK 25(16P13.3) WILD-TYPE   68   81
        clus
vv       DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  FEMALE                            6                             68
  MALE                              7                             81
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(16P13.3) MUTATED    10   2
  DEL PEAK 25(16P13.3) WILD-TYPE 133  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16P13.3) MUTATED     10    2
  DEL PEAK 25(16P13.3) WILD-TYPE  133   11
                                clus
vv                               DEL PEAK 25(16P13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    10
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 25(16P13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     133
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
D50V9, binary
                                cls
clus                               0   1
  DEL PEAK 25(16P13.3) MUTATED     0  13
  DEL PEAK 25(16P13.3) WILD-TYPE   6 143
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16P13.3) MUTATED      0   13
  DEL PEAK 25(16P13.3) WILD-TYPE    6  143
     clus
vv    DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  NO                             0                              6
  YES                           13                            143
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(16P13.3) MUTATED    10   0   1   0
  DEL PEAK 25(16P13.3) WILD-TYPE 111   2  11   3
D50V10, multiclass
    clus
vv   DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  R0                           10                            111
  R1                            0                              2
  R2                            1                             11
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(16P13.3) MUTATED       0                         0     5
  DEL PEAK 25(16P13.3) WILD-TYPE     1                         3    76
D50V12, multiclass
                           clus
vv                          DEL PEAK 25(16P13.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                5
                           clus
vv                          DEL PEAK 25(16P13.3) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 76
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(51) Variable = DEL PEAK 26(16Q23.1) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(16Q23.1) MUTATED    17   3
  DEL PEAK 26(16Q23.1) WILD-TYPE 111  19
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            20                            130 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                             3                             19 
$`DEL PEAK 26(16Q23.1) MUTATED`
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 
       10.39        32.02         1.02         6.05        19.99         7.99 
TCGA-AG-3732 TCGA-AG-3883 TCGA-AG-4005 TCGA-AH-6544 TCGA-AH-6644 TCGA-DC-6682 
       32.98         1.02        14.04         0.49         0.72        13.05 
TCGA-DY-A1DE TCGA-EI-6883 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6811 
      129.27        11.51        11.97         8.45         9.96         1.02 
TCGA-F5-6814 TCGA-G5-6233 
        0.53        18.28 

$`DEL PEAK 26(16Q23.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       12.72        37.74        10.39        14.50         8.45        15.39 
TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       20.02        36.03        12.00         8.02         7.07         2.01 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       24.00         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
       12.03         0.99        15.95        19.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3890 
        1.02         0.99         0.99        19.99        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       13.02        35.01        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       19.99        28.04        36.03         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       15.95        36.03         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       70.03        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.04         1.45         0.69 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        4.60         1.81        10.19         6.05         6.05         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        13.97        60.03         7.99        10.98 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02        12.99        12.00        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        30.05        12.95        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
        0.49         2.40        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       18.28        15.85        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6571 
        8.61        10.78        13.64        17.46        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
       14.86         0.39         0.66         0.69         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        55.76        47.08        26.43 

  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                          0.49                           0.39 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                        10.175                         15.620 
[1] "0.5 - 129.3 (10.2)" "0.4 - 126.4 (15.6)"
[1] "hr=" "1.6"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 26(16Q23.1) MUTATED         3        0         7         0         2
  DEL PEAK 26(16Q23.1) WILD-TYPE      27        8        31         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 26(16Q23.1) MUTATED           1          0          0          3
  DEL PEAK 26(16Q23.1) WILD-TYPE         4          9         23         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 26(16Q23.1) MUTATED          4         1
  DEL PEAK 26(16Q23.1) WILD-TYPE       14         8
D51V3, multiclass
            clus
vv           DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  STAGE I                               3                             27
  STAGE II                              0                              8
  STAGE IIA                             7                             31
  STAGE IIB                             0                              2
  STAGE IIC                             2                              0
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            0                             23
  STAGE IIIC                            3                             11
  STAGE IV                              4                             14
  STAGE IVA                             1                              8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 26(16Q23.1) MUTATED    0  4 16  3
  DEL PEAK 26(16Q23.1) WILD-TYPE  9 25 93 11
D51V4, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  T1                            0                              9
  T2                            4                             25
  T3                           16                             93
  T4                            3                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 26(16Q23.1) MUTATED   11  2  9
  DEL PEAK 26(16Q23.1) WILD-TYPE 72 43 23
D51V5, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  N0                           11                             72
  N1                            2                             43
  N2                            9                             23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 26(16Q23.1) MUTATED    17   4   0   2
  DEL PEAK 26(16Q23.1) WILD-TYPE 106  18   2  11
D51V6, multiclass
     clus
vv    DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  M0                            17                            106
  M1                             4                             18
  M1A                            0                              2
  MX                             2                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q23.1) MUTATED   11 12
  DEL PEAK 26(16Q23.1) WILD-TYPE 63 76
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     11   12
  DEL PEAK 26(16Q23.1) WILD-TYPE   63   76
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  FEMALE                           11                             63
  MALE                             12                             76
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED    20   2
  DEL PEAK 26(16Q23.1) WILD-TYPE 123  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     20    2
  DEL PEAK 26(16Q23.1) WILD-TYPE  123   11
                                clus
vv                               DEL PEAK 26(16Q23.1) MUTATED
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 26(16Q23.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     123
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
D51V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED     1  22
  DEL PEAK 26(16Q23.1) WILD-TYPE   5 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED      1   22
  DEL PEAK 26(16Q23.1) WILD-TYPE    5  134
     clus
vv    DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  NO                             1                              5
  YES                           22                            134
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(16Q23.1) MUTATED    16   0   1   0
  DEL PEAK 26(16Q23.1) WILD-TYPE 105   2  11   3
D51V10, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  R0                           16                            105
  R1                            0                              2
  R2                            1                             11
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D51V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(16Q23.1) MUTATED       0                         0    12
  DEL PEAK 26(16Q23.1) WILD-TYPE     1                         3    69
D51V12, multiclass
                           clus
vv                          DEL PEAK 26(16Q23.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               12
                           clus
vv                          DEL PEAK 26(16Q23.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(52) Variable = DEL PEAK 27(17P11.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 27(17P11.2) MUTATED   86 14
  DEL PEAK 27(17P11.2) WILD-TYPE 42  8
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           100                             50 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                            14                              8 
$`DEL PEAK 27(17P11.2) MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       17.95        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AG-3575 TCGA-AG-3578 
       37.74        14.50        15.39        20.02        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
        7.07         1.02        24.00         1.02        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
        2.01         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 
        1.02        32.98         0.99         1.02        17.03        35.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
        1.02        48.03        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       14.04         1.02        17.03        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       23.01        37.02        15.95         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 
       70.03        64.01        51.98         1.94        41.00         0.49 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72         4.60        10.19         6.05         6.05 
TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 
        6.97        13.97         7.99        11.01        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        7.10        30.05        13.05        10.06         5.29       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 
        2.40        20.91        17.00        18.28        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 TCGA-EI-7004 
       16.31        16.41        11.51        10.78        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 
        9.96        37.51        31.30        14.86         0.39         0.69 
TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 
        0.53         0.76         0.46        55.76 

$`DEL PEAK 27(17P11.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3580 
       24.13        10.39         8.45        10.39        36.03         8.02 
TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3612 TCGA-AG-3728 
        2.01        50.04        12.03         6.05        19.99        29.98 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4022 
        0.99        19.99        36.95        13.02        14.01         0.99 
TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G 
       20.98        36.03         9.07        10.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 
       61.97        38.04         1.45         1.81         9.37         4.73 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 
       60.03        10.98        15.02        12.99        12.00        36.00 
TCGA-DC-6681 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 
       12.95        32.61        20.55        19.96        15.85         8.61 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6233 
       13.64        17.46         1.02         0.66         1.12        18.28 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                          0.39                           0.66 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                        129.27                          61.97 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                        14.680                         13.825 
[1] "0.4 - 129.3 (14.7)" "0.7 - 62.0 (13.8)" 
[1] "hr=" "1.1"
D52V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 27(17P11.2) MUTATED        17        5        29         2         1
  DEL PEAK 27(17P11.2) WILD-TYPE      13        3         9         0         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 27(17P11.2) MUTATED           4          5         15         11
  DEL PEAK 27(17P11.2) WILD-TYPE         1          4          8          3
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 27(17P11.2) MUTATED         12         7
  DEL PEAK 27(17P11.2) WILD-TYPE        6         2
D52V3, multiclass
            clus
vv           DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  STAGE I                              17                             13
  STAGE II                              5                              3
  STAGE IIA                            29                              9
  STAGE IIB                             2                              0
  STAGE IIC                             1                              1
  STAGE III                             4                              1
  STAGE IIIA                            5                              4
  STAGE IIIB                           15                              8
  STAGE IIIC                           11                              3
  STAGE IV                             12                              6
  STAGE IVA                             7                              2
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 27(17P11.2) MUTATED    2 20 76 12
  DEL PEAK 27(17P11.2) WILD-TYPE  7  9 33  2
D52V4, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  T1                            2                              7
  T2                           20                              9
  T3                           76                             33
  T4                           12                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 27(17P11.2) MUTATED   56 30 23
  DEL PEAK 27(17P11.2) WILD-TYPE 27 15  9
D52V5, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  N0                           56                             27
  N1                           30                             15
  N2                           23                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 27(17P11.2) MUTATED   83 16   1  9
  DEL PEAK 27(17P11.2) WILD-TYPE 40  6   1  4
D52V6, multiclass
     clus
vv    DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  M0                            83                             40
  M1                            16                              6
  M1A                            1                              1
  MX                             9                              4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V7, binary
                                cls
clus                              0  1
  DEL PEAK 27(17P11.2) MUTATED   52 58
  DEL PEAK 27(17P11.2) WILD-TYPE 22 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED     52   58
  DEL PEAK 27(17P11.2) WILD-TYPE   22   30
        clus
vv       DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  FEMALE                           52                             22
  MALE                             58                             30
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                              0  1
  DEL PEAK 27(17P11.2) MUTATED   99  6
  DEL PEAK 27(17P11.2) WILD-TYPE 44  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED     99    6
  DEL PEAK 27(17P11.2) WILD-TYPE   44    7
                                clus
vv                               DEL PEAK 27(17P11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    99
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 27(17P11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      44
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED     4 106
  DEL PEAK 27(17P11.2) WILD-TYPE   2  50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED      4  106
  DEL PEAK 27(17P11.2) WILD-TYPE    2   50
     clus
vv    DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  NO                             4                              2
  YES                          106                             50
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 27(17P11.2) MUTATED   80  2  9  2
  DEL PEAK 27(17P11.2) WILD-TYPE 41  0  3  1
D52V10, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  R0                           80                             41
  R1                            2                              0
  R2                            9                              3
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D52V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(17P11.2) MUTATED       1                         0    56
  DEL PEAK 27(17P11.2) WILD-TYPE     0                         3    25
D52V12, multiclass
                           clus
vv                          DEL PEAK 27(17P11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               56
                           clus
vv                          DEL PEAK 27(17P11.2) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(53) Variable = DEL PEAK 28(18Q21.2) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 28(18Q21.2) MUTATED   112  19
  DEL PEAK 28(18Q21.2) WILD-TYPE  16   3
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                           131                             19 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                            19                              3 
$`DEL PEAK 28(18Q21.2) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       12.72        37.74        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       10.39        36.03        12.00        32.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
        2.01        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 
       50.04         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
        0.99        29.98         1.02        32.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        36.95        17.03        35.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         0.99        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N 
       37.02        15.95         9.07         1.02        12.00        31.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04         0.49         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        1.81        10.19         6.05         6.05         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        4.73        13.97        60.03         7.99        10.98        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02        12.99        12.00        13.97        15.02        36.00 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        7.10        30.05        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
      126.44        41.36        57.24       129.27        24.13        51.48 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        0.49         2.40        20.55        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       15.85        17.69        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       10.78        13.64        11.97         8.45        37.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       14.86         0.39         1.02         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.46        18.28        55.76        47.08        26.43 

$`DEL PEAK 28(18Q21.2) WILD-TYPE`
TCGA-AF-5654 TCGA-AG-3580 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 
        8.45         8.02        12.03        19.99         0.99        13.02 
TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       14.01        20.98        36.03        49.97        61.97         1.45 
TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 
       32.61        19.96         8.61        17.46         9.96         0.53 
TCGA-F5-6861 
        1.12 

  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                          0.39                           0.53 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                        129.27                          61.97 
  DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE 
                         14.86                          13.02 
[1] "0.4 - 129.3 (14.9)" "0.5 - 62.0 (13.0)" 
[1] "hr=" "1.2"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 28(18Q21.2) MUTATED        22        7        34         2         2
  DEL PEAK 28(18Q21.2) WILD-TYPE       8        1         4         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 28(18Q21.2) MUTATED           5          6         23         12
  DEL PEAK 28(18Q21.2) WILD-TYPE         0          3          0          2
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 28(18Q21.2) MUTATED         18         9
  DEL PEAK 28(18Q21.2) WILD-TYPE        0         0
D53V3, multiclass
            clus
vv           DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  STAGE I                              22                              8
  STAGE II                              7                              1
  STAGE IIA                            34                              4
  STAGE IIB                             2                              0
  STAGE IIC                             2                              0
  STAGE III                             5                              0
  STAGE IIIA                            6                              3
  STAGE IIIB                           23                              0
  STAGE IIIC                           12                              2
  STAGE IV                             18                              0
  STAGE IVA                             9                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  DEL PEAK 28(18Q21.2) MUTATED     5  23 101  13
  DEL PEAK 28(18Q21.2) WILD-TYPE   4   6   8   1
D53V4, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  T1                            5                              4
  T2                           23                              6
  T3                          101                              8
  T4                           13                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 28(18Q21.2) MUTATED   68 43 30
  DEL PEAK 28(18Q21.2) WILD-TYPE 15  2  2
D53V5, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  N0                           68                             15
  N1                           43                              2
  N2                           30                              2
[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"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 28(18Q21.2) MUTATED   105  22   2  12
  DEL PEAK 28(18Q21.2) WILD-TYPE  18   0   0   1
D53V6, multiclass
     clus
vv    DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  M0                           105                             18
  M1                            22                              0
  M1A                            2                              0
  MX                            12                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V7, binary
                                cls
clus                              0  1
  DEL PEAK 28(18Q21.2) MUTATED   65 78
  DEL PEAK 28(18Q21.2) WILD-TYPE  9 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED     65   78
  DEL PEAK 28(18Q21.2) WILD-TYPE    9   10
        clus
vv       DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  FEMALE                           65                              9
  MALE                             78                             10
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED   126  12
  DEL PEAK 28(18Q21.2) WILD-TYPE  17   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED    126   12
  DEL PEAK 28(18Q21.2) WILD-TYPE   17    1
                                clus
vv                               DEL PEAK 28(18Q21.2) MUTATED
  RECTAL ADENOCARCINOMA                                   126
  RECTAL MUCINOUS ADENOCARCINOMA                           12
                                clus
vv                               DEL PEAK 28(18Q21.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      17
  RECTAL MUCINOUS ADENOCARCINOMA                              1
[1] 2 2
[1] FALSE
D53V9, binary
                                cls
clus                               0   1
  DEL PEAK 28(18Q21.2) MUTATED     6 137
  DEL PEAK 28(18Q21.2) WILD-TYPE   0  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(18Q21.2) MUTATED      6  137
  DEL PEAK 28(18Q21.2) WILD-TYPE    0   19
     clus
vv    DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  NO                             6                              0
  YES                          137                             19
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 28(18Q21.2) MUTATED   104   2  12   3
  DEL PEAK 28(18Q21.2) WILD-TYPE  17   0   0   0
D53V10, multiclass
    clus
vv   DEL PEAK 28(18Q21.2) MUTATED DEL PEAK 28(18Q21.2) WILD-TYPE
  R0                          104                             17
  R1                            2                              0
  R2                           12                              0
  RX                            3                              0
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D53V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(18Q21.2) MUTATED       1                         3    72
  DEL PEAK 28(18Q21.2) WILD-TYPE     0                         0     9
D53V12, multiclass
                           clus
vv                          DEL PEAK 28(18Q21.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               72
                           clus
vv                          DEL PEAK 28(18Q21.2) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                  9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 29(18Q22.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(18Q22.1) MUTATED   108  19
  DEL PEAK 29(18Q22.1) WILD-TYPE  20   3
  DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE 
                           127                             23 
  DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE 
                            19                              3 
$`DEL PEAK 29(18Q22.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        17.95        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       12.72        37.74        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       10.39        36.03        12.00        32.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        2.01        24.00        46.03        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
       29.98        32.98         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       28.04        36.03        14.04         1.02        17.03         0.99 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       13.94         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
        9.07         1.02        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 
        0.49         0.69         0.72         4.60        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        13.97        60.03 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.99        10.98        11.01        15.02        12.99        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        36.00         7.10        30.05        12.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       13.05        10.06       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         0.49         2.40        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 
       17.00        18.28        15.85        17.69        16.34        16.31 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 
       16.41        11.51        10.78        13.64        11.97         8.45 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       37.51        31.30        14.86         0.39         1.02         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76         0.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 29(18Q22.1) WILD-TYPE`
TCGA-AF-5654 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3731 
        8.45         8.02         1.02        12.03        19.99         1.02 
TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A025 
        0.99        13.02        14.01        20.98        36.03        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 
       61.97         1.45         1.81         5.29        32.61        19.96 
TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
        8.61        17.46         9.96         0.53         1.12 

  DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE 
                          0.39                           0.53 
  DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE 
                        129.27                          61.97 
  DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE 
                         15.02                           9.96 
[1] "0.4 - 129.3 (15.0)" "0.5 - 62.0 (10.0)" 
[1] "hr=" "1.1"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 29(18Q22.1) MUTATED        22        6        34         2         2
  DEL PEAK 29(18Q22.1) WILD-TYPE       8        2         4         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 29(18Q22.1) MUTATED           3          6         22         12
  DEL PEAK 29(18Q22.1) WILD-TYPE         2          3          1          2
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 29(18Q22.1) MUTATED         17         9
  DEL PEAK 29(18Q22.1) WILD-TYPE        1         0
D54V3, multiclass
            clus
vv           DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE
  STAGE I                              22                              8
  STAGE II                              6                              2
  STAGE IIA                            34                              4
  STAGE IIB                             2                              0
  STAGE IIC                             2                              0
  STAGE III                             3                              2
  STAGE IIIA                            6                              3
  STAGE IIIB                           22                              1
  STAGE IIIC                           12                              2
  STAGE IV                             17                              1
  STAGE IVA                             9                              0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 29(18Q22.1) MUTATED    5 23 96 13
  DEL PEAK 29(18Q22.1) WILD-TYPE  4  6 13  1
D54V4, multiclass
    clus
vv   DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE
  T1                            5                              4
  T2                           23                              6
  T3                           96                             13
  T4                           13                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 29(18Q22.1) MUTATED   67 40 29
  DEL PEAK 29(18Q22.1) WILD-TYPE 16  5  3
D54V5, multiclass
    clus
vv   DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE
  N0                           67                             16
  N1                           40                              5
  N2                           29                              3
[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"
                                vv
clus                              M0  M1 M1A  MX
  DEL PEAK 29(18Q22.1) MUTATED   102  21   2  11
  DEL PEAK 29(18Q22.1) WILD-TYPE  21   1   0   2
D54V6, multiclass
     clus
vv    DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE
  M0                           102                             21
  M1                            21                              1
  M1A                            2                              0
  MX                            11                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V7, binary
                                cls
clus                              0  1
  DEL PEAK 29(18Q22.1) MUTATED   64 74
  DEL PEAK 29(18Q22.1) WILD-TYPE 10 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q22.1) MUTATED     64   74
  DEL PEAK 29(18Q22.1) WILD-TYPE   10   14
        clus
vv       DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE
  FEMALE                           64                             10
  MALE                             74                             14
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q22.1) MUTATED   124  10
  DEL PEAK 29(18Q22.1) WILD-TYPE  19   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q22.1) MUTATED    124   10
  DEL PEAK 29(18Q22.1) WILD-TYPE   19    3
                                clus
vv                               DEL PEAK 29(18Q22.1) MUTATED
  RECTAL ADENOCARCINOMA                                   124
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 29(18Q22.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      19
  RECTAL MUCINOUS ADENOCARCINOMA                              3
[1] 2 2
[1] FALSE
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q22.1) MUTATED     6 132
  DEL PEAK 29(18Q22.1) WILD-TYPE   0  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q22.1) MUTATED      6  132
  DEL PEAK 29(18Q22.1) WILD-TYPE    0   24
     clus
vv    DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE
  NO                             6                              0
  YES                          132                             24
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(18Q22.1) MUTATED   102   2  11   2
  DEL PEAK 29(18Q22.1) WILD-TYPE  19   0   1   1
D54V10, multiclass
    clus
vv   DEL PEAK 29(18Q22.1) MUTATED DEL PEAK 29(18Q22.1) WILD-TYPE
  R0                          102                             19
  R1                            2                              0
  R2                           11                              1
  RX                            2                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D54V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(18Q22.1) MUTATED       0                         3    70
  DEL PEAK 29(18Q22.1) WILD-TYPE     1                         0    11
D54V12, multiclass
                           clus
vv                          DEL PEAK 29(18Q22.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               70
                           clus
vv                          DEL PEAK 29(18Q22.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 11
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(55) Variable = DEL PEAK 30(19P13.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(19P13.3) MUTATED    24   7
  DEL PEAK 30(19P13.3) WILD-TYPE 104  15
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                            31                            119 
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                             7                             15 
$`DEL PEAK 30(19P13.3) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-4110 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3608 
       24.13        17.95        14.50        12.00         1.02        15.95 
TCGA-AG-3732 TCGA-AG-3893 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01Y 
       32.98        35.01        17.03        15.95         9.07        64.01 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5869 
        6.05         6.05         4.73        13.97        11.01        12.99 
TCGA-DC-6155 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
       13.97         7.10         5.29       129.27        24.13        51.48 
TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6885 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       17.00        16.34        13.64        31.30        14.86         0.39 
TCGA-G5-6233 
       18.28 

$`DEL PEAK 30(19P13.3) WILD-TYPE`
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       17.23        43.04        13.55        19.10        12.72        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 
       10.39         8.45        15.39        20.02        10.39        36.03 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         8.02         7.07         2.01        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       46.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        19.99        19.99         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 
        1.02         0.99         0.99        19.99         1.02        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       17.03        13.02        14.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 
       19.99        28.04        36.03        14.04         1.02         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       20.98        13.94         6.02        25.97        23.01        37.02 
TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A020 
       36.03         1.02        12.00        31.00        70.03        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       51.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04         0.49         1.45         0.69         0.72         4.60 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        1.81        10.19         6.97         9.37        60.03         7.99 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       10.98        15.02        12.00        15.02        36.00        30.05 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       12.95        13.05        10.06       126.44        41.36        57.24 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       32.61         0.49         2.40        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        17.46        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       37.51         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        55.76        47.08        26.43 

  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                          0.39                           0.46 
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE 
                         14.86                          14.01 
[1] "0.4 - 129.3 (14.9)" "0.5 - 126.4 (14.0)"
[1] "hr=" "1.8"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 30(19P13.3) MUTATED         5        3         8         0         1
  DEL PEAK 30(19P13.3) WILD-TYPE      25        5        30         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 30(19P13.3) MUTATED           1          2          4          3
  DEL PEAK 30(19P13.3) WILD-TYPE         4          7         19         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 30(19P13.3) MUTATED          5         4
  DEL PEAK 30(19P13.3) WILD-TYPE       13         5
D55V3, multiclass
            clus
vv           DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  STAGE I                               5                             25
  STAGE II                              3                              5
  STAGE IIA                             8                             30
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             1                              4
  STAGE IIIA                            2                              7
  STAGE IIIB                            4                             19
  STAGE IIIC                            3                             11
  STAGE IV                              5                             13
  STAGE IVA                             4                              5
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 30(19P13.3) MUTATED    0  6 28  2
  DEL PEAK 30(19P13.3) WILD-TYPE  9 23 81 12
D55V4, multiclass
    clus
vv   DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  T1                            0                              9
  T2                            6                             23
  T3                           28                             81
  T4                            2                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 30(19P13.3) MUTATED   16 12  8
  DEL PEAK 30(19P13.3) WILD-TYPE 67 33 24
D55V5, multiclass
    clus
vv   DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  N0                           16                             67
  N1                           12                             33
  N2                            8                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 30(19P13.3) MUTATED   27  8   0  1
  DEL PEAK 30(19P13.3) WILD-TYPE 96 14   2 12
D55V6, multiclass
     clus
vv    DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  M0                            27                             96
  M1                             8                             14
  M1A                            0                              2
  MX                             1                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V7, binary
                                cls
clus                              0  1
  DEL PEAK 30(19P13.3) MUTATED   16 20
  DEL PEAK 30(19P13.3) WILD-TYPE 58 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(19P13.3) MUTATED     16   20
  DEL PEAK 30(19P13.3) WILD-TYPE   58   68
        clus
vv       DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  FEMALE                           16                             58
  MALE                             20                             68
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                               0   1
  DEL PEAK 30(19P13.3) MUTATED    33   1
  DEL PEAK 30(19P13.3) WILD-TYPE 110  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(19P13.3) MUTATED     33    1
  DEL PEAK 30(19P13.3) WILD-TYPE  110   12
                                clus
vv                               DEL PEAK 30(19P13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    33
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 30(19P13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     110
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(19P13.3) MUTATED     1  35
  DEL PEAK 30(19P13.3) WILD-TYPE   5 121
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(19P13.3) MUTATED      1   35
  DEL PEAK 30(19P13.3) WILD-TYPE    5  121
     clus
vv    DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  NO                             1                              5
  YES                           35                            121
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 30(19P13.3) MUTATED   24  0  3  1
  DEL PEAK 30(19P13.3) WILD-TYPE 97  2  9  2
D55V10, multiclass
    clus
vv   DEL PEAK 30(19P13.3) MUTATED DEL PEAK 30(19P13.3) WILD-TYPE
  R0                           24                             97
  R1                            0                              2
  R2                            3                              9
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D55V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 30(19P13.3) MUTATED       1                         1    19
  DEL PEAK 30(19P13.3) WILD-TYPE     0                         2    62
D55V12, multiclass
                           clus
vv                          DEL PEAK 30(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               19
                           clus
vv                          DEL PEAK 30(19P13.3) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(56) Variable = DEL PEAK 31(20P12.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 31(20P12.1) MUTATED   42 14
  DEL PEAK 31(20P12.1) WILD-TYPE 86  8
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            56                             94 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                            14                              8 
$`DEL PEAK 31(20P12.1) MUTATED`
TCGA-AF-2689 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       17.95        10.39        36.03        32.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3608 
        2.01        24.00        34.03        50.04         6.05        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3883 
       19.99         7.99         0.99        29.98         0.99         1.02 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A014 
       32.02        36.03         1.02         0.99        13.94        15.95 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 
        1.02        12.00        31.00        70.03        64.01         1.94 
TCGA-AG-A02G TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 
       38.96         1.45         0.69         4.73        60.03        10.98 
TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC 
       12.00         7.10        30.05        13.05        10.06        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6512 
       57.24        24.13        32.61         2.40        15.85        17.69 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
       16.41        11.51        10.78         8.45        31.30        14.86 
TCGA-F5-6864 TCGA-G5-6641 
        0.46        26.43 

$`DEL PEAK 31(20P12.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 
       12.00         8.02         1.02        46.03         2.01        12.03 
TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 
        0.99        19.99         1.02        32.98         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       48.03        19.99        28.04        14.04        17.03        20.98 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        36.03         9.07 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98        49.97        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.49         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
        6.05         6.97         9.37        13.97         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       15.02        12.99        13.97        15.02        36.00        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
        5.29       126.44       129.27        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
        8.61        13.64        17.46        11.97         9.96        37.51 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76        18.28        55.76        47.08 

  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                          0.46                           0.39 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                         70.03                         129.27 
  DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE 
                         14.40                          14.27 
[1] "0.5 - 70.0 (14.4)"  "0.4 - 129.3 (14.3)"
[1] "hr=" "2.8"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 31(20P12.1) MUTATED         9        5        13         0         1
  DEL PEAK 31(20P12.1) WILD-TYPE      21        3        25         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 31(20P12.1) MUTATED           1          4          8          7
  DEL PEAK 31(20P12.1) WILD-TYPE         4          5         15          7
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 31(20P12.1) MUTATED          8         3
  DEL PEAK 31(20P12.1) WILD-TYPE       10         6
D56V3, multiclass
            clus
vv           DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  STAGE I                               9                             21
  STAGE II                              5                              3
  STAGE IIA                            13                             25
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             1                              4
  STAGE IIIA                            4                              5
  STAGE IIIB                            8                             15
  STAGE IIIC                            7                              7
  STAGE IV                              8                             10
  STAGE IVA                             3                              6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 31(20P12.1) MUTATED    2 11 42  5
  DEL PEAK 31(20P12.1) WILD-TYPE  7 18 67  9
D56V4, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  T1                            2                              7
  T2                           11                             18
  T3                           42                             67
  T4                            5                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 31(20P12.1) MUTATED   30 17 13
  DEL PEAK 31(20P12.1) WILD-TYPE 53 28 19
D56V5, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  N0                           30                             53
  N1                           17                             28
  N2                           13                             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 31(20P12.1) MUTATED   47 10   0  3
  DEL PEAK 31(20P12.1) WILD-TYPE 76 12   2 10
D56V6, multiclass
     clus
vv    DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  M0                            47                             76
  M1                            10                             12
  M1A                            0                              2
  MX                             3                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V7, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED   31 29
  DEL PEAK 31(20P12.1) WILD-TYPE 43 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     31   29
  DEL PEAK 31(20P12.1) WILD-TYPE   43   59
        clus
vv       DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  FEMALE                           31                             43
  MALE                             29                             59
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED   55  5
  DEL PEAK 31(20P12.1) WILD-TYPE 88  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED     55    5
  DEL PEAK 31(20P12.1) WILD-TYPE   88    8
                                clus
vv                               DEL PEAK 31(20P12.1) MUTATED
  RECTAL ADENOCARCINOMA                                    55
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 31(20P12.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      88
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
D56V9, binary
                                cls
clus                              0  1
  DEL PEAK 31(20P12.1) MUTATED    0 60
  DEL PEAK 31(20P12.1) WILD-TYPE  6 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(20P12.1) MUTATED      0   60
  DEL PEAK 31(20P12.1) WILD-TYPE    6   96
     clus
vv    DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  NO                             0                              6
  YES                           60                             96
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 31(20P12.1) MUTATED   45  1  7  1
  DEL PEAK 31(20P12.1) WILD-TYPE 76  1  5  2
D56V10, multiclass
    clus
vv   DEL PEAK 31(20P12.1) MUTATED DEL PEAK 31(20P12.1) WILD-TYPE
  R0                           45                             76
  R1                            1                              1
  R2                            7                              5
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D56V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(20P12.1) MUTATED       0                         1    26
  DEL PEAK 31(20P12.1) WILD-TYPE     1                         2    55
D56V12, multiclass
                           clus
vv                          DEL PEAK 31(20P12.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               26
                           clus
vv                          DEL PEAK 31(20P12.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(57) Variable = DEL PEAK 32(20P12.1) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 32(20P12.1) MUTATED   42 14
  DEL PEAK 32(20P12.1) WILD-TYPE 86  8
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                            56                             94 
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                            14                              8 
$`DEL PEAK 32(20P12.1) MUTATED`
TCGA-AF-2689 TCGA-AF-3913 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       17.95        10.39        36.03        32.02         7.07         1.02 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3608 
        2.01        24.00        34.03        50.04         6.05        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3883 
       19.99         7.99         0.99        29.98         0.99         1.02 
TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A014 
       32.02        36.03         1.02         0.99        13.94        15.95 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 
        1.02        12.00        31.00        70.03        64.01         1.94 
TCGA-AG-A02G TCGA-AH-6547 TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 
       38.96         1.45         0.69         4.73        60.03        10.98 
TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC 
       12.00         7.10        30.05        13.05        10.06        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6512 
       57.24        24.13        32.61         2.40        15.85        17.69 
TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 
       16.41        11.51        10.78         8.45        31.30        14.86 
TCGA-F5-6864 TCGA-G5-6641 
        0.46        26.43 

$`DEL PEAK 32(20P12.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       24.13        17.23        43.04        13.55        19.10        12.72 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 
       12.00         8.02         1.02        46.03         2.01        12.03 
TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 
        0.99        19.99         1.02        32.98         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       36.95        17.03        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A002 
       48.03        19.99        28.04        14.04        17.03        20.98 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 
        6.02        25.97        23.01        37.02        36.03         9.07 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       10.98        51.98        49.97        61.97        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.49         0.72         4.60         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
        6.05         6.97         9.37        13.97         7.99        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       15.02        12.99        13.97        15.02        36.00        12.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
        5.29       126.44       129.27        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        16.34        16.31 
TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 
        8.61        13.64        17.46        11.97         9.96        37.51 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76        18.28        55.76        47.08 

  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                          0.46                           0.39 
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                         70.03                         129.27 
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                         14.40                          14.27 
[1] "0.5 - 70.0 (14.4)"  "0.4 - 129.3 (14.3)"
[1] "hr=" "2.8"
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 32(20P12.1) MUTATED         9        5        13         0         1
  DEL PEAK 32(20P12.1) WILD-TYPE      21        3        25         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 32(20P12.1) MUTATED           1          4          8          7
  DEL PEAK 32(20P12.1) WILD-TYPE         4          5         15          7
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 32(20P12.1) MUTATED          8         3
  DEL PEAK 32(20P12.1) WILD-TYPE       10         6
D57V3, multiclass
            clus
vv           DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  STAGE I                               9                             21
  STAGE II                              5                              3
  STAGE IIA                            13                             25
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             1                              4
  STAGE IIIA                            4                              5
  STAGE IIIB                            8                             15
  STAGE IIIC                            7                              7
  STAGE IV                              8                             10
  STAGE IVA                             3                              6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 32(20P12.1) MUTATED    2 11 42  5
  DEL PEAK 32(20P12.1) WILD-TYPE  7 18 67  9
D57V4, multiclass
    clus
vv   DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  T1                            2                              7
  T2                           11                             18
  T3                           42                             67
  T4                            5                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 32(20P12.1) MUTATED   30 17 13
  DEL PEAK 32(20P12.1) WILD-TYPE 53 28 19
D57V5, multiclass
    clus
vv   DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  N0                           30                             53
  N1                           17                             28
  N2                           13                             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 32(20P12.1) MUTATED   47 10   0  3
  DEL PEAK 32(20P12.1) WILD-TYPE 76 12   2 10
D57V6, multiclass
     clus
vv    DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  M0                            47                             76
  M1                            10                             12
  M1A                            0                              2
  MX                             3                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V7, binary
                                cls
clus                              0  1
  DEL PEAK 32(20P12.1) MUTATED   31 29
  DEL PEAK 32(20P12.1) WILD-TYPE 43 59
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(20P12.1) MUTATED     31   29
  DEL PEAK 32(20P12.1) WILD-TYPE   43   59
        clus
vv       DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  FEMALE                           31                             43
  MALE                             29                             59
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                              0  1
  DEL PEAK 32(20P12.1) MUTATED   55  5
  DEL PEAK 32(20P12.1) WILD-TYPE 88  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(20P12.1) MUTATED     55    5
  DEL PEAK 32(20P12.1) WILD-TYPE   88    8
                                clus
vv                               DEL PEAK 32(20P12.1) MUTATED
  RECTAL ADENOCARCINOMA                                    55
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 32(20P12.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      88
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
D57V9, binary
                                cls
clus                              0  1
  DEL PEAK 32(20P12.1) MUTATED    0 60
  DEL PEAK 32(20P12.1) WILD-TYPE  6 96
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(20P12.1) MUTATED      0   60
  DEL PEAK 32(20P12.1) WILD-TYPE    6   96
     clus
vv    DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  NO                             0                              6
  YES                           60                             96
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 32(20P12.1) MUTATED   45  1  7  1
  DEL PEAK 32(20P12.1) WILD-TYPE 76  1  5  2
D57V10, multiclass
    clus
vv   DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  R0                           45                             76
  R1                            1                              1
  R2                            7                              5
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D57V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(20P12.1) MUTATED       0                         1    26
  DEL PEAK 32(20P12.1) WILD-TYPE     1                         2    55
D57V12, multiclass
                           clus
vv                          DEL PEAK 32(20P12.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               26
                           clus
vv                          DEL PEAK 32(20P12.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(58) Variable = DEL PEAK 33(21Q11.2) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 33(21Q11.2) MUTATED   55 12
  DEL PEAK 33(21Q11.2) WILD-TYPE 73 10
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                            67                             83 
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                            12                             10 
$`DEL PEAK 33(21Q11.2) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 
       24.13        17.95        17.23        19.10        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       20.02        10.39        36.03        12.00         7.07         1.02 
TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3728 
       24.00        46.03        34.03        12.03        19.99        29.98 
TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 
       19.99        17.03         1.02        48.03        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       14.04        17.03        12.00        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       10.98         1.94        38.96        61.97        41.00         0.49 
TCGA-AH-6643 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6157 
        0.69         4.73        13.97        10.98        13.97        36.00 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG 
        7.10        13.05        10.06       126.44        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 
       32.61         0.49         2.40        20.55        20.91        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       17.69        16.34        16.41        11.97         8.45        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6233 
        0.39         1.02         0.66         0.53         0.76        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 33(21Q11.2) WILD-TYPE`
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 
       43.04        13.55        12.72        37.74        10.39         8.45 
TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
       32.02         8.02         2.01         1.02         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        1.02        32.98         0.99         0.99         1.02        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4007 
       13.02        35.01        14.01        32.02        28.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
        0.99        20.98        13.94         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A023 
       37.02        15.95        36.03         9.07         1.02        51.98 
TCGA-AG-A025 TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       49.97        38.04         1.45         0.72         4.60         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       10.19         6.05         6.05         6.97         9.37        60.03 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        7.99        11.01        15.02        12.99        12.00        15.02 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF 
       30.05        12.95         5.29        41.36       129.27        24.13 
TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       19.96        17.00        18.28        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 
       10.78        13.64        17.46         9.96        37.51        14.86 
TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         1.12         0.46        55.76        47.08 

  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                          0.39                           0.46 
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                        126.44                         129.27 
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                         17.03                          12.99 
[1] "0.4 - 126.4 (17.0)" "0.5 - 129.3 (13.0)"
[1] "hr=" "1.2"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 33(21Q11.2) MUTATED        11        6        15         1         1
  DEL PEAK 33(21Q11.2) WILD-TYPE      19        2        23         1         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 33(21Q11.2) MUTATED           3          6         12          4
  DEL PEAK 33(21Q11.2) WILD-TYPE         2          3         11         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 33(21Q11.2) MUTATED          8         3
  DEL PEAK 33(21Q11.2) WILD-TYPE       10         6
D58V3, multiclass
            clus
vv           DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  STAGE I                              11                             19
  STAGE II                              6                              2
  STAGE IIA                            15                             23
  STAGE IIB                             1                              1
  STAGE IIC                             1                              1
  STAGE III                             3                              2
  STAGE IIIA                            6                              3
  STAGE IIIB                           12                             11
  STAGE IIIC                            4                             10
  STAGE IV                              8                             10
  STAGE IVA                             3                              6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 33(21Q11.2) MUTATED    1 17 47  6
  DEL PEAK 33(21Q11.2) WILD-TYPE  8 12 62  8
D58V4, multiclass
    clus
vv   DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  T1                            1                              8
  T2                           17                             12
  T3                           47                             62
  T4                            6                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 33(21Q11.2) MUTATED   34 24 13
  DEL PEAK 33(21Q11.2) WILD-TYPE 49 21 19
D58V5, multiclass
    clus
vv   DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  N0                           34                             49
  N1                           24                             21
  N2                           13                             19
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 33(21Q11.2) MUTATED   56  9   0  6
  DEL PEAK 33(21Q11.2) WILD-TYPE 67 13   2  7
D58V6, multiclass
     clus
vv    DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  M0                            56                             67
  M1                             9                             13
  M1A                            0                              2
  MX                             6                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V7, binary
                                cls
clus                              0  1
  DEL PEAK 33(21Q11.2) MUTATED   31 40
  DEL PEAK 33(21Q11.2) WILD-TYPE 43 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(21Q11.2) MUTATED     31   40
  DEL PEAK 33(21Q11.2) WILD-TYPE   43   48
        clus
vv       DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  FEMALE                           31                             43
  MALE                             40                             48
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                              0  1
  DEL PEAK 33(21Q11.2) MUTATED   64  3
  DEL PEAK 33(21Q11.2) WILD-TYPE 79 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(21Q11.2) MUTATED     64    3
  DEL PEAK 33(21Q11.2) WILD-TYPE   79   10
                                clus
vv                               DEL PEAK 33(21Q11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    64
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 33(21Q11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      79
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
D58V9, binary
                                cls
clus                              0  1
  DEL PEAK 33(21Q11.2) MUTATED    3 68
  DEL PEAK 33(21Q11.2) WILD-TYPE  3 88
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(21Q11.2) MUTATED      3   68
  DEL PEAK 33(21Q11.2) WILD-TYPE    3   88
     clus
vv    DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  NO                             3                              3
  YES                           68                             88
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 33(21Q11.2) MUTATED   53  1  4  0
  DEL PEAK 33(21Q11.2) WILD-TYPE 68  1  8  3
D58V10, multiclass
    clus
vv   DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  R0                           53                             68
  R1                            1                              1
  R2                            4                              8
  RX                            0                              3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D58V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(21Q11.2) MUTATED       0                         1    39
  DEL PEAK 33(21Q11.2) WILD-TYPE     1                         2    42
D58V12, multiclass
                           clus
vv                          DEL PEAK 33(21Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               39
                           clus
vv                          DEL PEAK 33(21Q11.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(59) Variable = DEL PEAK 34(22Q13.31) MUTATION ANALYSIS
D59V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 34(22Q13.31) MUTATED   47 11
  DEL PEAK 34(22Q13.31) WILD-TYPE 81 11
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             58                              92 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             11                              11 
$`DEL PEAK 34(22Q13.31) MUTATED`
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3575 
       13.55        19.10        14.50        15.39        10.39        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3593 
       32.02         7.07         1.02         2.01        24.00        34.03 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-3909 
       29.98         1.02        19.99         1.02         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       28.04        36.03        14.04        25.97        23.01        12.00 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6644 
       10.98         1.94        38.96        41.00         0.49         0.72 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 
       10.19         6.05         4.73        13.97        10.98        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
       12.99        13.97         7.10        30.05        13.05        10.06 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 
       41.36       129.27        51.48        32.61         2.40        20.55 
TCGA-EI-6508 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6810 
       20.91        17.69        16.41        11.97        14.86         0.39 
TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.76        18.28        26.43 

$`DEL PEAK 34(22Q13.31) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 
       24.13        17.95        17.23        43.04        12.72        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3586 
       10.39         8.45        20.02        36.03         8.02         1.02 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       46.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 
       15.95        19.99        19.99         7.99         0.99        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        0.99         0.99        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       14.01        48.03        32.02         1.02        17.03         0.99 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       20.98        13.94         6.02        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        9.07         1.02        31.00        70.03        64.01        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       49.97        61.97        38.04         1.45         0.69         4.60 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        1.81         6.05         6.97         9.37        60.03         7.99 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 
       15.02        12.00        15.02        36.00        12.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6509 
      126.44        57.24        24.13         0.49        19.96        17.00 
TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        16.34        16.31         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       10.78        13.64        17.46         8.45         9.96        37.51 
TCGA-F5-6571 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       31.30         1.02         0.69         0.53         1.12         0.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                           0.39                            0.46 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                         129.27                          126.44 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                         13.970                          15.435 
[1] "0.4 - 129.3 (14.0)" "0.5 - 126.4 (15.4)"
[1] "hr=" "2.3"
D59V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  DEL PEAK 34(22Q13.31) MUTATED        10        2        16         0
  DEL PEAK 34(22Q13.31) WILD-TYPE      20        6        22         2
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 34(22Q13.31) MUTATED           1         3          5         13
  DEL PEAK 34(22Q13.31) WILD-TYPE         1         2          4         10
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 34(22Q13.31) MUTATED            2       10         3
  DEL PEAK 34(22Q13.31) WILD-TYPE         12        8         6
D59V3, multiclass
            clus
vv           DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  STAGE I                               10                              20
  STAGE II                               2                               6
  STAGE IIA                             16                              22
  STAGE IIB                              0                               2
  STAGE IIC                              1                               1
  STAGE III                              3                               2
  STAGE IIIA                             5                               4
  STAGE IIIB                            13                              10
  STAGE IIIC                             2                              12
  STAGE IV                              10                               8
  STAGE IVA                              3                               6
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 34(22Q13.31) MUTATED    1 13 48  5
  DEL PEAK 34(22Q13.31) WILD-TYPE  8 16 61  9
D59V4, multiclass
    clus
vv   DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  T1                             1                               8
  T2                            13                              16
  T3                            48                              61
  T4                             5                               9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 34(22Q13.31) MUTATED   28 27 11
  DEL PEAK 34(22Q13.31) WILD-TYPE 55 18 21
D59V5, multiclass
    clus
vv   DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  N0                            28                              55
  N1                            27                              18
  N2                            11                              21
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              M0 M1 M1A MX
  DEL PEAK 34(22Q13.31) MUTATED   47 12   0  7
  DEL PEAK 34(22Q13.31) WILD-TYPE 76 10   2  6
D59V6, multiclass
     clus
vv    DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  M0                             47                              76
  M1                             12                              10
  M1A                             0                               2
  MX                              7                               6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V7, binary
                                 cls
clus                               0  1
  DEL PEAK 34(22Q13.31) MUTATED   28 39
  DEL PEAK 34(22Q13.31) WILD-TYPE 46 49
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.31) MUTATED     28   39
  DEL PEAK 34(22Q13.31) WILD-TYPE   46   49
        clus
vv       DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  FEMALE                            28                              46
  MALE                              39                              49
[1] 2 2
[1] FALSE
D59V8, binary
                                 cls
clus                               0  1
  DEL PEAK 34(22Q13.31) MUTATED   60  4
  DEL PEAK 34(22Q13.31) WILD-TYPE 83  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.31) MUTATED     60    4
  DEL PEAK 34(22Q13.31) WILD-TYPE   83    9
                                clus
vv                               DEL PEAK 34(22Q13.31) MUTATED
  RECTAL ADENOCARCINOMA                                     60
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               DEL PEAK 34(22Q13.31) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       83
  RECTAL MUCINOUS ADENOCARCINOMA                               9
[1] 2 2
[1] FALSE
D59V9, binary
                                 cls
clus                               0  1
  DEL PEAK 34(22Q13.31) MUTATED    3 64
  DEL PEAK 34(22Q13.31) WILD-TYPE  3 92
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.31) MUTATED      3   64
  DEL PEAK 34(22Q13.31) WILD-TYPE    3   92
     clus
vv    DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  NO                              3                               3
  YES                            64                              92
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 34(22Q13.31) MUTATED   46  1  7  0
  DEL PEAK 34(22Q13.31) WILD-TYPE 75  1  5  3
D59V10, multiclass
    clus
vv   DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  R0                            46                              75
  R1                             1                               1
  R2                             7                               5
  RX                             0                               3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D59V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 34(22Q13.31) MUTATED       0                         1    34
  DEL PEAK 34(22Q13.31) WILD-TYPE     1                         2    47
D59V12, multiclass
                           clus
vv                          DEL PEAK 34(22Q13.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                34
                           clus
vv                          DEL PEAK 34(22Q13.31) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  47
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(60) Variable = DEL PEAK 35(XP22.33) MUTATION ANALYSIS
D60V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(XP22.33) MUTATED    26   4
  DEL PEAK 35(XP22.33) WILD-TYPE 102  18
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                            30                            120 
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                             4                             18 
$`DEL PEAK 35(XP22.33) MUTATED`
TCGA-AF-2692 TCGA-AF-2693 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3593 
       13.55        19.10        12.00        32.02        24.00        34.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3893 TCGA-AG-4007 TCGA-AG-A008 
        2.01         6.05        32.98        35.01         1.02        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6544 TCGA-BM-6198 
        6.02        25.97        38.96        41.00         0.49        10.19 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6160 
        9.37        60.03        10.98        13.97        15.02        30.05 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
      129.27        32.61        11.97        37.51        31.30         0.39 

$`DEL PEAK 35(XP22.33) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 
       24.13        17.95        17.23        43.04        12.72        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50         8.45        15.39        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       36.03         8.02         7.07         1.02         2.01         1.02 
TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       46.03        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       19.99         7.99         0.99        29.98         1.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99        19.99         1.02        36.95        17.03        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00Y 
       36.03        14.04        17.03         0.99        20.98        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       37.02        15.95        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
       31.00        70.03        64.01        10.98        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
        1.94        61.97        38.04         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        4.60         1.81         6.05         6.05         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       13.97         7.99        11.01        15.02        12.99        12.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       36.00         7.10        12.95        13.05        10.06         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
      126.44        41.36        57.24        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        2.40        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       15.85        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       11.51        10.78        13.64        17.46         8.45         9.96 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       14.86         1.02         0.66         0.69         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76         0.46        18.28        55.76        47.08        26.43 

  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                          0.39                           0.46 
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                        17.060                         14.025 
[1] "0.4 - 129.3 (17.1)" "0.5 - 126.4 (14.0)"
[1] "hr=" "1.3"
D60V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 35(XP22.33) MUTATED         6        1        11         0         0
  DEL PEAK 35(XP22.33) WILD-TYPE      24        7        27         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 35(XP22.33) MUTATED           0          2          4          3
  DEL PEAK 35(XP22.33) WILD-TYPE         5          7         19         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 35(XP22.33) MUTATED          4         1
  DEL PEAK 35(XP22.33) WILD-TYPE       14         8
D60V3, multiclass
            clus
vv           DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  STAGE I                               6                             24
  STAGE II                              1                              7
  STAGE IIA                            11                             27
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             0                              5
  STAGE IIIA                            2                              7
  STAGE IIIB                            4                             19
  STAGE IIIC                            3                             11
  STAGE IV                              4                             14
  STAGE IVA                             1                              8
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 35(XP22.33) MUTATED    1  8 22  2
  DEL PEAK 35(XP22.33) WILD-TYPE  8 21 87 12
D60V4, multiclass
    clus
vv   DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  T1                            1                              8
  T2                            8                             21
  T3                           22                             87
  T4                            2                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 35(XP22.33) MUTATED   18  8  7
  DEL PEAK 35(XP22.33) WILD-TYPE 65 37 25
D60V5, multiclass
    clus
vv   DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  N0                           18                             65
  N1                            8                             37
  N2                            7                             25
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 M1A MX
  DEL PEAK 35(XP22.33) MUTATED   24  5   1  2
  DEL PEAK 35(XP22.33) WILD-TYPE 99 17   1 11
D60V6, multiclass
     clus
vv    DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  M0                            24                             99
  M1                             5                             17
  M1A                            1                              1
  MX                             2                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V7, binary
                                cls
clus                              0  1
  DEL PEAK 35(XP22.33) MUTATED   16 17
  DEL PEAK 35(XP22.33) WILD-TYPE 58 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XP22.33) MUTATED     16   17
  DEL PEAK 35(XP22.33) WILD-TYPE   58   71
        clus
vv       DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  FEMALE                           16                             58
  MALE                             17                             71
[1] 2 2
[1] FALSE
D60V8, binary
                                cls
clus                               0   1
  DEL PEAK 35(XP22.33) MUTATED    27   3
  DEL PEAK 35(XP22.33) WILD-TYPE 116  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XP22.33) MUTATED     27    3
  DEL PEAK 35(XP22.33) WILD-TYPE  116   10
                                clus
vv                               DEL PEAK 35(XP22.33) MUTATED
  RECTAL ADENOCARCINOMA                                    27
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 35(XP22.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     116
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
D60V9, binary
                                cls
clus                               0   1
  DEL PEAK 35(XP22.33) MUTATED     1  32
  DEL PEAK 35(XP22.33) WILD-TYPE   5 124
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XP22.33) MUTATED      1   32
  DEL PEAK 35(XP22.33) WILD-TYPE    5  124
     clus
vv    DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  NO                             1                              5
  YES                           32                            124
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 35(XP22.33) MUTATED   23  0  3  1
  DEL PEAK 35(XP22.33) WILD-TYPE 98  2  9  2
D60V10, multiclass
    clus
vv   DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  R0                           23                             98
  R1                            0                              2
  R2                            3                              9
  RX                            1                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D60V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 35(XP22.33) MUTATED       0                         0    16
  DEL PEAK 35(XP22.33) WILD-TYPE     1                         3    65
D60V12, multiclass
                           clus
vv                          DEL PEAK 35(XP22.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               16
                           clus
vv                          DEL PEAK 35(XP22.33) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 65
[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"
