[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/19775480/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/19781847/transformed.cor.cli.txt"

nPatients in clinical file=171, in cluster file=165, common to both=165
[1]  59 165
[1] "AMP PEAK  1(1Q21.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           48                           117 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           48                           117 
[1] "AMP PEAK  2(1Q32.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                           48                           117 
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                           48                           117 
[1] "AMP PEAK  3(5Q22.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           20                           145 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           20                           145 
[1] "AMP PEAK  4(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           54                           111 
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           54                           111 
[1] "AMP PEAK  5(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            53                            112 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            53                            112 
[1] "AMP PEAK  6(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            70                             95 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            70                             95 
[1] "AMP PEAK  7(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                           109                             56 
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                           109                             56 
[1] "AMP PEAK  8(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                            11                            154 
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                            11                            154 
[1] "AMP PEAK  9(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            45                            120 
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            45                            120 
[1] "AMP PEAK 10(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            28                            137 
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            28                            137 
[1] "AMP PEAK 11(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             41                             124 
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             41                             124 
[1] "AMP PEAK 12(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                            40                            125 
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                            40                            125 
[1] "AMP PEAK 13(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            126                              39 
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            126                              39 
[1] "AMP PEAK 14(13Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           125                             40 
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           125                             40 
[1] "AMP PEAK 15(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           120                             45 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           120                             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                            152 
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            13                            152 
[1] "AMP PEAK 17(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            47                            118 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            47                            118 
[1] "AMP PEAK 18(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          46                          119 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          46                          119 
[1] "AMP PEAK 19(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            39                            126 
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            39                            126 
[1] "AMP PEAK 20(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            36                            129 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            36                            129 
[1] "AMP PEAK 21(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            146                              19 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            146                              19 
[1] "AMP PEAK 22(20Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                            147                              18 
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                            147                              18 
[1] "AMP PEAK 23(20Q13.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                            148                              17 
  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                            148                              17 
[1] "AMP PEAK 24(XP22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                           32                           133 
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                           32                           133 
[1] "DEL PEAK  1(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            75                             90 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            75                             90 
[1] "DEL PEAK  2(1P33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         53                         112 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         53                         112 
[1] "DEL PEAK  3(1P13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           54                           111 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           54                           111 
[1] "DEL PEAK  4(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         13                         152 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         13                         152 
[1] "DEL PEAK  5(3P14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           31                           134 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           31                           134 
[1] "DEL PEAK  6(3Q26.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            18                            147 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            18                            147 
[1] "DEL PEAK  7(4P13) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         60                         105 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         60                         105 
[1] "DEL PEAK  8(4Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           73                            92 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           73                            92 
[1] "DEL PEAK  9(4Q35.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           72                            93 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           72                            93 
[1] "DEL PEAK 10(5Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                           53                           112 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                           53                           112 
[1] "DEL PEAK 11(5Q22.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           59                           106 
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           59                           106 
[1] "DEL PEAK 12(6P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           24                           141 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           24                           141 
[1] "DEL PEAK 13(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         30                         135 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         30                         135 
[1] "DEL PEAK 14(7Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            4                           161 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            4                           161 
[1] "DEL PEAK 15(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          100                            65 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                          100                            65 
[1] "DEL PEAK 16(8P11.21) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            45                            120 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            45                            120 
[1] "DEL PEAK 17(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            41                            124 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            41                            124 
[1] "DEL PEAK 18(10Q25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            48                            117 
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            48                            117 
[1] "DEL PEAK 19(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            38                            127 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            38                            127 
[1] "DEL PEAK 20(12P13.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                            33                            132 
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                            33                            132 
[1] "DEL PEAK 21(12Q22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                          26                          139 
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                          26                          139 
[1] "DEL PEAK 22(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                            70                             95 
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                            70                             95 
[1] "DEL PEAK 23(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                            72                             93 
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                            72                             93 
[1] "DEL PEAK 24(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE 
                            79                             86 
  DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE 
                            79                             86 
[1] "DEL PEAK 25(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE 
                             77                              88 
  DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE 
                             77                              88 
[1] "DEL PEAK 26(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                            13                            152 
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                            13                            152 
[1] "DEL PEAK 27(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            23                            142 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            23                            142 
[1] "DEL PEAK 28(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                           113                             52 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                           113                             52 
[1] "DEL PEAK 29(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                           145                             20 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                           145                             20 
[1] "DEL PEAK 30(18Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                           141                             24 
  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                           141                             24 
[1] "DEL PEAK 31(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            37                            128 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            37                            128 
[1] "DEL PEAK 32(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                            49                            116 
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                            49                            116 
[1] "DEL PEAK 33(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                            73                             92 
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                            73                             92 
[1] "DEL PEAK 34(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             68                              97 
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             68                              97 
[1] "DEL PEAK 35(XP22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                            34                            131 
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                            34                            131 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "RESIDUAL_TUMOR"                      
[16] "NUMBER_OF_LYMPH_NODES"               
[17] "RACE"                                
[18] "ETHNICITY"                           

Input Data has 18 rows and 165 columns.

[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=48,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=119,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=12,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=14,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "ETHNICITY excluded in the analysis because there is no case of (both >= 3) in the table below"
              HISPANIC OR LATINO NOT HISPANIC OR LATINO
freq.values   "1"                "83"                  
freq.contrast "83"               "1"                   
both >= 3     "FALSE"            "FALSE"               
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 165 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES" "RACE"                 
YEARS_TO_BIRTH, nv=48, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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  29 112  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  29 112  14 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  29 112  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  29 112  14 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
85 45 33 
[1] "table(vv)"
vv
N0 N1 N2 
85 45 33 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
85 45 33 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
85 45 33 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=2, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, nv=18, 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   40  6
  AMP PEAK  1(1Q21.3) WILD-TYPE 98 16
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           46                           114 
  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-3591 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3611 
       32.02        46.03        34.03        34.03        19.99        13.94 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 
       19.04        19.99        28.04        23.01        37.02        36.03 
TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       31.00        70.03        64.01         1.94        38.96        38.04 
TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 
        0.69         0.72        10.19         9.37         4.73        11.01 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6506 TCGA-EI-6882 
       13.97        15.02       129.27        24.13        20.55         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 
       10.78        13.64        11.97         9.96         0.39         0.69 
TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.76        18.28        47.08        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 
       39.48        17.23        43.04        34.49        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
       29.98        37.02        32.98         0.99         0.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        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-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
        6.02        25.97        15.95         9.07         1.02        12.00 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 
       10.98        51.98        49.97        61.97        41.00        38.56 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        1.45        26.43         1.81         6.05        33.17         6.97 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       12.39        78.12         7.17        21.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
        8.98        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36        57.24        51.48 
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-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-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.51        17.46         8.45        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
       32.19         0.66         0.53         1.12        12.46        55.76 

  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                         0.39                          0.49 
  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 
                       18.660                        17.015 
[1] "0.4 - 129.3 (18.7)" "0.5 - 126.4 (17.0)"
[1] "hr=" "1"  
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        28         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         19          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                            28
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           3                             6
  STAGE IIIB                           5                            19
  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 84  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                            84
  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 62 34 21
D1V5, multiclass
    clus
vv   AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  N0                          23                            62
  N1                          11                            34
  N2                          12                            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"
D1V6, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.3) MUTATED   34  5
  AMP PEAK  1(1Q21.3) WILD-TYPE 92 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     34    5
  AMP PEAK  1(1Q21.3) WILD-TYPE   92   19
   clus
vv  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  0                          34                            92
  1                           5                            19
[1] 2 2
[1] FALSE
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.3) MUTATED   21 27
  AMP PEAK  1(1Q21.3) WILD-TYPE 55 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     21   27
  AMP PEAK  1(1Q21.3) WILD-TYPE   55   62
        clus
vv       AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  FEMALE                          21                            55
  MALE                            27                            62
[1] 2 2
[1] FALSE
D1V8, binary
                               cls
clus                             0  1
  AMP PEAK  1(1Q21.3) MUTATED   26  8
  AMP PEAK  1(1Q21.3) WILD-TYPE 67 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     26    8
  AMP PEAK  1(1Q21.3) WILD-TYPE   67   11
     clus
vv    AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  NO                           26                            67
  YES                           8                            11
[1] 2 2
[1] FALSE
D1V9, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q21.3) MUTATED    41   3
  AMP PEAK  1(1Q21.3) WILD-TYPE 105  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     41    3
  AMP PEAK  1(1Q21.3) WILD-TYPE  105   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                                    105
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[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 90  1  9  4
D1V10, multiclass
    clus
vv   AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  R0                          33                            90
  R1                           1                             1
  R2                           3                             9
  RX                           0                             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"
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                         6    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                             6
  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   39  8
  AMP PEAK  2(1Q32.2) WILD-TYPE 99 14
  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                           47                           113 
  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-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3881 TCGA-AG-3882 
       34.03        34.03         6.05        13.94        19.04        19.99 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A01W 
       48.03        28.04        23.01        36.03        31.00        70.03 
TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       51.98         1.94        38.96        38.04        38.56         0.69 
TCGA-AH-6644 TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6155 
        0.72        10.19         9.37         4.73        11.01        13.97 
TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6882 
       15.02       129.27        24.13        32.61        20.55         8.61 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6810 
       10.78        13.64        11.97         8.45         9.96         0.39 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
        0.69         0.76        18.28        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        39.48        17.23        43.04        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        10.39        16.83        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
       20.05        24.00         1.02        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 
       12.03         0.99        15.95        19.99        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
        0.99         1.02        17.95        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-4021 TCGA-AG-4022 TCGA-AG-A002 
       14.04         1.02        17.03         3.98        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 
       13.94         6.02        25.97        37.02        15.95         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
        1.02        12.00        64.01        10.98        49.97        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       41.00         1.45        26.43         1.81         6.05        33.17 
TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
        6.97        12.39        78.12         7.17        21.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03         8.98        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48         0.49         2.40        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-6917 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       11.51        17.46        49.51        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 
        0.66         0.53         1.12        12.46        55.76 

  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE 
                         0.39                          0.49 
  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 
                        15.39                         17.03 
[1] "0.4 - 129.3 (15.4)" "0.5 - 126.4 (17.0)"
[1] "hr=" "1.4"
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        28         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         20          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                            28
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           4                             5
  STAGE IIIB                           4                            20
  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 85  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                            85
  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 64 33 20
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  N0                          21                            64
  N1                          12                            33
  N2                          13                            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"
D2V6, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q32.2) MUTATED   33  7
  AMP PEAK  2(1Q32.2) WILD-TYPE 93 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.2) MUTATED     33    7
  AMP PEAK  2(1Q32.2) WILD-TYPE   93   17
   clus
vv  AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  0                          33                            93
  1                           7                            17
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q32.2) MUTATED   22 26
  AMP PEAK  2(1Q32.2) WILD-TYPE 54 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.2) MUTATED     22   26
  AMP PEAK  2(1Q32.2) WILD-TYPE   54   63
        clus
vv       AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  FEMALE                          22                            54
  MALE                            26                            63
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q32.2) MUTATED   27  8
  AMP PEAK  2(1Q32.2) WILD-TYPE 66 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.2) MUTATED     27    8
  AMP PEAK  2(1Q32.2) WILD-TYPE   66   11
     clus
vv    AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  NO                           27                            66
  YES                           8                            11
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.2) MUTATED    41   4
  AMP PEAK  2(1Q32.2) WILD-TYPE 105   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.2) MUTATED     41    4
  AMP PEAK  2(1Q32.2) WILD-TYPE  105    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                                    105
  RECTAL MUCINOUS ADENOCARCINOMA                             9
[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 91  1  9  4
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q32.2) MUTATED AMP PEAK  2(1Q32.2) WILD-TYPE
  R0                          32                            91
  R1                           1                             1
  R2                           3                             9
  RX                           0                             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"
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                         6    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                             6
  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    20   0
  AMP PEAK  3(5Q22.3) WILD-TYPE 118  22
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                           20                           140 
  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-3885 TCGA-AG-3896 TCGA-AG-4007 TCGA-AG-A00H 
       20.02        19.99        17.95         1.02         1.02        25.97 
TCGA-AG-A014 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       15.95        12.00        31.00        38.04        38.56         0.69 
TCGA-AH-6644 TCGA-DC-6683 TCGA-EI-6506 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-7002 
        0.72         5.03        20.55        16.31        11.51        11.97 
TCGA-F5-6465 TCGA-F5-6811 
       49.51        32.19 

$`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        39.48        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 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        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        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
       50.04        12.03         6.05         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        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-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 
       32.02        19.99        28.04        36.03        14.04        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y 
       37.02        36.03         9.07         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-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
       41.00         1.45        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         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-6507 
       24.13        51.48        32.61         0.49         2.40        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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       16.41         8.61        10.78        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
        9.96        31.30        28.57         0.39         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        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                         0.69                          0.39 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                        49.51                        129.27 
  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE 
                        17.13                         17.03 
[1] "0.7 - 49.5 (17.1)"  "0.4 - 129.3 (17.0)"
[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        35         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         20         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                            35
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            0                             5
  STAGE IIIA                           1                             8
  STAGE IIIB                           4                            20
  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 97 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                            97
  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 76 39 29
D3V5, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  N0                           9                            76
  N1                           6                            39
  N2                           4                            29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    15   4
  AMP PEAK  3(5Q22.3) WILD-TYPE 111  20
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     15    4
  AMP PEAK  3(5Q22.3) WILD-TYPE  111   20
   clus
vv  AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  0                          15                           111
  1                           4                            20
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(5Q22.3) MUTATED    8 12
  AMP PEAK  3(5Q22.3) WILD-TYPE 68 77
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED      8   12
  AMP PEAK  3(5Q22.3) WILD-TYPE   68   77
        clus
vv       AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  FEMALE                           8                            68
  MALE                            12                            77
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                             0  1
  AMP PEAK  3(5Q22.3) MUTATED   10  3
  AMP PEAK  3(5Q22.3) WILD-TYPE 83 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     10    3
  AMP PEAK  3(5Q22.3) WILD-TYPE   83   16
     clus
vv    AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  NO                           10                            83
  YES                           3                            16
[1] 2 2
[1] FALSE
D3V9, binary
                               cls
clus                              0   1
  AMP PEAK  3(5Q22.3) MUTATED    20   0
  AMP PEAK  3(5Q22.3) WILD-TYPE 126  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(5Q22.3) MUTATED     20    0
  AMP PEAK  3(5Q22.3) WILD-TYPE  126   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                                    126
  RECTAL MUCINOUS ADENOCARCINOMA                            13
[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 108   2  10   4
D3V10, multiclass
    clus
vv   AMP PEAK  3(5Q22.3) MUTATED AMP PEAK  3(5Q22.3) WILD-TYPE
  R0                          15                           108
  R1                           0                             2
  R2                           2                            10
  RX                           0                             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"
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                         6    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                             6
  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   43  7
  AMP PEAK  4(6P21.1) WILD-TYPE 95 15
  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                           50                           110 
  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-AF-A56L TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       15.39        65.98        36.03        24.00        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 
       34.03         6.05        19.99        19.99        20.98        29.98 
TCGA-AG-3883 TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
        1.02         1.02        14.04         1.02         3.98        46.03 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A01N TCGA-AH-6644 TCGA-BM-6198 
       36.03         9.07        12.00        31.00         0.72        10.19 
TCGA-CI-6619 TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        6.05         9.37        21.01         5.03         8.98        15.02 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 
       27.95         4.01       129.27        24.13        51.48        20.55 
TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 
       15.85        17.69        49.51        28.57         0.39         0.66 
TCGA-G5-6233 TCGA-G5-6641 
       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 
       39.48        17.23        13.55        34.49        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       10.39        86.63        11.84        36.03        12.00        32.02 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 TCGA-AG-3594 
        8.02         7.07        20.05         1.02        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        13.94         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        0.99        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       14.01        48.03        32.02        19.99        28.04        36.03 
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-A014 TCGA-AG-A01J TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       37.02        15.95         1.02        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-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 
       38.04        38.56         1.45         0.69        26.43         1.81 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
       33.17         6.97         4.73        12.39        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       11.01        15.02        13.97        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 
        5.03         5.29       126.44        41.36        57.24        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-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-F5-6571 
       13.64        17.46        11.97         8.45         9.96        31.30 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       32.19         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE 
                         0.39                          0.49 
  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 
                       19.545                        16.620 
[1] "0.4 - 129.3 (19.5)" "0.5 - 126.4 (16.6)"
[1] "hr=" "1.1"
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        31         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  4(6P21.1) MUTATED           2          1         10          7
  AMP PEAK  4(6P21.1) WILD-TYPE         3          8         14          7
                               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                            31
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            2                             3
  STAGE IIIA                           1                             8
  STAGE IIIB                          10                            14
  STAGE IIIC                           7                             7
  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 39  5
  AMP PEAK  4(6P21.1) WILD-TYPE  5 23 73  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                          39                            73
  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 17
  AMP PEAK  4(6P21.1) WILD-TYPE 66 28 16
D4V5, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  N0                          19                            66
  N1                          17                            28
  N2                          17                            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"
D4V6, binary
                               cls
clus                             0  1
  AMP PEAK  4(6P21.1) MUTATED   33 13
  AMP PEAK  4(6P21.1) WILD-TYPE 93 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     33   13
  AMP PEAK  4(6P21.1) WILD-TYPE   93   11
   clus
vv  AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  0                          33                            93
  1                          13                            11
[1] 2 2
[1] FALSE
D4V7, binary
                               cls
clus                             0  1
  AMP PEAK  4(6P21.1) MUTATED   22 32
  AMP PEAK  4(6P21.1) WILD-TYPE 54 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     22   32
  AMP PEAK  4(6P21.1) WILD-TYPE   54   57
        clus
vv       AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  FEMALE                          22                            54
  MALE                            32                            57
[1] 2 2
[1] FALSE
D4V8, binary
                               cls
clus                             0  1
  AMP PEAK  4(6P21.1) MUTATED   25  9
  AMP PEAK  4(6P21.1) WILD-TYPE 68 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     25    9
  AMP PEAK  4(6P21.1) WILD-TYPE   68   10
     clus
vv    AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  NO                           25                            68
  YES                           9                            10
[1] 2 2
[1] FALSE
D4V9, binary
                               cls
clus                             0  1
  AMP PEAK  4(6P21.1) MUTATED   51  1
  AMP PEAK  4(6P21.1) WILD-TYPE 95 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(6P21.1) MUTATED     51    1
  AMP PEAK  4(6P21.1) WILD-TYPE   95   12
                                clus
vv                               AMP PEAK  4(6P21.1) MUTATED
  RECTAL ADENOCARCINOMA                                   51
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK  4(6P21.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     95
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  4(6P21.1) MUTATED   36  0  7  1
  AMP PEAK  4(6P21.1) WILD-TYPE 87  2  5  3
D4V10, multiclass
    clus
vv   AMP PEAK  4(6P21.1) MUTATED AMP PEAK  4(6P21.1) WILD-TYPE
  R0                          36                            87
  R1                           0                             2
  R2                           7                             5
  RX                           1                             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                         4    27
  AMP PEAK  4(6P21.1) WILD-TYPE     1                         2    54
D4V12, multiclass
                           clus
vv                          AMP PEAK  4(6P21.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              27
                           clus
vv                          AMP PEAK  4(6P21.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  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   40 12
  AMP PEAK  5(8P11.23) WILD-TYPE 98 10
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            52                            108 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                            12                             10 
$`AMP PEAK  5(8P11.23) MUTATED`
TCGA-AF-3911 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 
       37.74        20.02        10.39        65.98        36.03        36.03 
TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3887 
       24.00        34.03        34.03         2.01         0.99        36.95 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 
       35.01         1.02        48.03        32.02        36.03         1.02 
TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-AG-A032 TCGA-AH-6544 
       46.03        15.95        31.00        51.98        38.04        38.56 
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        78.12 
TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A1DC 
        7.17        15.02        27.95        10.98         4.01        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 
       57.24        24.13        51.48         0.49        17.00        15.85 
TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 
       16.31        11.51        10.78        49.51        28.57        32.19 
TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6572 
        0.69        12.46        18.28        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        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K 
       34.49        10.39        14.50        16.83        15.39        86.63 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 
       11.84        12.00        32.02         8.02         7.07        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
        1.02        46.03        34.03        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99         1.02        17.95        17.03        13.02 
TCGA-AG-3894 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 
       14.01        19.99        28.04        14.04        17.03         3.98 
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-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y 
       36.03         9.07         1.02        12.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
       10.98        49.97         1.94        38.96        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 
        1.45        26.43         1.81        10.19        33.17         6.97 
TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       12.39        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       13.97        19.99         5.95         5.03         5.29       126.44 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      129.27        32.61         2.40        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6885 
       18.28        17.69        16.34        16.41         8.61        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 
       17.46        11.97         8.45         9.96        31.30         0.39 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6641 
        0.66         0.53         1.12         0.76        55.76        26.43 

  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                          0.49                           0.39 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                         78.12                         129.27 
  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE 
                        24.065                         16.375 
[1] "0.5 - 78.1 (24.1)"  "0.4 - 129.3 (16.4)"
[1] "hr=" "1.8"
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        27         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  5(8P11.23) MUTATED           0          2          6          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                             27
  STAGE IIB                             1                              1
  STAGE IIC                             2                              0
  STAGE III                             0                              5
  STAGE IIIA                            2                              7
  STAGE IIIB                            6                             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 37  7
  AMP PEAK  5(8P11.23) WILD-TYPE  8 22 75  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                           37                             75
  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 14
  AMP PEAK  5(8P11.23) WILD-TYPE 61 32 19
D5V5, multiclass
    clus
vv   AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  N0                           24                             61
  N1                           13                             32
  N2                           14                             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"
D5V6, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.23) MUTATED   36 11
  AMP PEAK  5(8P11.23) WILD-TYPE 90 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED     36   11
  AMP PEAK  5(8P11.23) WILD-TYPE   90   13
   clus
vv  AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  0                           36                             90
  1                           11                             13
[1] 2 2
[1] FALSE
D5V7, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.23) MUTATED   19 34
  AMP PEAK  5(8P11.23) WILD-TYPE 57 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED     19   34
  AMP PEAK  5(8P11.23) WILD-TYPE   57   55
        clus
vv       AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  FEMALE                           19                             57
  MALE                             34                             55
[1] 2 2
[1] FALSE
D5V8, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.23) MUTATED   28  7
  AMP PEAK  5(8P11.23) WILD-TYPE 65 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED     28    7
  AMP PEAK  5(8P11.23) WILD-TYPE   65   12
     clus
vv    AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  NO                            28                             65
  YES                            7                             12
[1] 2 2
[1] FALSE
D5V9, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.23) MUTATED   51  2
  AMP PEAK  5(8P11.23) WILD-TYPE 95 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.23) MUTATED     51    2
  AMP PEAK  5(8P11.23) WILD-TYPE   95   11
                                clus
vv                               AMP PEAK  5(8P11.23) MUTATED
  RECTAL ADENOCARCINOMA                                    51
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK  5(8P11.23) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      95
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  5(8P11.23) MUTATED   30  0  7  3
  AMP PEAK  5(8P11.23) WILD-TYPE 93  2  5  1
D5V10, multiclass
    clus
vv   AMP PEAK  5(8P11.23) MUTATED AMP PEAK  5(8P11.23) WILD-TYPE
  R0                           30                             93
  R1                            0                              2
  R2                            7                              5
  RX                            3                              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                         2    31
  AMP PEAK  5(8P11.23) WILD-TYPE     1                         4    50
D5V12, multiclass
                           clus
vv                          AMP PEAK  5(8P11.23) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               31
                           clus
vv                          AMP PEAK  5(8P11.23) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  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   55 13
  AMP PEAK  6(8P11.21) WILD-TYPE 83  9
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            68                             92 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                            13                              9 
$`AMP PEAK  6(8P11.21) MUTATED`
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 
       20.02        10.39        65.98        36.03        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3732 
        1.02        34.03        34.03         2.01         0.99        32.98 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
       19.04         1.02        36.95         1.02        48.03        32.02 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A00Y TCGA-AG-A014 
       28.04        14.04         1.02        46.03        23.01        15.95 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 
        9.07         1.02        31.00        64.01        51.98         1.94 
TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       38.96        38.04        38.56         1.45         0.69         0.72 
TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6155 
        6.05         9.37         4.73        78.12         7.17        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       15.02        27.95        10.98         4.01         5.03       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6509 
       41.36        57.24       129.27        24.13         0.49        17.00 
TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-F5-6465 
       15.85        16.31        11.51        10.78        13.64        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
       28.57        32.19         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       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        39.48        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 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       86.63        11.84        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       20.05        46.03        34.03        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98        37.02         0.99         0.99        19.99 
TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3909 
       17.95        17.03        13.02        35.01        14.01        19.99 
TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        17.03         3.98        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        26.43         1.81        10.19 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       33.17         6.97        12.39        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DG 
        5.03         8.98        19.99         5.95         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 
                          0.49                           0.39 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                        129.27                          86.63 
  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE 
                         18.66                          16.93 
[1] "0.5 - 129.3 (18.7)" "0.4 - 86.6 (16.9)" 
[1] "hr=" "1.3"
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        22         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  6(8P11.21) MUTATED           1          4          8          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                             22
  STAGE IIB                             1                              1
  STAGE IIC                             2                              0
  STAGE III                             1                              4
  STAGE IIIA                            4                              5
  STAGE IIIB                            8                             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 48  8
  AMP PEAK  6(8P11.21) WILD-TYPE  7 18 64  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                           48                             64
  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 16
  AMP PEAK  6(8P11.21) WILD-TYPE 51 27 17
D6V5, multiclass
    clus
vv   AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  N0                           34                             51
  N1                           18                             27
  N2                           16                             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"
D6V6, binary
                                cls
clus                              0  1
  AMP PEAK  6(8P11.21) MUTATED   48 14
  AMP PEAK  6(8P11.21) WILD-TYPE 78 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED     48   14
  AMP PEAK  6(8P11.21) WILD-TYPE   78   10
   clus
vv  AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  0                           48                             78
  1                           14                             10
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                              0  1
  AMP PEAK  6(8P11.21) MUTATED   31 39
  AMP PEAK  6(8P11.21) WILD-TYPE 45 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED     31   39
  AMP PEAK  6(8P11.21) WILD-TYPE   45   50
        clus
vv       AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  FEMALE                           31                             45
  MALE                             39                             50
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                              0  1
  AMP PEAK  6(8P11.21) MUTATED   37  6
  AMP PEAK  6(8P11.21) WILD-TYPE 56 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED     37    6
  AMP PEAK  6(8P11.21) WILD-TYPE   56   13
     clus
vv    AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  NO                            37                             56
  YES                            6                             13
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                              0  1
  AMP PEAK  6(8P11.21) MUTATED   65  3
  AMP PEAK  6(8P11.21) WILD-TYPE 81 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8P11.21) MUTATED     65    3
  AMP PEAK  6(8P11.21) WILD-TYPE   81   10
                                clus
vv                               AMP PEAK  6(8P11.21) MUTATED
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK  6(8P11.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      81
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  6(8P11.21) MUTATED   41  2  9  3
  AMP PEAK  6(8P11.21) WILD-TYPE 82  0  3  1
D6V10, multiclass
    clus
vv   AMP PEAK  6(8P11.21) MUTATED AMP PEAK  6(8P11.21) WILD-TYPE
  R0                           41                             82
  R1                            2                              0
  R2                            9                              3
  RX                            3                              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                         2    37
  AMP PEAK  6(8P11.21) WILD-TYPE     1                         4    44
D6V12, multiclass
                           clus
vv                          AMP PEAK  6(8P11.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               37
                           clus
vv                          AMP PEAK  6(8P11.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  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   87 19
  AMP PEAK  7(8Q24.21) WILD-TYPE 51  3
  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE 
                           106                             54 
  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        39.48        17.23        43.04        13.55        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        10.39        16.83        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 
       65.98        36.03        32.02        36.03        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
       46.03        34.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
        0.99        19.99         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 
        0.99        19.04         1.02        36.95        17.03         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-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A00H TCGA-AG-A00Y 
        1.02        17.03         3.98        46.03        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 
       38.56         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        78.12         7.17        21.01        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        4.01         5.03       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        49.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
       28.57         0.39        32.19         0.53         0.76        12.46 
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-AF-A56N TCGA-AG-3575 TCGA-AG-3580 
       19.10        14.50        15.39        11.84        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 
        7.07        20.05        34.03        12.03        15.95        19.99 
TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       13.94        20.98        29.98         0.99        19.99        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       13.02        35.01        14.01        20.98        13.94         6.02 
TCGA-AG-A015 TCGA-AG-A01L TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AH-6897 
       36.03        12.00        10.98        49.97        38.96        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-DC-5337 TCGA-DC-6160 
        1.81        33.17         6.97        12.39        15.02        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 
        5.95         5.29       129.27        51.48        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 
       20.91        18.28        17.69        16.41         8.61        17.46 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       11.97         8.45        31.30         0.66         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 
                        17.755                         15.670 
[1] "0.4 - 126.4 (17.8)" "0.7 - 129.3 (15.7)"
[1] "hr=" "2"  
D7V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  7(8Q24.21) MUTATED        16        6        29         1         2
  AMP PEAK  7(8Q24.21) WILD-TYPE      14        2        11         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  7(8Q24.21) MUTATED           3          5         14         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                            29                             11
  STAGE IIB                             1                              1
  STAGE IIC                             2                              0
  STAGE III                             3                              2
  STAGE IIIA                            5                              4
  STAGE IIIB                           14                             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 76 10
  AMP PEAK  7(8Q24.21) WILD-TYPE  5 11 36  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                           76                             36
  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   55 28 24
  AMP PEAK  7(8Q24.21) WILD-TYPE 30 17  9
D7V5, multiclass
    clus
vv   AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  N0                           55                             30
  N1                           28                             17
  N2                           24                              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"
D7V6, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q24.21) MUTATED   80 18
  AMP PEAK  7(8Q24.21) WILD-TYPE 46  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.21) MUTATED     80   18
  AMP PEAK  7(8Q24.21) WILD-TYPE   46    6
   clus
vv  AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  0                           80                             46
  1                           18                              6
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q24.21) MUTATED   49 60
  AMP PEAK  7(8Q24.21) WILD-TYPE 27 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.21) MUTATED     49   60
  AMP PEAK  7(8Q24.21) WILD-TYPE   27   29
        clus
vv       AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  FEMALE                           49                             27
  MALE                             60                             29
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                              0  1
  AMP PEAK  7(8Q24.21) MUTATED   58 13
  AMP PEAK  7(8Q24.21) WILD-TYPE 35  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.21) MUTATED     58   13
  AMP PEAK  7(8Q24.21) WILD-TYPE   35    6
     clus
vv    AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  NO                            58                             35
  YES                           13                              6
[1] 2 2
[1] FALSE
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q24.21) MUTATED   101   5
  AMP PEAK  7(8Q24.21) WILD-TYPE  45   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.21) MUTATED    101    5
  AMP PEAK  7(8Q24.21) WILD-TYPE   45    8
                                clus
vv                               AMP PEAK  7(8Q24.21) MUTATED
  RECTAL ADENOCARCINOMA                                   101
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK  7(8Q24.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      45
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  7(8Q24.21) MUTATED   77  2 10  3
  AMP PEAK  7(8Q24.21) WILD-TYPE 46  0  2  1
D7V10, multiclass
    clus
vv   AMP PEAK  7(8Q24.21) MUTATED AMP PEAK  7(8Q24.21) WILD-TYPE
  R0                           77                             46
  R1                            2                              0
  R2                           10                              2
  RX                            3                              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                         5    55
  AMP PEAK  7(8Q24.21) WILD-TYPE     1                         1    26
D7V12, multiclass
                           clus
vv                          AMP PEAK  7(8Q24.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               55
                           clus
vv                          AMP PEAK  7(8Q24.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              1
  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    10   1
  AMP PEAK  8(10Q22.2) WILD-TYPE 128  21
  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE 
                            11                            149 
  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-3881 TCGA-AG-3999 TCGA-AG-A014 
       39.48        46.03        50.04        19.04        28.04        15.95 
TCGA-AG-A01W TCGA-AG-A020 TCGA-BM-6198 TCGA-CI-6619 TCGA-DC-4745 
       70.03        10.98        10.19         6.05        21.01 

$`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        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        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        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 
        1.02        34.03        34.03        34.03         2.01        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
        6.05         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.99         1.02        17.95        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-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 
       32.02        19.99        36.03        14.04         1.02        17.03 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L 
       23.01        37.02        36.03         9.07         1.02        12.00 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       31.00        64.01        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        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
        0.72        26.43         1.81        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        12.39        78.12         7.17        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       19.99         5.95         4.01         5.03         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-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         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 
       12.46        18.28        55.76        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 
                         21.01                          17.00 
[1] "6.0 - 70.0 (21.0)"  "0.4 - 129.3 (17.0)"
[1] "hr=" "2.4"
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        38         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         22         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                             38
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            2                             22
  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  27 103  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                            103
  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 80 41 31
D8V5, multiclass
    clus
vv   AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  N0                            5                             80
  N1                            4                             41
  N2                            2                             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"
D8V6, binary
                                cls
clus                               0   1
  AMP PEAK  8(10Q22.2) MUTATED     8   2
  AMP PEAK  8(10Q22.2) WILD-TYPE 118  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(10Q22.2) MUTATED      8    2
  AMP PEAK  8(10Q22.2) WILD-TYPE  118   22
   clus
vv  AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  0                            8                            118
  1                            2                             22
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(10Q22.2) MUTATED    6  5
  AMP PEAK  8(10Q22.2) WILD-TYPE 70 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(10Q22.2) MUTATED      6    5
  AMP PEAK  8(10Q22.2) WILD-TYPE   70   84
        clus
vv       AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  FEMALE                            6                             70
  MALE                              5                             84
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                              0  1
  AMP PEAK  8(10Q22.2) MUTATED    5  2
  AMP PEAK  8(10Q22.2) WILD-TYPE 88 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(10Q22.2) MUTATED      5    2
  AMP PEAK  8(10Q22.2) WILD-TYPE   88   17
     clus
vv    AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  NO                             5                             88
  YES                            2                             17
[1] 2 2
[1] FALSE
D8V9, binary
                                cls
clus                               0   1
  AMP PEAK  8(10Q22.2) MUTATED     9   1
  AMP PEAK  8(10Q22.2) WILD-TYPE 137  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(10Q22.2) MUTATED      9    1
  AMP PEAK  8(10Q22.2) WILD-TYPE  137   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                                     137
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[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 114   2  12   4
D8V10, multiclass
    clus
vv   AMP PEAK  8(10Q22.2) MUTATED AMP PEAK  8(10Q22.2) WILD-TYPE
  R0                            9                            114
  R1                            0                              2
  R2                            0                             12
  RX                            0                              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"
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                         6    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                              6
  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    37   7
  AMP PEAK  9(11P15.5) WILD-TYPE 101  15
  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE 
                            44                            116 
  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 
       39.48        17.23        13.55        10.39        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3583 
       10.39        65.98        36.03        12.00         8.02        20.05 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3611 
       46.03        34.03        34.03        34.03        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H 
       19.99         0.99        14.01        36.03         1.02        25.97 
TCGA-AG-A01N TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-4957 TCGA-DC-4749 
       31.00        26.43        10.19         9.37        12.39        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       15.02         5.03         8.98        27.95        19.99       126.44 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 TCGA-F5-6810 TCGA-F5-6811 
        0.49         2.40        20.55        16.31         0.39        32.19 
TCGA-F5-6861 TCGA-G5-6233 
        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        34.49        37.74        14.50 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       15.39        86.63        11.84        32.02         7.07        36.03 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       24.00         1.02         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 
        0.99        15.95        20.98         7.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 
       17.95        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-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        3.98        46.03        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        38.56         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        33.17         6.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6156 
        4.73        78.12         7.17        21.01        13.97        15.02 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       10.98         5.95         4.01         5.03         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        49.51        31.30        28.57 
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        12.46        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                           0.53 
  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 
                         17.03                          17.03 
[1] "0.4 - 126.4 (17.0)" "0.5 - 129.3 (17.0)"
[1] "hr=" "1.6"
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        26         1         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  9(11P15.5) MUTATED           2          3          3          3
  AMP PEAK  9(11P15.5) WILD-TYPE         3          6         21         11
                                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                             26
  STAGE IIB                             1                              1
  STAGE IIC                             1                              1
  STAGE III                             2                              3
  STAGE IIIA                            3                              6
  STAGE IIIB                            3                             21
  STAGE IIIC                            3                             11
  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 30  4
  AMP PEAK  9(11P15.5) WILD-TYPE  6 21 82 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                           30                             82
  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  9
  AMP PEAK  9(11P15.5) WILD-TYPE 57 37 24
D9V5, multiclass
    clus
vv   AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  N0                           28                             57
  N1                            8                             37
  N2                            9                             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"
D9V6, binary
                                cls
clus                              0  1
  AMP PEAK  9(11P15.5) MUTATED   36  6
  AMP PEAK  9(11P15.5) WILD-TYPE 90 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED     36    6
  AMP PEAK  9(11P15.5) WILD-TYPE   90   18
   clus
vv  AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  0                           36                             90
  1                            6                             18
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                              0  1
  AMP PEAK  9(11P15.5) MUTATED   21 24
  AMP PEAK  9(11P15.5) WILD-TYPE 55 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED     21   24
  AMP PEAK  9(11P15.5) WILD-TYPE   55   65
        clus
vv       AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  FEMALE                           21                             55
  MALE                             24                             65
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                              0  1
  AMP PEAK  9(11P15.5) MUTATED   25  7
  AMP PEAK  9(11P15.5) WILD-TYPE 68 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED     25    7
  AMP PEAK  9(11P15.5) WILD-TYPE   68   12
     clus
vv    AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  NO                            25                             68
  YES                            7                             12
[1] 2 2
[1] FALSE
D9V9, binary
                                cls
clus                               0   1
  AMP PEAK  9(11P15.5) MUTATED    43   1
  AMP PEAK  9(11P15.5) WILD-TYPE 103  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11P15.5) MUTATED     43    1
  AMP PEAK  9(11P15.5) WILD-TYPE  103   12
                                clus
vv                               AMP PEAK  9(11P15.5) MUTATED
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK  9(11P15.5) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     103
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  9(11P15.5) MUTATED   35  0  3  1
  AMP PEAK  9(11P15.5) WILD-TYPE 88  2  9  3
D9V10, multiclass
    clus
vv   AMP PEAK  9(11P15.5) MUTATED AMP PEAK  9(11P15.5) WILD-TYPE
  R0                           35                             88
  R1                            0                              2
  R2                            3                              9
  RX                            1                              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                         4    23
  AMP PEAK  9(11P15.5) WILD-TYPE     1                         2    58
D9V12, multiclass
                           clus
vv                          AMP PEAK  9(11P15.5) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               23
                           clus
vv                          AMP PEAK  9(11P15.5) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  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    24   3
  AMP PEAK 10(11Q13.3) WILD-TYPE 114  19
  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                            27                            133 
  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-AF-A56L TCGA-AG-3575 TCGA-AG-3592 TCGA-AG-3612 
       17.23        10.39        65.98        12.00        34.03        19.99 
TCGA-AG-3883 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A00H TCGA-AG-A01N TCGA-AG-A01Y 
        1.02        36.03         1.02        25.97        31.00        64.01 
TCGA-AH-6897 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       26.43         9.37         4.73        11.01         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-EI-6514 
       15.02        27.95        10.98         5.29       129.27        16.31 
TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 
       13.64         0.39        32.19 

$`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        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       86.63        11.84        36.03        32.02         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
       29.98        37.02        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
       19.99        17.95        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-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        23.01        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 
        1.02        12.00        70.03        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        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        1.45         0.69         0.72         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       33.17         6.97        12.39        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        13.97        19.99         5.95         4.01         5.03 
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-6881 TCGA-EI-6882 
       18.28        15.85        17.69        16.34        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-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       49.51        31.30        28.57         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        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       26.43 

  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE 
                          0.39                           0.49 
  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 
                         15.02                          17.46 
[1] "0.4 - 129.3 (15.0)" "0.5 - 126.4 (17.5)"
[1] "hr=" "1.3"
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        33         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 10(11Q13.3) MUTATED           1          0          2          2
  AMP PEAK 10(11Q13.3) WILD-TYPE         4          9         22         12
                                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                             33
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            2                             22
  STAGE IIIC                            2                             12
  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 17  3
  AMP PEAK 10(11Q13.3) WILD-TYPE  8 22 95 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                           17                             95
  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  5
  AMP PEAK 10(11Q13.3) WILD-TYPE 67 40 28
D10V5, multiclass
    clus
vv   AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  N0                           18                             67
  N1                            5                             40
  N2                            5                             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"
D10V6, binary
                                cls
clus                               0   1
  AMP PEAK 10(11Q13.3) MUTATED    21   6
  AMP PEAK 10(11Q13.3) WILD-TYPE 105  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED     21    6
  AMP PEAK 10(11Q13.3) WILD-TYPE  105   18
   clus
vv  AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  0                           21                            105
  1                            6                             18
[1] 2 2
[1] FALSE
D10V7, binary
                                cls
clus                              0  1
  AMP PEAK 10(11Q13.3) MUTATED   13 15
  AMP PEAK 10(11Q13.3) WILD-TYPE 63 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED     13   15
  AMP PEAK 10(11Q13.3) WILD-TYPE   63   74
        clus
vv       AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  FEMALE                           13                             63
  MALE                             15                             74
[1] 2 2
[1] FALSE
D10V8, binary
                                cls
clus                              0  1
  AMP PEAK 10(11Q13.3) MUTATED   16  1
  AMP PEAK 10(11Q13.3) WILD-TYPE 77 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED     16    1
  AMP PEAK 10(11Q13.3) WILD-TYPE   77   18
     clus
vv    AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  NO                            16                             77
  YES                            1                             18
[1] 2 2
[1] FALSE
D10V9, binary
                                cls
clus                               0   1
  AMP PEAK 10(11Q13.3) MUTATED    27   1
  AMP PEAK 10(11Q13.3) WILD-TYPE 119  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 10(11Q13.3) MUTATED     27    1
  AMP PEAK 10(11Q13.3) WILD-TYPE  119   12
                                clus
vv                               AMP PEAK 10(11Q13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    27
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK 10(11Q13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     119
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK 10(11Q13.3) MUTATED    19   0   2   2
  AMP PEAK 10(11Q13.3) WILD-TYPE 104   2  10   2
D10V10, multiclass
    clus
vv   AMP PEAK 10(11Q13.3) MUTATED AMP PEAK 10(11Q13.3) WILD-TYPE
  R0                           19                            104
  R1                            0                              2
  R2                            2                             10
  RX                            2                              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                         4    14
  AMP PEAK 10(11Q13.3) WILD-TYPE     0                         2    67
D10V12, multiclass
                           clus
vv                          AMP PEAK 10(11Q13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               14
                           clus
vv                          AMP PEAK 10(11Q13.3) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              2
  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    33   7
  AMP PEAK 11(12P13.33) WILD-TYPE 105  15
  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE 
                             40                             120 
  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        34.49        37.74        14.50        16.83        10.39 
TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3611 
       36.03        46.03         2.01         6.05        19.99        13.94 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
        7.99        37.02        19.04         1.02        36.95         1.02 
TCGA-AG-4001 TCGA-AG-4022 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G TCGA-AG-A02N 
       36.03        46.03        15.95        36.03        38.96        61.97 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
        4.73        78.12         4.01         5.03         5.29       126.44 
TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
       57.24        32.61        19.96        18.28        17.69        13.64 
TCGA-EI-7002 TCGA-F5-6812 TCGA-G5-6233 TCGA-G5-6641 
       11.97         0.66        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        39.48        17.23        43.04        13.55        10.39 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 
       15.39        20.02        86.63        65.98        11.84        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        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99        20.98         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 
       32.98         0.99         0.99        19.99        17.95        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-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 
       28.04        14.04         1.02        17.03         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       13.94         6.02        25.97        23.01        37.02         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-A02X TCGA-AG-A032 TCGA-AH-6544 
       51.98        49.97         1.94        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 
        6.05        33.17         6.97         9.37        12.39         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC 
       15.02        27.95        10.98        19.99         5.95        41.36 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         0.49         2.40        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        15.85        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        11.51        10.78        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 
       49.51        31.30        28.57         0.39        32.19         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        12.46        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 
                         18.660                          16.375 
[1] "0.7 - 126.4 (18.7)" "0.4 - 129.3 (16.4)"
[1] "hr=" "1.1"
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        30         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         20
                                 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                              30
  STAGE IIB                              0                               2
  STAGE IIC                              1                               1
  STAGE III                              0                               5
  STAGE IIIA                             2                               7
  STAGE IIIB                             4                              20
  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 87 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                              87
  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 61 36 25
D11V5, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  N0                            24                              61
  N1                             9                              36
  N2                             8                              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"
D11V6, binary
                                 cls
clus                               0  1
  AMP PEAK 11(12P13.33) MUTATED   30  4
  AMP PEAK 11(12P13.33) WILD-TYPE 96 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     30    4
  AMP PEAK 11(12P13.33) WILD-TYPE   96   20
   clus
vv  AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  0                            30                              96
  1                             4                              20
[1] 2 2
[1] FALSE
D11V7, binary
                                 cls
clus                               0  1
  AMP PEAK 11(12P13.33) MUTATED   17 24
  AMP PEAK 11(12P13.33) WILD-TYPE 59 65
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     17   24
  AMP PEAK 11(12P13.33) WILD-TYPE   59   65
        clus
vv       AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  FEMALE                            17                              59
  MALE                              24                              65
[1] 2 2
[1] FALSE
D11V8, binary
                                 cls
clus                               0  1
  AMP PEAK 11(12P13.33) MUTATED   22  7
  AMP PEAK 11(12P13.33) WILD-TYPE 71 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     22    7
  AMP PEAK 11(12P13.33) WILD-TYPE   71   12
     clus
vv    AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  NO                             22                              71
  YES                             7                              12
[1] 2 2
[1] FALSE
D11V9, binary
                                 cls
clus                                0   1
  AMP PEAK 11(12P13.33) MUTATED    33   5
  AMP PEAK 11(12P13.33) WILD-TYPE 113   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 11(12P13.33) MUTATED     33    5
  AMP PEAK 11(12P13.33) WILD-TYPE  113    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                                      113
  RECTAL MUCINOUS ADENOCARCINOMA                               8
[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 95  2  9  2
D11V10, multiclass
    clus
vv   AMP PEAK 11(12P13.33) MUTATED AMP PEAK 11(12P13.33) WILD-TYPE
  R0                            28                              95
  R1                             0                               2
  R2                             3                               9
  RX                             2                               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"
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                         6    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                               6
  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    32   7
  AMP PEAK 12(12P12.1) WILD-TYPE 106  15
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                            39                            121 
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                             7                             15 
$`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        34.49        37.74        14.50        16.83        10.39 
TCGA-AG-3574 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3611 
       36.03        46.03         2.01         6.05        19.99        13.94 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 
        7.99        37.02        19.04         1.02        36.95         1.02 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A02G 
       28.04        36.03         3.98        15.95        36.03        38.96 
TCGA-AG-A02N TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 
       61.97        33.17         4.73        78.12         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 
        5.29        32.61        19.96        18.28        17.69        13.64 
TCGA-EI-7002 TCGA-G5-6233 TCGA-G5-6641 
       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        39.48        17.23        43.04        13.55        10.39 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 
       15.39        20.02        86.63        65.98        11.84        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        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99        20.98         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 
       32.98         0.99         0.99        19.99        17.95        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-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02        17.03        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        6.02        25.97        23.01        37.02         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-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        6.97         9.37        12.39         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       15.02         5.03         8.98        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       10.98        19.99         5.95       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         0.49         2.40        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        17.00        15.85        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
        8.61        11.51        10.78        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         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        12.46        55.76 
TCGA-G5-6572 
       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 
                         78.12                         129.27 
  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE 
                         18.28                          16.41 
[1] "1.0 - 78.1 (18.3)"  "0.4 - 129.3 (16.4)"
[1] "hr=" "1.5"
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        32         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         21          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                             32
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             0                              5
  STAGE IIIA                            2                              7
  STAGE IIIB                            3                             21
  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 88 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                             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
  AMP PEAK 12(12P12.1) MUTATED   21  9 10
  AMP PEAK 12(12P12.1) WILD-TYPE 64 36 23
D12V5, multiclass
    clus
vv   AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  N0                           21                             64
  N1                            9                             36
  N2                           10                             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"
D12V6, binary
                                cls
clus                              0  1
  AMP PEAK 12(12P12.1) MUTATED   27  6
  AMP PEAK 12(12P12.1) WILD-TYPE 99 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12P12.1) MUTATED     27    6
  AMP PEAK 12(12P12.1) WILD-TYPE   99   18
   clus
vv  AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  0                           27                             99
  1                            6                             18
[1] 2 2
[1] FALSE
D12V7, binary
                                cls
clus                              0  1
  AMP PEAK 12(12P12.1) MUTATED   17 23
  AMP PEAK 12(12P12.1) WILD-TYPE 59 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12P12.1) MUTATED     17   23
  AMP PEAK 12(12P12.1) WILD-TYPE   59   66
        clus
vv       AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  FEMALE                           17                             59
  MALE                             23                             66
[1] 2 2
[1] FALSE
D12V8, binary
                                cls
clus                              0  1
  AMP PEAK 12(12P12.1) MUTATED   25  6
  AMP PEAK 12(12P12.1) WILD-TYPE 68 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12P12.1) MUTATED     25    6
  AMP PEAK 12(12P12.1) WILD-TYPE   68   13
     clus
vv    AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  NO                            25                             68
  YES                            6                             13
[1] 2 2
[1] FALSE
D12V9, binary
                                cls
clus                               0   1
  AMP PEAK 12(12P12.1) MUTATED    32   5
  AMP PEAK 12(12P12.1) WILD-TYPE 114   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(12P12.1) MUTATED     32    5
  AMP PEAK 12(12P12.1) WILD-TYPE  114    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                                     114
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[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 96  2  8  2
D12V10, multiclass
    clus
vv   AMP PEAK 12(12P12.1) MUTATED AMP PEAK 12(12P12.1) WILD-TYPE
  R0                           27                             96
  R1                            0                              2
  R2                            4                              8
  RX                            2                              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"
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                         6    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                              6
  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   102  20
  AMP PEAK 13(13Q12.13) WILD-TYPE  36   2
  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE 
                            122                              38 
  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        39.48        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        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 
       10.39        86.63        65.98        11.84         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       20.05         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        2.01         0.99        19.99        13.94        19.99        20.98 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99        29.98         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       36.95        17.03        35.01        14.01         1.02        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-4021 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
        3.98        46.03         6.02        25.97        23.01        37.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A025 
       15.95        36.03         9.07        12.00        51.98        49.97 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
        1.94        38.96        38.04        38.56         0.69         0.72 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       26.43         6.05        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        5.03         8.98        15.02        27.95        10.98        19.99 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         5.03       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-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-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-F5-6811 
        9.96        49.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.69         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       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 
       34.49        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        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-A002 
       32.98         0.99        19.04        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-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-DC-6155 
       61.97        41.00         1.45         1.81        10.19        13.97 
TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
        5.95         5.29        19.96         8.61        13.64        17.46 
TCGA-F5-6814 TCGA-F5-6861 
        0.53         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 
                         17.460                          13.955 
[1] "0.4 - 129.3 (17.5)" "0.5 - 70.0 (14.0)" 
[1] "hr=" "3.1"
D13V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 13(13Q12.13) MUTATED        21        2        30         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         21
  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                             30                              10
  STAGE IIB                              2                               0
  STAGE IIC                              2                               0
  STAGE III                              4                               1
  STAGE IIIA                             6                               3
  STAGE IIIB                            21                               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 85 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                            85                              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   57 37 30
  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                            57                              28
  N1                            37                               8
  N2                            30                               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"
D13V6, binary
                                 cls
clus                               0  1
  AMP PEAK 13(13Q12.13) MUTATED   94 19
  AMP PEAK 13(13Q12.13) WILD-TYPE 32  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED     94   19
  AMP PEAK 13(13Q12.13) WILD-TYPE   32    5
   clus
vv  AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  0                            94                              32
  1                            19                               5
[1] 2 2
[1] FALSE
D13V7, binary
                                 cls
clus                               0  1
  AMP PEAK 13(13Q12.13) MUTATED   57 69
  AMP PEAK 13(13Q12.13) WILD-TYPE 19 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED     57   69
  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                            57                              19
  MALE                              69                              20
[1] 2 2
[1] FALSE
D13V8, binary
                                 cls
clus                               0  1
  AMP PEAK 13(13Q12.13) MUTATED   70 16
  AMP PEAK 13(13Q12.13) WILD-TYPE 23  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED     70   16
  AMP PEAK 13(13Q12.13) WILD-TYPE   23    3
     clus
vv    AMP PEAK 13(13Q12.13) MUTATED AMP PEAK 13(13Q12.13) WILD-TYPE
  NO                             70                              23
  YES                            16                               3
[1] 2 2
[1] FALSE
D13V9, binary
                                 cls
clus                                0   1
  AMP PEAK 13(13Q12.13) MUTATED   117   5
  AMP PEAK 13(13Q12.13) WILD-TYPE  29   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(13Q12.13) MUTATED    117    5
  AMP PEAK 13(13Q12.13) WILD-TYPE   29    8
                                clus
vv                               AMP PEAK 13(13Q12.13) MUTATED
  RECTAL ADENOCARCINOMA                                    117
  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
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 13(13Q12.13) MUTATED   90  2  9  3
  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                            90                              33
  R1                             2                               0
  R2                             9                               3
  RX                             3                               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                         6    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                             6
  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   102  19
  AMP PEAK 14(13Q12.2) WILD-TYPE  36   3
  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE 
                           121                             39 
  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        39.48        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-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       86.63        65.98        11.84         7.07        36.03        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
        1.02        46.03        34.03        34.03        34.03         2.01 
TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 
        0.99        19.99        13.94        19.99        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       29.98         0.99        19.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 
       17.03        35.01        14.01         1.02        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       28.04        36.03        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 
       46.03         6.02        25.97        23.01        37.02        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       36.03         9.07        12.00        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 
       38.96        41.00        38.04        38.56         0.69         0.72 
TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       26.43         6.05         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
        8.98        15.02        27.95        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.03       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-6508 
       51.48        32.61         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-7002 TCGA-EI-7004 TCGA-F5-6464 
       16.41        11.51        10.78        11.97         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.76        12.46        18.28        55.76        47.08 
TCGA-G5-6641 
       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 
       34.49        16.83        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-3881 TCGA-AG-3892 TCGA-AG-3898 
       37.02        32.98         0.99        19.04        13.02        48.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       20.98        13.94         1.02        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 
       10.98        61.97         1.45         1.81        10.19        33.17 
TCGA-DC-6155 TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 
       13.97         5.95         5.29        19.96         8.61        13.64 
TCGA-EI-6917 TCGA-F5-6814 TCGA-F5-6861 
       17.46         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 
                         17.69                          13.97 
[1] "0.4 - 129.3 (17.7)" "0.5 - 70.0 (14.0)" 
[1] "hr=" "1.9"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 14(13Q12.2) MUTATED        21        2        30         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         21         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                            30                             10
  STAGE IIB                             2                              0
  STAGE IIC                             2                              0
  STAGE III                             4                              1
  STAGE IIIA                            6                              3
  STAGE IIIB                           21                              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 84 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                           84                             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   57 36 30
  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                           57                             28
  N1                           36                              9
  N2                           30                              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"
D14V6, binary
                                cls
clus                              0  1
  AMP PEAK 14(13Q12.2) MUTATED   94 18
  AMP PEAK 14(13Q12.2) WILD-TYPE 32  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED     94   18
  AMP PEAK 14(13Q12.2) WILD-TYPE   32    6
   clus
vv  AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  0                           94                             32
  1                           18                              6
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                              0  1
  AMP PEAK 14(13Q12.2) MUTATED   55 70
  AMP PEAK 14(13Q12.2) WILD-TYPE 21 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED     55   70
  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                           55                             21
  MALE                             70                             19
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                              0  1
  AMP PEAK 14(13Q12.2) MUTATED   68 16
  AMP PEAK 14(13Q12.2) WILD-TYPE 25  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED     68   16
  AMP PEAK 14(13Q12.2) WILD-TYPE   25    3
     clus
vv    AMP PEAK 14(13Q12.2) MUTATED AMP PEAK 14(13Q12.2) WILD-TYPE
  NO                            68                             25
  YES                           16                              3
[1] 2 2
[1] FALSE
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q12.2) MUTATED   116   5
  AMP PEAK 14(13Q12.2) WILD-TYPE  30   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q12.2) MUTATED    116    5
  AMP PEAK 14(13Q12.2) WILD-TYPE   30    8
                                clus
vv                               AMP PEAK 14(13Q12.2) MUTATED
  RECTAL ADENOCARCINOMA                                   116
  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
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 14(13Q12.2) MUTATED   90  2  9  3
  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                           90                             33
  R1                            2                              0
  R2                            9                              3
  RX                            3                              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                         6    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                            6
  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   99 17
  AMP PEAK 15(13Q22.1) WILD-TYPE 39  5
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                           116                             44 
  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                            17                              5 
$`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        39.48        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-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       86.63        65.98        11.84         7.07        36.03        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3605 
        1.02        46.03        34.03        34.03        34.03         0.99 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 
       19.99        13.94        19.99        20.98         0.99        29.98 
TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.99         1.02        17.95        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        46.03         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01L 
       25.97        23.01        15.95        36.03         9.07        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       70.03        64.01        51.98        49.97         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       38.04        38.56         0.69         0.72        26.43         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        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        11.01        15.02         5.03         8.98        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         4.01         5.03         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-6509 TCGA-EI-6510 TCGA-EI-6511 
       32.61         0.49        20.55        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-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
       32.19         0.66         0.69         0.76        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       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 
       34.49        16.83        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-3881 TCGA-AG-3892 
        7.99        37.02        32.98         0.99        19.04        13.02 
TCGA-AG-3898 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01J 
       48.03         3.98        20.98        13.94        37.02         1.02 
TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 
       31.00        10.98        61.97        41.00         1.45         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6681 TCGA-EF-5831 TCGA-EI-6507 
       10.19        33.17        13.97         5.95         2.40        19.96 
TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6814 
       20.91         8.61        13.64        17.46         8.45         0.53 
TCGA-F5-6861 TCGA-F5-6864 
        1.12        12.46 

  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE 
                          0.39                           0.53 
  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 
                        18.115                         13.790 
[1] "0.4 - 129.3 (18.1)" "0.5 - 62.0 (13.8)" 
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 15(13Q22.1) MUTATED        20        5        27         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         13
  AMP PEAK 15(13Q22.1) WILD-TYPE         1          3          5          1
                                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                            27                             13
  STAGE IIB                             2                              0
  STAGE IIC                             2                              0
  STAGE III                             4                              1
  STAGE IIIA                            6                              3
  STAGE IIIB                           19                              5
  STAGE IIIC                           13                              1
  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 81 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                           81                             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   56 35 27
  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                           56                             29
  N1                           35                             10
  N2                           27                              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"
D15V6, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   90 17
  AMP PEAK 15(13Q22.1) WILD-TYPE 36  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     90   17
  AMP PEAK 15(13Q22.1) WILD-TYPE   36    7
   clus
vv  AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  0                           90                             36
  1                           17                              7
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   53 67
  AMP PEAK 15(13Q22.1) WILD-TYPE 23 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     53   67
  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                           53                             23
  MALE                             67                             22
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                              0  1
  AMP PEAK 15(13Q22.1) MUTATED   63 16
  AMP PEAK 15(13Q22.1) WILD-TYPE 30  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED     63   16
  AMP PEAK 15(13Q22.1) WILD-TYPE   30    3
     clus
vv    AMP PEAK 15(13Q22.1) MUTATED AMP PEAK 15(13Q22.1) WILD-TYPE
  NO                            63                             30
  YES                           16                              3
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                               0   1
  AMP PEAK 15(13Q22.1) MUTATED   112   4
  AMP PEAK 15(13Q22.1) WILD-TYPE  34   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(13Q22.1) MUTATED    112    4
  AMP PEAK 15(13Q22.1) WILD-TYPE   34    9
                                clus
vv                               AMP PEAK 15(13Q22.1) MUTATED
  RECTAL ADENOCARCINOMA                                   112
  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
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 15(13Q22.1) MUTATED   85  2  8  4
  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                           85                             38
  R1                            2                              0
  R2                            8                              4
  RX                            4                              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                         6    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                            6
  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 127  20
  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                            13                            147 
  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 
       34.49        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         7.17        41.36         8.45         9.96 
TCGA-F5-6864 
       12.46 

$`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        39.48        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        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        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        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        13.94        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        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-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         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-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-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-6897 TCGA-AH-6903 TCGA-CI-6619 
       38.56         1.45         0.72        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4745 
       33.17         6.97         4.73        12.39        78.12        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        57.24       129.27        24.13        51.48 
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-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
       11.97        49.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
        0.66         0.69         0.53         1.12         0.76        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE 
                          0.69                           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 
                         12.46                          17.03 
[1] "0.7 - 70.0 (12.5)"  "0.4 - 129.3 (17.0)"
[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        37         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 16(15Q26.1) MUTATED           0          0          3          3
  AMP PEAK 16(15Q26.1) WILD-TYPE         5          9         21         11
                                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                             37
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             0                              5
  STAGE IIIA                            0                              9
  STAGE IIIB                            3                             21
  STAGE IIIC                            3                             11
  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  28 103  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                            103
  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 79 43 28
D16V5, multiclass
    clus
vv   AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  N0                            6                             79
  N1                            2                             43
  N2                            5                             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"
D16V6, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.1) MUTATED    11   0
  AMP PEAK 16(15Q26.1) WILD-TYPE 115  24
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED     11    0
  AMP PEAK 16(15Q26.1) WILD-TYPE  115   24
   clus
vv  AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  0                           11                            115
  1                            0                             24
[1] 2 2
[1] FALSE
D16V7, binary
                                cls
clus                              0  1
  AMP PEAK 16(15Q26.1) MUTATED    8  5
  AMP PEAK 16(15Q26.1) WILD-TYPE 68 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED      8    5
  AMP PEAK 16(15Q26.1) WILD-TYPE   68   84
        clus
vv       AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  FEMALE                            8                             68
  MALE                              5                             84
[1] 2 2
[1] FALSE
D16V8, binary
                                cls
clus                              0  1
  AMP PEAK 16(15Q26.1) MUTATED    6  3
  AMP PEAK 16(15Q26.1) WILD-TYPE 87 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED      6    3
  AMP PEAK 16(15Q26.1) WILD-TYPE   87   16
     clus
vv    AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  NO                             6                             87
  YES                            3                             16
[1] 2 2
[1] FALSE
D16V9, binary
                                cls
clus                               0   1
  AMP PEAK 16(15Q26.1) MUTATED    11   2
  AMP PEAK 16(15Q26.1) WILD-TYPE 135  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(15Q26.1) MUTATED     11    2
  AMP PEAK 16(15Q26.1) WILD-TYPE  135   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                                     135
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[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 113   2  12   3
D16V10, multiclass
    clus
vv   AMP PEAK 16(15Q26.1) MUTATED AMP PEAK 16(15Q26.1) WILD-TYPE
  R0                           10                            113
  R1                            0                              2
  R2                            0                             12
  RX                            1                              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"
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                         6    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                              6
  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   40  6
  AMP PEAK 17(16P11.2) WILD-TYPE 98 16
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                            46                            114 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                             6                             16 
$`AMP PEAK 17(16P11.2) MUTATED`
TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       39.48        37.74        10.39        15.39        20.02        86.63 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3725 
       65.98        36.03        34.03         6.05        13.94        20.98 
TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3909 TCGA-AG-4001 
        7.99        37.02        17.95        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        46.03        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        78.12        11.01         5.03         8.98         5.03 
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        49.51 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
       28.57         0.39        32.19         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        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       14.50        16.83        10.39        11.84        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        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        19.99        19.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 
       32.02        28.04        14.04        17.03         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       13.94         6.02        25.97        23.01        37.02         1.02 
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-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00        38.56         1.45         0.69        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        1.81         6.05        33.17         4.73        12.39         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       21.01        15.02        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         4.01         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       57.24       129.27        32.61         2.40        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
       20.91        17.00        18.28        15.85        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        8.45         9.96        31.30         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        1.12        12.46        18.28        55.76        47.08        26.43 

  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                          0.39                           0.53 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                         86.63                         129.27 
  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE 
                        17.820                         16.915 
[1] "0.4 - 86.6 (17.8)"  "0.5 - 129.3 (16.9)"
[1] "hr=" "1.2"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 17(16P11.2) MUTATED         6        1         8         2         0
  AMP PEAK 17(16P11.2) WILD-TYPE      24        7        32         0         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 17(16P11.2) MUTATED           1          1         11          5
  AMP PEAK 17(16P11.2) WILD-TYPE         4          8         13          9
                                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                             8                             32
  STAGE IIB                             2                              0
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            1                              8
  STAGE IIIB                           11                             13
  STAGE IIIC                            5                              9
  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 32  6
  AMP PEAK 17(16P11.2) WILD-TYPE  7 22 80  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                           32                             80
  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   18 18 10
  AMP PEAK 17(16P11.2) WILD-TYPE 67 27 23
D17V5, multiclass
    clus
vv   AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  N0                           18                             67
  N1                           18                             27
  N2                           10                             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"
D17V6, binary
                                cls
clus                              0  1
  AMP PEAK 17(16P11.2) MUTATED   31 11
  AMP PEAK 17(16P11.2) WILD-TYPE 95 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED     31   11
  AMP PEAK 17(16P11.2) WILD-TYPE   95   13
   clus
vv  AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  0                           31                             95
  1                           11                             13
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                              0  1
  AMP PEAK 17(16P11.2) MUTATED   20 27
  AMP PEAK 17(16P11.2) WILD-TYPE 56 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED     20   27
  AMP PEAK 17(16P11.2) WILD-TYPE   56   62
        clus
vv       AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  FEMALE                           20                             56
  MALE                             27                             62
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                              0  1
  AMP PEAK 17(16P11.2) MUTATED   25  7
  AMP PEAK 17(16P11.2) WILD-TYPE 68 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED     25    7
  AMP PEAK 17(16P11.2) WILD-TYPE   68   12
     clus
vv    AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  NO                            25                             68
  YES                            7                             12
[1] 2 2
[1] FALSE
D17V9, binary
                                cls
clus                              0  1
  AMP PEAK 17(16P11.2) MUTATED   47  0
  AMP PEAK 17(16P11.2) WILD-TYPE 99 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(16P11.2) MUTATED     47    0
  AMP PEAK 17(16P11.2) WILD-TYPE   99   13
                                clus
vv                               AMP PEAK 17(16P11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    47
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 17(16P11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      99
  RECTAL MUCINOUS ADENOCARCINOMA                             13
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 17(16P11.2) MUTATED   30  0  7  2
  AMP PEAK 17(16P11.2) WILD-TYPE 93  2  5  2
D17V10, multiclass
    clus
vv   AMP PEAK 17(16P11.2) MUTATED AMP PEAK 17(16P11.2) WILD-TYPE
  R0                           30                             93
  R1                            0                              2
  R2                            7                              5
  RX                            2                              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                         4    22
  AMP PEAK 17(16P11.2) WILD-TYPE     1                         2    59
D17V12, multiclass
                           clus
vv                          AMP PEAK 17(16P11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               22
                           clus
vv                          AMP PEAK 17(16P11.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  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   40  4
  AMP PEAK 18(17Q12) WILD-TYPE 98 18
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                          44                          116 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                           4                           18 
$`AMP PEAK 18(17Q12) MUTATED`
TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 
       17.23        86.63        65.98        11.84        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       36.03        46.03        34.03        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3898 TCGA-AG-3902 
       19.99         0.99        19.99         1.02        48.03        32.02 
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-A01Y TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6623 
       64.01        51.98         0.69        26.43         6.05         9.37 
TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DG TCGA-EI-6509 
        8.98         4.01         5.03         5.29        51.48        17.00 
TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 
       18.28        16.31        11.97        32.19         0.69        12.46 
TCGA-G5-6235 TCGA-G5-6641 
       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        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       37.74        10.39        14.50        16.83        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        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        6.05         0.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3887 
       37.02        32.98         0.99        19.04        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3909 
       17.03        13.02        35.01        14.01         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04        14.04         3.98        46.03        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        38.56         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        33.17         6.97         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
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        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       28.57         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 
                        0.69                         0.39 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                       86.63                       129.27 
  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE 
                      17.015                       17.245 
[1] "0.7 - 86.6 (17.0)"  "0.4 - 129.3 (17.2)"
[1] "hr=" "2.1"
D18V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 18(17Q12) MUTATED         8        3        12         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          5          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                          12                           28
  STAGE IIB                           0                            2
  STAGE IIC                           0                            2
  STAGE III                           1                            4
  STAGE IIIA                          1                            8
  STAGE IIIB                          5                           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 30  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                         30                           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   25  9 12
  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                         25                           60
  N1                          9                           36
  N2                         12                           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"
D18V6, binary
                              cls
clus                            0  1
  AMP PEAK 18(17Q12) MUTATED   33  9
  AMP PEAK 18(17Q12) WILD-TYPE 93 15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED     33    9
  AMP PEAK 18(17Q12) WILD-TYPE   93   15
   clus
vv  AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  0                         33                           93
  1                          9                           15
[1] 2 2
[1] FALSE
D18V7, binary
                              cls
clus                            0  1
  AMP PEAK 18(17Q12) MUTATED   18 28
  AMP PEAK 18(17Q12) WILD-TYPE 58 61
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED     18   28
  AMP PEAK 18(17Q12) WILD-TYPE   58   61
        clus
vv       AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  FEMALE                         18                           58
  MALE                           28                           61
[1] 2 2
[1] FALSE
D18V8, binary
                              cls
clus                            0  1
  AMP PEAK 18(17Q12) MUTATED   28  3
  AMP PEAK 18(17Q12) WILD-TYPE 65 16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED     28    3
  AMP PEAK 18(17Q12) WILD-TYPE   65   16
     clus
vv    AMP PEAK 18(17Q12) MUTATED AMP PEAK 18(17Q12) WILD-TYPE
  NO                          28                           65
  YES                          3                           16
[1] 2 2
[1] FALSE
D18V9, binary
                              cls
clus                             0   1
  AMP PEAK 18(17Q12) MUTATED    44   2
  AMP PEAK 18(17Q12) WILD-TYPE 102  11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 18(17Q12) MUTATED     44    2
  AMP PEAK 18(17Q12) WILD-TYPE  102   11
                                clus
vv                               AMP PEAK 18(17Q12) MUTATED
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          2
                                clus
vv                               AMP PEAK 18(17Q12) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   102
  RECTAL MUCINOUS ADENOCARCINOMA                           11
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 18(17Q12) MUTATED   32  1  6  2
  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                         32                           91
  R1                          1                            1
  R2                          6                            6
  RX                          2                            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                         3    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                          3
  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    33   4
  AMP PEAK 19(17Q24.1) WILD-TYPE 105  18
  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                            37                            123 
  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-AF-A56K TCGA-AF-A56N TCGA-AG-3575 
       39.48        17.23        13.55        86.63        11.84        12.00 
TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3608 TCGA-AG-3609 
        7.07        46.03        34.03        50.04        15.95        19.99 
TCGA-AG-3612 TCGA-AG-3882 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-A014 
       19.99        19.99        36.03         1.02        17.03        15.95 
TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A023 TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 
        9.07        31.00        51.98         0.69        26.43         6.05 
TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 
        8.98         4.01         5.03       129.27        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 TCGA-F5-6864 
        2.40        18.28        16.31        11.97        32.19        12.46 
TCGA-G5-6235 
       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        34.49        37.74        10.39 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       14.50        16.83        15.39        20.02        10.39        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        32.02         8.02        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
        1.02        34.03        34.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        13.94        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3883 
       37.02        32.98         0.99         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        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-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        3.98        46.03        20.98        13.94         6.02        25.97 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01W 
       23.01        37.02        36.03         1.02        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
       64.01        10.98        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-6903 
       41.00        38.04        38.56         1.45         0.72         1.81 
TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
       10.19        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.29       126.44        41.36        57.24        24.13        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        15.85        17.69 
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-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46         8.45         9.96        49.51        31.30        28.57 
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-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       18.28        47.08        26.43 

  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE 
                          0.49                           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 
                         17.03                          17.03 
[1] "0.5 - 129.3 (17.0)" "0.4 - 126.4 (17.0)"
[1] "hr=" "1.7"
D19V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 19(17Q24.1) MUTATED         5        1        13         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          5          3
  AMP PEAK 19(17Q24.1) WILD-TYPE         4          9         19         11
                                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                            13                             27
  STAGE IIB                             1                              1
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            5                             19
  STAGE IIIC                            3                             11
  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 27  5
  AMP PEAK 19(17Q24.1) WILD-TYPE  9 22 85  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                           27                             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 19(17Q24.1) MUTATED   22  7 10
  AMP PEAK 19(17Q24.1) WILD-TYPE 63 38 23
D19V5, multiclass
    clus
vv   AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  N0                           22                             63
  N1                            7                             38
  N2                           10                             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"
D19V6, binary
                                cls
clus                              0  1
  AMP PEAK 19(17Q24.1) MUTATED   27  9
  AMP PEAK 19(17Q24.1) WILD-TYPE 99 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED     27    9
  AMP PEAK 19(17Q24.1) WILD-TYPE   99   15
   clus
vv  AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  0                           27                             99
  1                            9                             15
[1] 2 2
[1] FALSE
D19V7, binary
                                cls
clus                              0  1
  AMP PEAK 19(17Q24.1) MUTATED   18 21
  AMP PEAK 19(17Q24.1) WILD-TYPE 58 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED     18   21
  AMP PEAK 19(17Q24.1) WILD-TYPE   58   68
        clus
vv       AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  FEMALE                           18                             58
  MALE                             21                             68
[1] 2 2
[1] FALSE
D19V8, binary
                                cls
clus                              0  1
  AMP PEAK 19(17Q24.1) MUTATED   23  3
  AMP PEAK 19(17Q24.1) WILD-TYPE 70 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED     23    3
  AMP PEAK 19(17Q24.1) WILD-TYPE   70   16
     clus
vv    AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  NO                            23                             70
  YES                            3                             16
[1] 2 2
[1] FALSE
D19V9, binary
                                cls
clus                               0   1
  AMP PEAK 19(17Q24.1) MUTATED    38   0
  AMP PEAK 19(17Q24.1) WILD-TYPE 108  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 19(17Q24.1) MUTATED     38    0
  AMP PEAK 19(17Q24.1) WILD-TYPE  108   13
                                clus
vv                               AMP PEAK 19(17Q24.1) MUTATED
  RECTAL ADENOCARCINOMA                                    38
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 19(17Q24.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     108
  RECTAL MUCINOUS ADENOCARCINOMA                             13
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 19(17Q24.1) MUTATED   28  1  5  0
  AMP PEAK 19(17Q24.1) WILD-TYPE 95  1  7  4
D19V10, multiclass
    clus
vv   AMP PEAK 19(17Q24.1) MUTATED AMP PEAK 19(17Q24.1) WILD-TYPE
  R0                           28                             95
  R1                            1                              1
  R2                            5                              7
  RX                            0                              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"
D19V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 19(17Q24.1) MUTATED       0                         2    20
  AMP PEAK 19(17Q24.1) WILD-TYPE     1                         4    61
D19V12, multiclass
                           clus
vv                          AMP PEAK 19(17Q24.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               20
                           clus
vv                          AMP PEAK 19(17Q24.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  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    29   6
  AMP PEAK 20(19P13.2) WILD-TYPE 109  16
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                            35                            125 
  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-AF-A56K TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3591 
       17.23        10.39        86.63        65.98        36.03        34.03 
TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3878 TCGA-AG-3885 
       34.03         6.05        19.99        13.94         0.99        17.95 
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        46.03        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        21.01        11.01         8.98 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DD TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6506 
       27.95         4.01        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        39.48        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.04        19.99         1.02        36.95        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-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
       17.03         3.98        20.98        13.94         6.02        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-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
       70.03        64.01        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 
        9.37         4.73        12.39        78.12         7.17        15.02 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03        13.97        15.02        10.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG 
        5.03         5.29       126.44        41.36       129.27        51.48 
TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61         2.40        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       15.85        16.34        16.41         8.61        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         0.66         0.69         0.53         1.12 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        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 
                         86.63                         129.27 
  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE 
                         17.69                          17.00 
[1] "0.5 - 86.6 (17.7)"  "0.4 - 129.3 (17.0)"
[1] "hr=" "1.3"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 20(19P13.2) MUTATED         4        2         8         1         1
  AMP PEAK 20(19P13.2) WILD-TYPE      26        6        32         1         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 20(19P13.2) MUTATED           1          0          7          6
  AMP PEAK 20(19P13.2) WILD-TYPE         4          9         17          8
                                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                             8                             32
  STAGE IIB                             1                              1
  STAGE IIC                             1                              1
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            7                             17
  STAGE IIIC                            6                              8
  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 26  5
  AMP PEAK 20(19P13.2) WILD-TYPE  9 24 86  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                           26                             86
  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   17 10  9
  AMP PEAK 20(19P13.2) WILD-TYPE 68 35 24
D20V5, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  N0                           17                             68
  N1                           10                             35
  N2                            9                             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"
D20V6, binary
                                cls
clus                              0  1
  AMP PEAK 20(19P13.2) MUTATED   29  6
  AMP PEAK 20(19P13.2) WILD-TYPE 97 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     29    6
  AMP PEAK 20(19P13.2) WILD-TYPE   97   18
   clus
vv  AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  0                           29                             97
  1                            6                             18
[1] 2 2
[1] FALSE
D20V7, binary
                                cls
clus                              0  1
  AMP PEAK 20(19P13.2) MUTATED   18 18
  AMP PEAK 20(19P13.2) WILD-TYPE 58 71
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     18   18
  AMP PEAK 20(19P13.2) WILD-TYPE   58   71
        clus
vv       AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  FEMALE                           18                             58
  MALE                             18                             71
[1] 2 2
[1] FALSE
D20V8, binary
                                cls
clus                              0  1
  AMP PEAK 20(19P13.2) MUTATED   18  5
  AMP PEAK 20(19P13.2) WILD-TYPE 75 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     18    5
  AMP PEAK 20(19P13.2) WILD-TYPE   75   14
     clus
vv    AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  NO                            18                             75
  YES                            5                             14
[1] 2 2
[1] FALSE
D20V9, binary
                                cls
clus                               0   1
  AMP PEAK 20(19P13.2) MUTATED    36   0
  AMP PEAK 20(19P13.2) WILD-TYPE 110  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 20(19P13.2) MUTATED     36    0
  AMP PEAK 20(19P13.2) WILD-TYPE  110   13
                                clus
vv                               AMP PEAK 20(19P13.2) MUTATED
  RECTAL ADENOCARCINOMA                                    36
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 20(19P13.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     110
  RECTAL MUCINOUS ADENOCARCINOMA                             13
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 20(19P13.2) MUTATED   28  1  3  1
  AMP PEAK 20(19P13.2) WILD-TYPE 95  1  9  3
D20V10, multiclass
    clus
vv   AMP PEAK 20(19P13.2) MUTATED AMP PEAK 20(19P13.2) WILD-TYPE
  R0                           28                             95
  R1                            1                              1
  R2                            3                              9
  RX                            1                              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                         4    15
  AMP PEAK 20(19P13.2) WILD-TYPE     1                         2    66
D20V12, multiclass
                           clus
vv                          AMP PEAK 20(19P13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               15
                           clus
vv                          AMP PEAK 20(19P13.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  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   121  20
  AMP PEAK 21(20Q11.21) WILD-TYPE  17   2
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                            141                              19 
  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE 
                             20                               2 
$`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        39.48        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        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 
       86.63        65.98        11.84        36.03         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98        37.02         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         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-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        46.03        13.94         6.02        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-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         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        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       15.02        27.95        10.98        19.99         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
        5.03       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-6508 
       51.48        32.61         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-F5-6464 
       16.41        11.51        10.78        13.64        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       49.51        31.30        28.57         0.39        32.19         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        12.46        18.28 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        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        34.49        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 
       32.98        19.04        13.02         3.98        20.98        49.97 
TCGA-AG-A02N TCGA-CI-6620 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 
       61.97        33.17         5.29        19.96         8.61        17.46 
TCGA-EI-7004 
        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 
                          17.03                           17.46 
[1] "0.4 - 129.3 (17.0)" "2.0 - 62.0 (17.5)" 
[1] "hr=" "1.2"
D21V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 21(20Q11.21) MUTATED        26        5        33         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         24
  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                             33                               7
  STAGE IIB                              2                               0
  STAGE IIC                              2                               0
  STAGE III                              5                               0
  STAGE IIIA                             8                               1
  STAGE IIIB                            24                               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 98 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                            98                              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   71 43 30
  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                            71                              14
  N1                            43                               2
  N2                            30                               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"
D21V6, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q11.21) MUTATED   109  22
  AMP PEAK 21(20Q11.21) WILD-TYPE  17   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED    109   22
  AMP PEAK 21(20Q11.21) WILD-TYPE   17    2
   clus
vv  AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  0                           109                              17
  1                            22                               2
[1] 2 2
[1] FALSE
D21V7, binary
                                 cls
clus                               0  1
  AMP PEAK 21(20Q11.21) MUTATED   67 79
  AMP PEAK 21(20Q11.21) WILD-TYPE  9 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED     67   79
  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                            67                               9
  MALE                              79                              10
[1] 2 2
[1] FALSE
D21V8, binary
                                 cls
clus                               0  1
  AMP PEAK 21(20Q11.21) MUTATED   78 17
  AMP PEAK 21(20Q11.21) WILD-TYPE 15  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED     78   17
  AMP PEAK 21(20Q11.21) WILD-TYPE   15    2
     clus
vv    AMP PEAK 21(20Q11.21) MUTATED AMP PEAK 21(20Q11.21) WILD-TYPE
  NO                             78                              15
  YES                            17                               2
[1] 2 2
[1] FALSE
D21V9, binary
                                 cls
clus                                0   1
  AMP PEAK 21(20Q11.21) MUTATED   135   7
  AMP PEAK 21(20Q11.21) WILD-TYPE  11   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 21(20Q11.21) MUTATED    135    7
  AMP PEAK 21(20Q11.21) WILD-TYPE   11    6
                                clus
vv                               AMP PEAK 21(20Q11.21) MUTATED
  RECTAL ADENOCARCINOMA                                    135
  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
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 21(20Q11.21) MUTATED   108   2  11   3
  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                           108                              15
  R1                             2                               0
  R2                            11                               1
  RX                             3                               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                         6    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                             6
  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   122  20
  AMP PEAK 22(20Q11.23) WILD-TYPE  16   2
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                            142                              18 
  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE 
                             20                               2 
$`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        39.48        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        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 
       86.63        65.98        11.84        36.03         8.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98        37.02         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        17.03        35.01        14.01         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-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H 
        1.02        17.03        46.03        13.94         6.02        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-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 
       12.00        31.00        70.03        64.01        10.98        51.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.94        38.96        41.00        38.04        38.56         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        4.01         5.03       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-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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.31        16.41        11.51        10.78        13.64        11.97 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        9.96        49.51        31.30        28.57         0.39        32.19 
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        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       18.28        55.76        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        34.49        12.00        32.02         2.01         6.05 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 
       32.98        19.04        13.02         3.98        20.98        49.97 
TCGA-AG-A02N TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       61.97         5.29        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 
                         17.030                          15.505 
[1] "0.4 - 129.3 (17.0)" "2.0 - 62.0 (15.5)" 
[1] "hr=" "1.1"
D22V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 22(20Q11.23) MUTATED        26        5        33         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         24
  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                             33                               7
  STAGE IIB                              2                               0
  STAGE IIC                              2                               0
  STAGE III                              5                               0
  STAGE IIIA                             8                               1
  STAGE IIIB                            24                               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 99 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                            99                              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   71 44 30
  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                            71                              14
  N1                            44                               1
  N2                            30                               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"
D22V6, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.23) MUTATED   109  23
  AMP PEAK 22(20Q11.23) WILD-TYPE  17   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.23) MUTATED    109   23
  AMP PEAK 22(20Q11.23) WILD-TYPE   17    1
   clus
vv  AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  0                           109                              17
  1                            23                               1
[1] 2 2
[1] FALSE
D22V7, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.23) MUTATED   68 79
  AMP PEAK 22(20Q11.23) WILD-TYPE  8 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.23) MUTATED     68   79
  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                            68                               8
  MALE                              79                              10
[1] 2 2
[1] FALSE
D22V8, binary
                                 cls
clus                               0  1
  AMP PEAK 22(20Q11.23) MUTATED   79 17
  AMP PEAK 22(20Q11.23) WILD-TYPE 14  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.23) MUTATED     79   17
  AMP PEAK 22(20Q11.23) WILD-TYPE   14    2
     clus
vv    AMP PEAK 22(20Q11.23) MUTATED AMP PEAK 22(20Q11.23) WILD-TYPE
  NO                             79                              14
  YES                            17                               2
[1] 2 2
[1] FALSE
D22V9, binary
                                 cls
clus                                0   1
  AMP PEAK 22(20Q11.23) MUTATED   136   7
  AMP PEAK 22(20Q11.23) WILD-TYPE  10   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 22(20Q11.23) MUTATED    136    7
  AMP PEAK 22(20Q11.23) WILD-TYPE   10    6
                                clus
vv                               AMP PEAK 22(20Q11.23) MUTATED
  RECTAL ADENOCARCINOMA                                    136
  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
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 22(20Q11.23) MUTATED   108   2  11   3
  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                           108                              15
  R1                             2                               0
  R2                            11                               1
  RX                             3                               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                         6    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                             6
  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(20Q13.31) MUTATION ANALYSIS
D23V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 23(20Q13.31) MUTATED   123  20
  AMP PEAK 23(20Q13.31) WILD-TYPE  15   2
  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                            143                              17 
  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                             20                               2 
$`AMP PEAK 23(20Q13.31) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        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        16.83        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3580 
       10.39        86.63        65.98        11.84        36.03         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        7.07        36.03        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03        34.03        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
        0.99        29.98        37.02         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        17.03        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-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        17.03        46.03        13.94         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-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-AG-A032 TCGA-AH-6544 
       51.98         1.94        38.96        41.00        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 
        6.05        33.17         6.97         9.37         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        11.01        15.02         5.03 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        8.98        13.97        15.02        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03       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-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31        16.41        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         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 
       12.46        18.28        55.76        47.08        26.43 

$`AMP PEAK 23(20Q13.31) WILD-TYPE`
TCGA-AF-3400 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 
       34.49        12.00        32.02         2.01         6.05        32.98 
TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N 
       19.04        13.02         3.98        20.98        49.97        61.97 
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 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                           0.39                            2.01 
  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                         129.27                           61.97 
  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE 
                          17.03                           17.46 
[1] "0.4 - 129.3 (17.0)" "2.0 - 62.0 (17.5)" 
[1] "hr=" "1.1"
D23V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 23(20Q13.31) MUTATED        26        5        34         2
  AMP PEAK 23(20Q13.31) WILD-TYPE       4        3         6         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 23(20Q13.31) MUTATED           2         5          8         24
  AMP PEAK 23(20Q13.31) WILD-TYPE         0         0          1          0
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 23(20Q13.31) MUTATED           13       17         8
  AMP PEAK 23(20Q13.31) WILD-TYPE          1        1         1
D23V3, multiclass
            clus
vv           AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  STAGE I                               26                               4
  STAGE II                               5                               3
  STAGE IIA                             34                               6
  STAGE IIB                              2                               0
  STAGE IIC                              2                               0
  STAGE III                              5                               0
  STAGE IIIA                             8                               1
  STAGE IIIB                            24                               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 23(20Q13.31) MUTATED     7  27 100  13
  AMP PEAK 23(20Q13.31) WILD-TYPE   2   2  12   1
D23V4, multiclass
    clus
vv   AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  T1                             7                               2
  T2                            27                               2
  T3                           100                              12
  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(20Q13.31) MUTATED   72 44 30
  AMP PEAK 23(20Q13.31) WILD-TYPE 13  1  3
D23V5, multiclass
    clus
vv   AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  N0                            72                              13
  N1                            44                               1
  N2                            30                               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"
D23V6, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q13.31) MUTATED   110  23
  AMP PEAK 23(20Q13.31) WILD-TYPE  16   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.31) MUTATED    110   23
  AMP PEAK 23(20Q13.31) WILD-TYPE   16    1
   clus
vv  AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  0                           110                              16
  1                            23                               1
[1] 2 2
[1] FALSE
D23V7, binary
                                 cls
clus                               0  1
  AMP PEAK 23(20Q13.31) MUTATED   69 79
  AMP PEAK 23(20Q13.31) WILD-TYPE  7 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.31) MUTATED     69   79
  AMP PEAK 23(20Q13.31) WILD-TYPE    7   10
        clus
vv       AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  FEMALE                            69                               7
  MALE                              79                              10
[1] 2 2
[1] FALSE
D23V8, binary
                                 cls
clus                               0  1
  AMP PEAK 23(20Q13.31) MUTATED   80 17
  AMP PEAK 23(20Q13.31) WILD-TYPE 13  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.31) MUTATED     80   17
  AMP PEAK 23(20Q13.31) WILD-TYPE   13    2
     clus
vv    AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  NO                             80                              13
  YES                            17                               2
[1] 2 2
[1] FALSE
D23V9, binary
                                 cls
clus                                0   1
  AMP PEAK 23(20Q13.31) MUTATED   136   7
  AMP PEAK 23(20Q13.31) WILD-TYPE  10   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 23(20Q13.31) MUTATED    136    7
  AMP PEAK 23(20Q13.31) WILD-TYPE   10    6
                                clus
vv                               AMP PEAK 23(20Q13.31) MUTATED
  RECTAL ADENOCARCINOMA                                    136
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 23(20Q13.31) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       10
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 23(20Q13.31) MUTATED   109   2  11   3
  AMP PEAK 23(20Q13.31) WILD-TYPE  14   0   1   1
D23V10, multiclass
    clus
vv   AMP PEAK 23(20Q13.31) MUTATED AMP PEAK 23(20Q13.31) WILD-TYPE
  R0                           109                              14
  R1                             2                               0
  R2                            11                               1
  RX                             3                               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(20Q13.31) MUTATED       0                         6    76
  AMP PEAK 23(20Q13.31) WILD-TYPE     1                         0     5
D23V12, multiclass
                           clus
vv                          AMP PEAK 23(20Q13.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                76
                           clus
vv                          AMP PEAK 23(20Q13.31) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               0
  WHITE                                                   5
[1] 3 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    26   5
  AMP PEAK 24(XP22.2) WILD-TYPE 112  17
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                           31                           129 
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                            5                            17 
$`AMP PEAK 24(XP22.2) MUTATED`
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3591 
       10.39        16.83        20.02        86.63        36.03        34.03 
TCGA-AG-3592 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3999 TCGA-AG-4021 TCGA-AG-4022 
       34.03        19.99        19.99        28.04         3.98        46.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A02N 
       15.95        36.03         9.07        31.00        64.01        61.97 
TCGA-AG-A032 TCGA-AH-6644 TCGA-AH-6897 TCGA-DC-4745 TCGA-DC-6154 TCGA-DT-5265 
       38.04         0.72        26.43        21.01         8.98         5.29 
TCGA-DY-A1H8 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6863 
       32.61        18.28        17.69        13.64        11.97         0.76 
TCGA-G5-6235 
       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        39.48        17.23        43.04        13.55        19.10 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L 
       34.49        37.74        14.50        15.39        10.39        65.98 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3594 
       20.05        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-3611 
       50.04        12.03         6.05         0.99        15.95        13.94 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       20.98         7.99         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
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        38.56         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        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
        9.37         4.73        12.39        78.12         7.17        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       15.02         5.03        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03       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        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       32.19         0.66         0.69         0.53         1.12        12.46 
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 
                        86.63                        129.27 
  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE 
                        20.02                         16.31 
[1] "0.7 - 86.6 (20.0)"  "0.4 - 129.3 (16.3)"
[1] "hr=" "1.1"
D24V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 24(XP22.2) MUTATED         4        5         3         0         0
  AMP PEAK 24(XP22.2) WILD-TYPE      26        3        37         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         17         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                            3                            37
  STAGE IIB                            0                             2
  STAGE IIC                            0                             2
  STAGE III                            0                             5
  STAGE IIIA                           2                             7
  STAGE IIIB                           7                            17
  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 21  3
  AMP PEAK 24(XP22.2) WILD-TYPE  8 22 91 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                          21                            91
  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   14 11  6
  AMP PEAK 24(XP22.2) WILD-TYPE 71 34 27
D24V5, multiclass
    clus
vv   AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  N0                          14                            71
  N1                          11                            34
  N2                           6                            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"
D24V6, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP22.2) MUTATED    22   7
  AMP PEAK 24(XP22.2) WILD-TYPE 104  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP22.2) MUTATED     22    7
  AMP PEAK 24(XP22.2) WILD-TYPE  104   17
   clus
vv  AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  0                          22                           104
  1                           7                            17
[1] 2 2
[1] FALSE
D24V7, binary
                               cls
clus                             0  1
  AMP PEAK 24(XP22.2) MUTATED   18 14
  AMP PEAK 24(XP22.2) WILD-TYPE 58 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP22.2) MUTATED     18   14
  AMP PEAK 24(XP22.2) WILD-TYPE   58   75
        clus
vv       AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  FEMALE                          18                            58
  MALE                            14                            75
[1] 2 2
[1] FALSE
D24V8, binary
                               cls
clus                             0  1
  AMP PEAK 24(XP22.2) MUTATED   21  3
  AMP PEAK 24(XP22.2) WILD-TYPE 72 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP22.2) MUTATED     21    3
  AMP PEAK 24(XP22.2) WILD-TYPE   72   16
     clus
vv    AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  NO                           21                            72
  YES                           3                            16
[1] 2 2
[1] FALSE
D24V9, binary
                               cls
clus                              0   1
  AMP PEAK 24(XP22.2) MUTATED    31   1
  AMP PEAK 24(XP22.2) WILD-TYPE 115  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 24(XP22.2) MUTATED     31    1
  AMP PEAK 24(XP22.2) WILD-TYPE  115   12
                                clus
vv                               AMP PEAK 24(XP22.2) MUTATED
  RECTAL ADENOCARCINOMA                                   31
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK 24(XP22.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    115
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 24(XP22.2) MUTATED   24  1  4  1
  AMP PEAK 24(XP22.2) WILD-TYPE 99  1  8  3
D24V10, multiclass
    clus
vv   AMP PEAK 24(XP22.2) MUTATED AMP PEAK 24(XP22.2) WILD-TYPE
  R0                          24                            99
  R1                           1                             1
  R2                           4                             8
  RX                           1                             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"
D24V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 24(XP22.2) MUTATED       1                         2    13
  AMP PEAK 24(XP22.2) WILD-TYPE     0                         4    68
D24V12, multiclass
                           clus
vv                          AMP PEAK 24(XP22.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              13
                           clus
vv                          AMP PEAK 24(XP22.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             4
  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 = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.11) MUTATED   61 10
  DEL PEAK  1(1P36.11) WILD-TYPE 77 12
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            71                             89 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            10                             12 
$`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-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 
       14.50        15.39        86.63        65.98        11.84        32.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 
       36.03        20.05        24.00        46.03        34.03         6.05 
TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 
       19.99         0.99        29.98        37.02        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
        1.02        36.95        17.03         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       28.04        36.03        13.94        25.97        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       70.03        64.01        51.98         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4749 
       38.56         0.69        10.19         6.97         4.73        11.01 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
        5.03         8.98        13.97        15.02        27.95        19.99 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 
        5.95         5.03       126.44       129.27        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6702 
        2.40        20.55        15.85        11.97         8.45        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       32.19         0.69        12.46        47.08        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 
       39.48        34.49        37.74        16.83        20.02        10.39 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3591 
       36.03        12.00         8.02         7.07         1.02        34.03 
TCGA-AG-3592 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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3742 
       13.94        19.99        20.98         7.99        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 
        0.99        17.95        13.02        35.01        14.01        32.02 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       14.04         1.02        17.03         3.98        46.03        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        26.43         1.81         6.05        33.17         9.37 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6158 
       12.39        78.12         7.17        21.01        15.02        10.98 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        4.01         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        49.51        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 
                          0.49                           0.39 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                        129.27                          78.12 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                         19.99                          16.31 
[1] "0.5 - 129.3 (20.0)" "0.4 - 78.1 (16.3)" 
[1] "hr=" "1.3"
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  1(1P36.11) MUTATED        12        3        17         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         12          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
D25V3, 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                            17                             23
  STAGE IIB                             2                              0
  STAGE IIC                             0                              2
  STAGE III                             2                              3
  STAGE IIIA                            3                              6
  STAGE IIIB                           12                             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 48 10
  DEL PEAK  1(1P36.11) WILD-TYPE  7 15 64  4
D25V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            2                              7
  T2                           14                             15
  T3                           48                             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   34 22 18
  DEL PEAK  1(1P36.11) WILD-TYPE 51 23 15
D25V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           34                             51
  N1                           22                             23
  N2                           18                             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"
D25V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   55 13
  DEL PEAK  1(1P36.11) WILD-TYPE 71 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     55   13
  DEL PEAK  1(1P36.11) WILD-TYPE   71   11
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                           55                             71
  1                           13                             11
[1] 2 2
[1] FALSE
D25V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   34 41
  DEL PEAK  1(1P36.11) WILD-TYPE 42 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     34   41
  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                           34                             42
  MALE                             41                             48
[1] 2 2
[1] FALSE
D25V8, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   38 11
  DEL PEAK  1(1P36.11) WILD-TYPE 55  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     38   11
  DEL PEAK  1(1P36.11) WILD-TYPE   55    8
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                            38                             55
  YES                           11                              8
[1] 2 2
[1] FALSE
D25V9, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   64  7
  DEL PEAK  1(1P36.11) WILD-TYPE 82  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     64    7
  DEL PEAK  1(1P36.11) WILD-TYPE   82    6
                                clus
vv                               DEL PEAK  1(1P36.11) MUTATED
  RECTAL ADENOCARCINOMA                                    64
  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
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  1(1P36.11) MUTATED   54  1  7  1
  DEL PEAK  1(1P36.11) WILD-TYPE 69  1  5  3
D25V10, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  R0                           54                             69
  R1                            1                              1
  R2                            7                              5
  RX                            1                              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"
D25V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.11) MUTATED       0                         6    35
  DEL PEAK  1(1P36.11) WILD-TYPE     1                         0    46
D25V12, multiclass
                           clus
vv                          DEL PEAK  1(1P36.11) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            6
  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(26) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  2(1P33) MUTATED   45  6
  DEL PEAK  2(1P33) WILD-TYPE 93 16
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         51                         109 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                          6                          16 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K 
       24.13        17.23        13.55        14.50        15.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 
       65.98        11.84        32.02        36.03        24.00        34.03 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 
       29.98        37.02        19.04        19.99         1.02        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       19.99        28.04        36.03        25.97        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       70.03         1.94        38.96        38.04        38.56         0.69 
TCGA-BM-6198 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-4749 
       10.19         9.37         4.73        12.39        21.01        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
        5.03        13.97        27.95        19.99       126.44       129.27 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 
        0.49        20.55        15.85        13.64        11.97        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-G5-6572 
       32.19         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 
       39.48        43.04        19.10        34.49        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       16.83        20.02        10.39        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
        7.07        20.05         1.02        46.03        34.03        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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       32.98         0.99         0.99         1.02        17.95        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4005 
       17.03        13.02        35.01        14.01        32.02        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02        17.03         3.98        46.03        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        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
       33.17         6.97        78.12         7.17        15.02         8.98 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       15.02        10.98         5.95         4.01         5.03         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        49.51        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        12.46        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                       78.12 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                      20.55                       16.31 
[1] "0.5 - 129.3 (20.6)" "0.4 - 78.1 (16.3)" 
[1] "hr=" "1.7"
D26V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  2(1P33) MUTATED         7        2        15         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          6
  DEL PEAK  2(1P33) WILD-TYPE         4          7         15          8
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  2(1P33) MUTATED          6         2
  DEL PEAK  2(1P33) WILD-TYPE       12         7
D26V3, multiclass
            clus
vv           DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  STAGE I                            7                          23
  STAGE II                           2                           6
  STAGE IIA                         15                          25
  STAGE IIB                          1                           1
  STAGE IIC                          0                           2
  STAGE III                          1                           4
  STAGE IIIA                         2                           7
  STAGE IIIB                         9                          15
  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  2(1P33) MUTATED    1  8 39  4
  DEL PEAK  2(1P33) WILD-TYPE  8 21 73 10
D26V4, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         1                           8
  T2                         8                          21
  T3                        39                          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   25 18  9
  DEL PEAK  2(1P33) WILD-TYPE 60 27 24
D26V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        25                          60
  N1                        18                          27
  N2                         9                          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"
D26V6, binary
                             cls
clus                           0  1
  DEL PEAK  2(1P33) MUTATED   40  8
  DEL PEAK  2(1P33) WILD-TYPE 86 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     40    8
  DEL PEAK  2(1P33) WILD-TYPE   86   16
   clus
vv  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  0                        40                          86
  1                         8                          16
[1] 2 2
[1] FALSE
D26V7, binary
                             cls
clus                           0  1
  DEL PEAK  2(1P33) MUTATED   25 28
  DEL PEAK  2(1P33) WILD-TYPE 51 61
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     25   28
  DEL PEAK  2(1P33) WILD-TYPE   51   61
        clus
vv       DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  FEMALE                        25                          51
  MALE                          28                          61
[1] 2 2
[1] FALSE
D26V8, binary
                             cls
clus                           0  1
  DEL PEAK  2(1P33) MUTATED   29  8
  DEL PEAK  2(1P33) WILD-TYPE 64 11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     29    8
  DEL PEAK  2(1P33) WILD-TYPE   64   11
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                         29                          64
  YES                         8                          11
[1] 2 2
[1] FALSE
D26V9, binary
                             cls
clus                           0  1
  DEL PEAK  2(1P33) MUTATED   49  1
  DEL PEAK  2(1P33) WILD-TYPE 97 12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     49    1
  DEL PEAK  2(1P33) WILD-TYPE   97   12
                                clus
vv                               DEL PEAK  2(1P33) MUTATED
  RECTAL ADENOCARCINOMA                                 49
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  2(1P33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   97
  RECTAL MUCINOUS ADENOCARCINOMA                          12
[1] 2 2
[1] FALSE
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  2(1P33) MUTATED   36  1  4  1
  DEL PEAK  2(1P33) WILD-TYPE 87  1  8  3
D26V10, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  R0                        36                          87
  R1                         1                           1
  R2                         4                           8
  RX                         1                           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  2(1P33) MUTATED       0                         5    26
  DEL PEAK  2(1P33) WILD-TYPE     1                         1    55
D26V12, multiclass
                           clus
vv                          DEL PEAK  2(1P33) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         5
  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(27) Variable = DEL PEAK  3(1P13.2) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(1P13.2) MUTATED   44  9
  DEL PEAK  3(1P13.2) WILD-TYPE 94 13
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           53                           107 
  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-AF-A56L 
       24.13        17.23        13.55        14.50        15.39        65.98 
TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 
       11.84        32.02        36.03        24.00        34.03         2.01 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3909 
       29.98        37.02        19.04        19.99         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       28.04        36.03         3.98        25.97        23.01        12.00 
TCGA-AG-A01W TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 
       70.03         1.94        38.04        38.56         0.69        10.19 
TCGA-CI-6623 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 
        9.37        11.01         5.03        13.97        27.95        19.99 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 
      126.44        41.36       129.27         0.49        20.55        17.00 
TCGA-EI-6511 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 
       15.85        11.51        13.64        11.97        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6572 
        0.66         0.69         0.76        18.28        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 
       39.48        43.04        19.10        34.49        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 
       16.83        20.02        10.39        86.63        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        8.02         7.07        20.05         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 
       34.03        50.04        12.03         6.05         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
       32.98         0.99         0.99         1.02        17.95        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        46.03        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        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05        33.17         6.97         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
        7.17        21.01        15.02         8.98        15.02        10.98 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DD TCGA-DY-A1DF 
        5.95         4.01         5.03         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        49.51        31.30         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6641 
        0.53         1.12        12.46        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                         86.63 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                        19.04                         16.41 
[1] "0.5 - 129.3 (19.0)" "0.4 - 86.6 (16.4)" 
[1] "hr=" "1.4"
D27V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  3(1P13.2) MUTATED         6        2        16         1         2
  DEL PEAK  3(1P13.2) WILD-TYPE      24        6        24         1         0
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  3(1P13.2) MUTATED           0          1          9          7
  DEL PEAK  3(1P13.2) WILD-TYPE         5          8         15          7
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  3(1P13.2) MUTATED          6         2
  DEL PEAK  3(1P13.2) WILD-TYPE       12         7
D27V3, 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                           16                            24
  STAGE IIB                            1                             1
  STAGE IIC                            2                             0
  STAGE III                            0                             5
  STAGE IIIA                           1                             8
  STAGE IIIB                           9                            15
  STAGE IIIC                           7                             7
  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 41  5
  DEL PEAK  3(1P13.2) WILD-TYPE  8 23 71  9
D27V4, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  T1                           1                             8
  T2                           6                            23
  T3                          41                            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
  DEL PEAK  3(1P13.2) MUTATED   26 15 12
  DEL PEAK  3(1P13.2) WILD-TYPE 59 30 21
D27V5, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  N0                          26                            59
  N1                          15                            30
  N2                          12                            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"
D27V6, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P13.2) MUTATED   42  8
  DEL PEAK  3(1P13.2) WILD-TYPE 84 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     42    8
  DEL PEAK  3(1P13.2) WILD-TYPE   84   16
   clus
vv  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  0                          42                            84
  1                           8                            16
[1] 2 2
[1] FALSE
D27V7, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P13.2) MUTATED   25 29
  DEL PEAK  3(1P13.2) WILD-TYPE 51 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     25   29
  DEL PEAK  3(1P13.2) WILD-TYPE   51   60
        clus
vv       DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  FEMALE                          25                            51
  MALE                            29                            60
[1] 2 2
[1] FALSE
D27V8, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P13.2) MUTATED   29  8
  DEL PEAK  3(1P13.2) WILD-TYPE 64 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     29    8
  DEL PEAK  3(1P13.2) WILD-TYPE   64   11
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  NO                           29                            64
  YES                           8                            11
[1] 2 2
[1] FALSE
D27V9, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P13.2) MUTATED   49  2
  DEL PEAK  3(1P13.2) WILD-TYPE 97 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     49    2
  DEL PEAK  3(1P13.2) WILD-TYPE   97   11
                                clus
vv                               DEL PEAK  3(1P13.2) MUTATED
  RECTAL ADENOCARCINOMA                                   49
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK  3(1P13.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     97
  RECTAL MUCINOUS ADENOCARCINOMA                            11
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  3(1P13.2) MUTATED   39  1  4  1
  DEL PEAK  3(1P13.2) WILD-TYPE 84  1  8  3
D27V10, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  R0                          39                            84
  R1                           1                             1
  R2                           4                             8
  RX                           1                             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  3(1P13.2) MUTATED       0                         4    29
  DEL PEAK  3(1P13.2) WILD-TYPE     1                         2    52
D27V12, multiclass
                           clus
vv                          DEL PEAK  3(1P13.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              29
                           clus
vv                          DEL PEAK  3(1P13.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  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(28) Variable = DEL PEAK  4(2P12) MUTATION ANALYSIS
D28V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2P12) MUTATED    12   1
  DEL PEAK  4(2P12) WILD-TYPE 126  21
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         13                         147 
  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-3611 
       15.39        32.02        36.03         6.05        19.99        13.94 
TCGA-AG-3881 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-A00H TCGA-AG-A02X TCGA-DC-6156 
       19.04         1.02        28.04        25.97        41.00        15.02 
TCGA-F5-6571 
       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        39.48        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 
       34.49        37.74        10.39        14.50        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       34.03        34.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        0.99        15.95        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       29.98        37.02        32.98         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        36.95        17.03        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       14.01        48.03        32.02        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02        17.03         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
        6.02        23.01        37.02        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-A032 
       51.98        49.97         1.94        38.96        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       10.19         6.05        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
        5.03         8.98        13.97        27.95        10.98        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
        5.95         4.01         5.03         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-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-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        49.51        28.57         0.39        32.19         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        12.46        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 
                      19.99                       17.00 
[1] "1.0 - 41.0 (20.0)"  "0.4 - 129.3 (17.0)"
[1] "hr=" "1.4"
D28V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  4(2P12) MUTATED         2        0         5         0         0
  DEL PEAK  4(2P12) WILD-TYPE      28        8        35         2         2
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  4(2P12) MUTATED           0          0          1          3
  DEL PEAK  4(2P12) WILD-TYPE         5          9         23         11
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  4(2P12) MUTATED          1         1
  DEL PEAK  4(2P12) WILD-TYPE       17         8
D28V3, multiclass
            clus
vv           DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  STAGE I                            2                          28
  STAGE II                           0                           8
  STAGE IIA                          5                          35
  STAGE IIB                          0                           2
  STAGE IIC                          0                           2
  STAGE III                          0                           5
  STAGE IIIA                         0                           9
  STAGE IIIB                         1                          23
  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  10   1
  DEL PEAK  4(2P12) WILD-TYPE   9  27 102  13
D28V4, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  T1                         0                           9
  T2                         2                          27
  T3                        10                         102
  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    7  2  4
  DEL PEAK  4(2P12) WILD-TYPE 78 43 29
D28V5, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  N0                         7                          78
  N1                         2                          43
  N2                         4                          29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    10   2
  DEL PEAK  4(2P12) WILD-TYPE 116  22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     10    2
  DEL PEAK  4(2P12) WILD-TYPE  116   22
   clus
vv  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  0                        10                         116
  1                         2                          22
[1] 2 2
[1] FALSE
D28V7, binary
                             cls
clus                           0  1
  DEL PEAK  4(2P12) MUTATED    7  6
  DEL PEAK  4(2P12) WILD-TYPE 69 83
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      7    6
  DEL PEAK  4(2P12) WILD-TYPE   69   83
        clus
vv       DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  FEMALE                         7                          69
  MALE                           6                          83
[1] 2 2
[1] FALSE
D28V8, binary
                             cls
clus                           0  1
  DEL PEAK  4(2P12) MUTATED    8  3
  DEL PEAK  4(2P12) WILD-TYPE 85 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      8    3
  DEL PEAK  4(2P12) WILD-TYPE   85   16
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  NO                          8                          85
  YES                         3                          16
[1] 2 2
[1] FALSE
D28V9, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    11   1
  DEL PEAK  4(2P12) WILD-TYPE 135  12
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     11    1
  DEL PEAK  4(2P12) WILD-TYPE  135   12
                                clus
vv                               DEL PEAK  4(2P12) MUTATED
  RECTAL ADENOCARCINOMA                                 11
  RECTAL MUCINOUS ADENOCARCINOMA                         1
                                clus
vv                               DEL PEAK  4(2P12) WILD-TYPE
  RECTAL ADENOCARCINOMA                                  135
  RECTAL MUCINOUS ADENOCARCINOMA                          12
[1] 2 2
[1] FALSE
                             vv
clus                           R0  R1  R2  RX
  DEL PEAK  4(2P12) MUTATED    10   0   1   0
  DEL PEAK  4(2P12) WILD-TYPE 113   2  11   4
D28V10, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  R0                        10                         113
  R1                         0                           2
  R2                         1                          11
  RX                         0                           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"
D28V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2P12) MUTATED       0                         0     3
  DEL PEAK  4(2P12) WILD-TYPE     1                         6    78
D28V12, multiclass
                           clus
vv                          DEL PEAK  4(2P12) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         0
  WHITE                                             3
                           clus
vv                          DEL PEAK  4(2P12) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              78
[1] 3 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  5(3P14.2) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P14.2) MUTATED    26   5
  DEL PEAK  5(3P14.2) WILD-TYPE 112  17
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           31                           129 
  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-AF-A56K TCGA-AF-A56N 
       43.04        19.10        34.49        14.50        86.63        11.84 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3592 TCGA-AG-3731 
        8.02         7.07        20.05        24.00        34.03        37.02 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-4007 TCGA-AG-4008 
       32.98        19.04        19.99        17.95         1.02        17.03 
TCGA-AG-A00C TCGA-AG-A02G TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
        6.02        38.96        38.56        10.19         6.05         9.37 
TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6508 TCGA-F5-6810 
       15.02        10.98         4.01         5.29        20.91         0.39 
TCGA-G5-6233 
       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        39.48        17.23        13.55        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 
       16.83        15.39        20.02        10.39        65.98        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       12.00        32.02        36.03         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
       15.95        19.99        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3887 
        0.99        29.98         0.99         0.99         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-4021 
       32.02        19.99        28.04        36.03        14.04         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94        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-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        41.00        38.04         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 
       26.43         1.81        33.17         6.97         4.73        12.39 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        21.01        11.01         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        15.02        27.95        19.99         5.95         5.03 
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-6507 TCGA-EI-6509 
       32.61         0.49         2.40        20.55        19.96        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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
        8.45         9.96        49.51        31.30        28.57        32.19 
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        12.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                         0.39                          0.49 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                        86.63                        129.27 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                        17.95                         17.00 
[1] "0.4 - 86.6 (17.9)"  "0.5 - 129.3 (17.0)"
[1] "hr=" "1.6"
D29V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  5(3P14.2) MUTATED         9        1         8         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         20         14
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  5(3P14.2) MUTATED          6         1
  DEL PEAK  5(3P14.2) WILD-TYPE       12         8
D29V3, 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                            8                            32
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            0                             5
  STAGE IIIA                           0                             9
  STAGE IIIB                           4                            20
  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 19  2
  DEL PEAK  5(3P14.2) WILD-TYPE  5 23 93 12
D29V4, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  T1                           4                             5
  T2                           6                            23
  T3                          19                            93
  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   18  8  5
  DEL PEAK  5(3P14.2) WILD-TYPE 67 37 28
D29V5, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  N0                          18                            67
  N1                           8                            37
  N2                           5                            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"
D29V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P14.2) MUTATED    21   7
  DEL PEAK  5(3P14.2) WILD-TYPE 105  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     21    7
  DEL PEAK  5(3P14.2) WILD-TYPE  105   17
   clus
vv  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  0                          21                           105
  1                           7                            17
[1] 2 2
[1] FALSE
D29V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED    8 23
  DEL PEAK  5(3P14.2) WILD-TYPE 68 66
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED      8   23
  DEL PEAK  5(3P14.2) WILD-TYPE   68   66
        clus
vv       DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  FEMALE                           8                            68
  MALE                            23                            66
[1] 2 2
[1] FALSE
D29V8, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   21  5
  DEL PEAK  5(3P14.2) WILD-TYPE 72 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     21    5
  DEL PEAK  5(3P14.2) WILD-TYPE   72   14
     clus
vv    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  NO                           21                            72
  YES                           5                            14
[1] 2 2
[1] FALSE
D29V9, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P14.2) MUTATED    25   3
  DEL PEAK  5(3P14.2) WILD-TYPE 121  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     25    3
  DEL PEAK  5(3P14.2) WILD-TYPE  121   10
                                clus
vv                               DEL PEAK  5(3P14.2) MUTATED
  RECTAL ADENOCARCINOMA                                   25
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  5(3P14.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    121
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK  5(3P14.2) MUTATED    20   0   5   1
  DEL PEAK  5(3P14.2) WILD-TYPE 103   2   7   3
D29V10, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  R0                          20                           103
  R1                           0                             2
  R2                           5                             7
  RX                           1                             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  5(3P14.2) MUTATED       1                         2    14
  DEL PEAK  5(3P14.2) WILD-TYPE     0                         4    67
D29V12, multiclass
                           clus
vv                          DEL PEAK  5(3P14.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              14
                           clus
vv                          DEL PEAK  5(3P14.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             4
  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(30) Variable = DEL PEAK  6(3Q26.31) MUTATION ANALYSIS
D30V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  6(3Q26.31) MUTATED    15   3
  DEL PEAK  6(3Q26.31) WILD-TYPE 123  19
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            18                            142 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                             3                             19 
$`DEL PEAK  6(3Q26.31) MUTATED`
TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3599 TCGA-AG-3609 
       34.49        14.50        32.02        20.05        12.03        19.99 
TCGA-AG-3731 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A02G TCGA-CI-6619 TCGA-DC-6682 
       37.02        36.03        14.04        38.96         6.05         4.01 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-7002 TCGA-G5-6233 
        5.29        19.96        20.91         8.61        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        39.48        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        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       86.63        65.98        11.84        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
       34.03        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       15.95        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       29.98        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 
        1.02        17.95        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-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
        1.02        17.03         3.98        46.03        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-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        38.56         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        1.81        10.19        33.17         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       19.99         5.95         5.03       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-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-6885 TCGA-EI-6917 
       16.31        16.41        11.51        10.78        13.64        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        31.30        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19         0.66         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        55.76        47.08        26.43 

  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                          4.01                           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 
                        19.120                         17.015 
[1] "4.0 - 39.0 (19.1)"  "0.4 - 129.3 (17.0)"
[1] "hr=" "1.9"
D30V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  6(3Q26.31) MUTATED         1        1         6         0         1
  DEL PEAK  6(3Q26.31) WILD-TYPE      29        7        34         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  6(3Q26.31) MUTATED           0          0          1          1
  DEL PEAK  6(3Q26.31) WILD-TYPE         5          9         23         13
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK  6(3Q26.31) MUTATED          6         1
  DEL PEAK  6(3Q26.31) WILD-TYPE       12         8
D30V3, multiclass
            clus
vv           DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  STAGE I                               1                             29
  STAGE II                              1                              7
  STAGE IIA                             6                             34
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             0                              5
  STAGE IIIA                            0                              9
  STAGE IIIB                            1                             23
  STAGE IIIC                            1                             13
  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  6(3Q26.31) MUTATED    0  2 15  1
  DEL PEAK  6(3Q26.31) WILD-TYPE  9 27 97 13
D30V4, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  T1                            0                              9
  T2                            2                             27
  T3                           15                             97
  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  6(3Q26.31) MUTATED    8  4  6
  DEL PEAK  6(3Q26.31) WILD-TYPE 77 41 27
D30V5, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  N0                            8                             77
  N1                            4                             41
  N2                            6                             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"
D30V6, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q26.31) MUTATED    11   6
  DEL PEAK  6(3Q26.31) WILD-TYPE 115  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED     11    6
  DEL PEAK  6(3Q26.31) WILD-TYPE  115   18
   clus
vv  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  0                           11                            115
  1                            6                             18
[1] 2 2
[1] FALSE
D30V7, binary
                                cls
clus                              0  1
  DEL PEAK  6(3Q26.31) MUTATED    4 14
  DEL PEAK  6(3Q26.31) WILD-TYPE 72 75
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED      4   14
  DEL PEAK  6(3Q26.31) WILD-TYPE   72   75
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  FEMALE                            4                             72
  MALE                             14                             75
[1] 2 2
[1] FALSE
D30V8, binary
                                cls
clus                              0  1
  DEL PEAK  6(3Q26.31) MUTATED   15  1
  DEL PEAK  6(3Q26.31) WILD-TYPE 78 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED     15    1
  DEL PEAK  6(3Q26.31) WILD-TYPE   78   18
     clus
vv    DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  NO                            15                             78
  YES                            1                             18
[1] 2 2
[1] FALSE
D30V9, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q26.31) MUTATED    11   5
  DEL PEAK  6(3Q26.31) WILD-TYPE 135   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED     11    5
  DEL PEAK  6(3Q26.31) WILD-TYPE  135    8
                                clus
vv                               DEL PEAK  6(3Q26.31) MUTATED
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK  6(3Q26.31) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     135
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  6(3Q26.31) MUTATED    13   0   3   1
  DEL PEAK  6(3Q26.31) WILD-TYPE 110   2   9   3
D30V10, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  R0                           13                            110
  R1                            0                              2
  R2                            3                              9
  RX                            1                              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"
D30V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3Q26.31) MUTATED       1                         0     9
  DEL PEAK  6(3Q26.31) WILD-TYPE     0                         6    72
D30V12, multiclass
                           clus
vv                          DEL PEAK  6(3Q26.31) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                9
                           clus
vv                          DEL PEAK  6(3Q26.31) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              6
  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(31) Variable = DEL PEAK  7(4P13) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  7(4P13) MUTATED   54  5
  DEL PEAK  7(4P13) WILD-TYPE 84 17
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         59                         101 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                          5                          17 
$`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        34.49        37.74        14.50 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3593 
       15.39        10.39        65.98        36.03        34.03        34.03 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       13.94        19.99        20.98        29.98        37.02        32.98 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
       19.04         1.02        17.95        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        33.17         5.03 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE 
       15.02        27.95        10.98        19.99       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        28.57         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 
       39.48        13.55        19.10        10.39        16.83        20.02 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       86.63        11.84        36.03        12.00        32.02         8.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
        7.07        20.05        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-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 
       19.99         7.99         0.99         0.99         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 
       36.95        13.02        14.01         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       46.03        20.98         6.02        37.02        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-A032 TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        61.97        38.04        38.56         1.45 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        0.72        26.43         1.81         6.97         9.37         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
        8.98        13.97         5.95         4.01         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 
       41.36        57.24        24.13        51.48         0.49        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        17.69        16.31 
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-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 
        9.96        49.51        32.19         0.66         0.53         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.76        12.46        18.28        55.76        47.08 

  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                       0.39                        0.49 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                     129.27                       86.63 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                      20.98                       14.01 
[1] "0.4 - 129.3 (21.0)" "0.5 - 86.6 (14.0)" 
[1] "hr=" "2.3"
D31V2, 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        24         2         2
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  7(4P13) MUTATED           1          3         11          7
  DEL PEAK  7(4P13) WILD-TYPE         4          6         13          7
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  7(4P13) MUTATED          7         4
  DEL PEAK  7(4P13) WILD-TYPE       11         5
D31V3, 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                          24
  STAGE IIB                          0                           2
  STAGE IIC                          0                           2
  STAGE III                          1                           4
  STAGE IIIA                         3                           6
  STAGE IIIB                        11                          13
  STAGE IIIC                         7                           7
  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 43  4
  DEL PEAK  7(4P13) WILD-TYPE  7 18 69 10
D31V4, multiclass
    clus
vv   DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  T1                         2                           7
  T2                        11                          18
  T3                        43                          69
  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 13
  DEL PEAK  7(4P13) WILD-TYPE 58 25 20
D31V5, multiclass
    clus
vv   DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  N0                        27                          58
  N1                        20                          25
  N2                        13                          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"
D31V6, binary
                             cls
clus                           0  1
  DEL PEAK  7(4P13) MUTATED   45  9
  DEL PEAK  7(4P13) WILD-TYPE 81 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED     45    9
  DEL PEAK  7(4P13) WILD-TYPE   81   15
   clus
vv  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  0                        45                          81
  1                         9                          15
[1] 2 2
[1] FALSE
D31V7, binary
                             cls
clus                           0  1
  DEL PEAK  7(4P13) MUTATED   23 37
  DEL PEAK  7(4P13) WILD-TYPE 53 52
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED     23   37
  DEL PEAK  7(4P13) WILD-TYPE   53   52
        clus
vv       DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  FEMALE                        23                          53
  MALE                          37                          52
[1] 2 2
[1] FALSE
D31V8, binary
                             cls
clus                           0  1
  DEL PEAK  7(4P13) MUTATED   33 10
  DEL PEAK  7(4P13) WILD-TYPE 60  9
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED     33   10
  DEL PEAK  7(4P13) WILD-TYPE   60    9
     clus
vv    DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  NO                         33                          60
  YES                        10                           9
[1] 2 2
[1] FALSE
D31V9, binary
                             cls
clus                           0  1
  DEL PEAK  7(4P13) MUTATED   55  3
  DEL PEAK  7(4P13) WILD-TYPE 91 10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED     55    3
  DEL PEAK  7(4P13) WILD-TYPE   91   10
                                clus
vv                               DEL PEAK  7(4P13) MUTATED
  RECTAL ADENOCARCINOMA                                 55
  RECTAL MUCINOUS ADENOCARCINOMA                         3
                                clus
vv                               DEL PEAK  7(4P13) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   91
  RECTAL MUCINOUS ADENOCARCINOMA                          10
[1] 2 2
[1] FALSE
                             vv
clus                          R0 R1 R2 RX
  DEL PEAK  7(4P13) MUTATED   47  0  3  1
  DEL PEAK  7(4P13) WILD-TYPE 76  2  9  3
D31V10, multiclass
    clus
vv   DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  R0                        47                          76
  R1                         0                           2
  R2                         3                           9
  RX                         1                           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"
D31V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(4P13) MUTATED       0                         3    28
  DEL PEAK  7(4P13) WILD-TYPE     1                         3    53
D31V12, multiclass
                           clus
vv                          DEL PEAK  7(4P13) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         3
  WHITE                                            28
                           clus
vv                          DEL PEAK  7(4P13) WILD-TYPE
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  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(32) Variable = DEL PEAK  8(4Q22.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(4Q22.1) MUTATED   65  5
  DEL PEAK  8(4Q22.1) WILD-TYPE 73 17
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           70                            90 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                            5                            17 
$`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        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 
       37.74        14.50        15.39        65.98        36.03        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 
       34.03         6.05        13.94        19.99        20.98        29.98 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3898 
       32.98        19.04         1.02        17.95         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        38.56         0.69        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 
        6.05        33.17         4.73        11.01         5.03        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE 
       27.95        10.98        19.99         4.01       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        28.57         0.39        32.19 
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-AF-A56K 
       39.48        10.39        16.83        20.02        10.39        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       11.84        36.03        12.00        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3594 
       20.05        24.00         1.02        46.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       50.04        12.03         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        0.99        37.02         0.99         0.99        19.99        36.95 
TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-4021 
       17.03        13.02        35.01        14.01        32.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       46.03        20.98        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G 
        1.02        31.00        10.98        51.98        49.97        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       61.97        38.04         1.45         0.72        26.43         1.81 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        12.39        78.12         7.17        21.01 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       15.02         8.98        13.97         5.95         5.03         5.29 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24        24.13        51.48        32.61         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 
       20.55        19.96        18.28        17.69        16.31         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        13.64        17.46         9.96        49.51 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        12.46        55.76        47.08 

  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                         0.39                          0.49 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                       129.27                         86.63 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                       18.115                        16.130 
[1] "0.4 - 129.3 (18.1)" "0.5 - 86.6 (16.1)" 
[1] "hr=" "2.6"
D32V2, 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        20         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  8(4Q22.1) MUTATED           2          2         13          9
  DEL PEAK  8(4Q22.1) WILD-TYPE         3          7         11          5
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  8(4Q22.1) MUTATED          5         5
  DEL PEAK  8(4Q22.1) WILD-TYPE       13         4
D32V3, 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                            20
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            2                             3
  STAGE IIIA                           2                             7
  STAGE IIIB                          13                            11
  STAGE IIIC                           9                             5
  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 53  7
  DEL PEAK  8(4Q22.1) WILD-TYPE  7 18 59  7
D32V4, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  T1                           2                             7
  T2                          11                            18
  T3                          53                            59
  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 17
  DEL PEAK  8(4Q22.1) WILD-TYPE 50 24 16
D32V5, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  N0                          35                            50
  N1                          21                            24
  N2                          17                            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"
D32V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   57  9
  DEL PEAK  8(4Q22.1) WILD-TYPE 69 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     57    9
  DEL PEAK  8(4Q22.1) WILD-TYPE   69   15
   clus
vv  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  0                          57                            69
  1                           9                            15
[1] 2 2
[1] FALSE
D32V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   29 44
  DEL PEAK  8(4Q22.1) WILD-TYPE 47 45
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     29   44
  DEL PEAK  8(4Q22.1) WILD-TYPE   47   45
        clus
vv       DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  FEMALE                          29                            47
  MALE                            44                            45
[1] 2 2
[1] FALSE
D32V8, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   38 11
  DEL PEAK  8(4Q22.1) WILD-TYPE 55  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     38   11
  DEL PEAK  8(4Q22.1) WILD-TYPE   55    8
     clus
vv    DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  NO                           38                            55
  YES                          11                             8
[1] 2 2
[1] FALSE
D32V9, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   65  4
  DEL PEAK  8(4Q22.1) WILD-TYPE 81  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     65    4
  DEL PEAK  8(4Q22.1) WILD-TYPE   81    9
                                clus
vv                               DEL PEAK  8(4Q22.1) MUTATED
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               DEL PEAK  8(4Q22.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     81
  RECTAL MUCINOUS ADENOCARCINOMA                             9
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  8(4Q22.1) MUTATED   56  1  3  1
  DEL PEAK  8(4Q22.1) WILD-TYPE 67  1  9  3
D32V10, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  R0                          56                            67
  R1                           1                             1
  R2                           3                             9
  RX                           1                             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  8(4Q22.1) MUTATED       0                         3    39
  DEL PEAK  8(4Q22.1) WILD-TYPE     1                         3    42
D32V12, multiclass
                           clus
vv                          DEL PEAK  8(4Q22.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              39
                           clus
vv                          DEL PEAK  8(4Q22.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             3
  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(33) Variable = DEL PEAK  9(4Q35.1) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(4Q35.1) MUTATED   61  8
  DEL PEAK  9(4Q35.1) WILD-TYPE 77 14
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           69                            91 
  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        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 
       37.74        10.39        14.50        15.39        65.98        36.03 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 TCGA-AG-3612 
       46.03        34.03        34.03         6.05        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 
       20.98        29.98        32.98         0.99        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       17.95        48.03        19.99        28.04        36.03        14.04 
TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
        3.98        13.94        25.97        23.01        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 
       64.01        41.00        38.56         0.69        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 
       33.17         4.73        11.01         5.03        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 
       10.98        19.99       126.44       129.27        24.13         2.40 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6464 
       17.00        15.85        16.34        16.41        11.97         9.96 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       31.30        28.57         0.39        32.19         0.66         0.53 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6641 
       12.46        18.28        26.43 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N 
       39.48        16.83        20.02        10.39        86.63        11.84 
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        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
        0.99        15.95        19.99         7.99         0.99        37.02 
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-3896 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4022 
       14.01         1.02        32.02         1.02        17.03        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98         6.02        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
        1.02        31.00        10.98        51.98        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
       38.96        61.97        38.04         1.45         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        1.81         6.97         9.37        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 
       21.01        15.02         8.98        13.97         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        5.03         5.29        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-6512 
        0.49        20.55        19.96        20.91        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-EI-7004 TCGA-F5-6465 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 
        8.45        49.51         0.69         1.12         0.76        55.76 
TCGA-G5-6572 
       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                         86.63 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                        19.04                         15.95 
[1] "0.4 - 129.3 (19.0)" "0.5 - 86.6 (15.9)" 
[1] "hr=" "1.4"
D33V2, 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        21         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  9(4Q35.1) MUTATED           2          2         12         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
D33V3, 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                            21
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            2                             3
  STAGE IIIA                           2                             7
  STAGE IIIB                          12                            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 53  4
  DEL PEAK  9(4Q35.1) WILD-TYPE  6 17 59 10
D33V4, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  T1                           3                             6
  T2                          12                            17
  T3                          53                            59
  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 18
  DEL PEAK  9(4Q35.1) WILD-TYPE 51 25 15
D33V5, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  N0                          34                            51
  N1                          20                            25
  N2                          18                            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"
D33V6, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   55 10
  DEL PEAK  9(4Q35.1) WILD-TYPE 71 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     55   10
  DEL PEAK  9(4Q35.1) WILD-TYPE   71   14
   clus
vv  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  0                          55                            71
  1                          10                            14
[1] 2 2
[1] FALSE
D33V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   30 42
  DEL PEAK  9(4Q35.1) WILD-TYPE 46 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     30   42
  DEL PEAK  9(4Q35.1) WILD-TYPE   46   47
        clus
vv       DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  FEMALE                          30                            46
  MALE                            42                            47
[1] 2 2
[1] FALSE
D33V8, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   39 11
  DEL PEAK  9(4Q35.1) WILD-TYPE 54  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     39   11
  DEL PEAK  9(4Q35.1) WILD-TYPE   54    8
     clus
vv    DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  NO                           39                            54
  YES                          11                             8
[1] 2 2
[1] FALSE
D33V9, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   65  3
  DEL PEAK  9(4Q35.1) WILD-TYPE 81 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     65    3
  DEL PEAK  9(4Q35.1) WILD-TYPE   81   10
                                clus
vv                               DEL PEAK  9(4Q35.1) MUTATED
  RECTAL ADENOCARCINOMA                                   65
  RECTAL MUCINOUS ADENOCARCINOMA                           3
                                clus
vv                               DEL PEAK  9(4Q35.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     81
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  9(4Q35.1) MUTATED   55  0  3  1
  DEL PEAK  9(4Q35.1) WILD-TYPE 68  2  9  3
D33V10, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  R0                          55                            68
  R1                           0                             2
  R2                           3                             9
  RX                           1                             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  9(4Q35.1) MUTATED       0                         4    39
  DEL PEAK  9(4Q35.1) WILD-TYPE     1                         2    42
D33V12, multiclass
                           clus
vv                          DEL PEAK  9(4Q35.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              39
                           clus
vv                          DEL PEAK  9(4Q35.1) 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(34) Variable = DEL PEAK 10(5Q12.1) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(5Q12.1) MUTATED   43  9
  DEL PEAK 10(5Q12.1) WILD-TYPE 95 13
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                           52                           108 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                            9                            13 
$`DEL PEAK 10(5Q12.1) 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-AF-A56K TCGA-AG-3591 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 
       10.39        86.63        34.03        13.94        20.98        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3896 
       37.02        32.98        19.04        19.99        17.03         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A00Y 
       48.03        28.04        36.03        17.03         3.98        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 
       33.17         7.17         5.03        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       10.98         4.01       126.44        57.24       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6881 TCGA-EI-6885 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 
       20.55        16.41        13.64        11.97         8.45        49.51 
TCGA-F5-6702 TCGA-F5-6811 TCGA-G5-6233 TCGA-G5-6641 
       28.57        32.19        18.28        26.43 

$`DEL PEAK 10(5Q12.1) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 
       39.48        13.55        19.10        34.49        14.50        16.83 
TCGA-AF-6655 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        65.98        11.84        36.03        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        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        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-3742 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99         0.99         1.02        17.95        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-A00C TCGA-AG-A00H 
        1.02        46.03        20.98        13.94         6.02        25.97 
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-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 
       31.00        10.98        51.98        49.97        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         1.45         0.69         0.72        26.43         1.81 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        12.39        78.12 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
       21.01        11.01        15.02         8.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        5.03         5.29        41.36        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        2.40        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31         8.61        11.51        10.78 
TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 
       17.46         9.96        31.30         0.39         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        12.46        55.76        47.08 

  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                         1.02                          0.39 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                       129.27                         78.12 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                       21.995                        15.435 
[1] "1.0 - 129.3 (22.0)" "0.4 - 78.1 (15.4)" 
[1] "hr=" "1.2"
D34V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 10(5Q12.1) MUTATED         8        3        16         0         1
  DEL PEAK 10(5Q12.1) WILD-TYPE      22        5        24         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 10(5Q12.1) MUTATED           1          3          5          4
  DEL PEAK 10(5Q12.1) WILD-TYPE         4          6         19         10
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 10(5Q12.1) MUTATED          7         5
  DEL PEAK 10(5Q12.1) WILD-TYPE       11         4
D34V3, multiclass
            clus
vv           DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  STAGE I                              8                            22
  STAGE II                             3                             5
  STAGE IIA                           16                            24
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           3                             6
  STAGE IIIB                           5                            19
  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(5Q12.1) MUTATED    2  9 38  4
  DEL PEAK 10(5Q12.1) WILD-TYPE  7 20 74 10
D34V4, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  T1                           2                             7
  T2                           9                            20
  T3                          38                            74
  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(5Q12.1) MUTATED   27 15 11
  DEL PEAK 10(5Q12.1) WILD-TYPE 58 30 22
D34V5, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  N0                          27                            58
  N1                          15                            30
  N2                          11                            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"
D34V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q12.1) MUTATED   37 10
  DEL PEAK 10(5Q12.1) WILD-TYPE 89 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED     37   10
  DEL PEAK 10(5Q12.1) WILD-TYPE   89   14
   clus
vv  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  0                          37                            89
  1                          10                            14
[1] 2 2
[1] FALSE
D34V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q12.1) MUTATED   27 26
  DEL PEAK 10(5Q12.1) WILD-TYPE 49 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED     27   26
  DEL PEAK 10(5Q12.1) WILD-TYPE   49   63
        clus
vv       DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  FEMALE                          27                            49
  MALE                            26                            63
[1] 2 2
[1] FALSE
D34V8, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q12.1) MUTATED   34  6
  DEL PEAK 10(5Q12.1) WILD-TYPE 59 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED     34    6
  DEL PEAK 10(5Q12.1) WILD-TYPE   59   13
     clus
vv    DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  NO                           34                            59
  YES                           6                            13
[1] 2 2
[1] FALSE
D34V9, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q12.1) MUTATED   50  2
  DEL PEAK 10(5Q12.1) WILD-TYPE 96 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED     50    2
  DEL PEAK 10(5Q12.1) WILD-TYPE   96   11
                                clus
vv                               DEL PEAK 10(5Q12.1) MUTATED
  RECTAL ADENOCARCINOMA                                   50
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 10(5Q12.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     96
  RECTAL MUCINOUS ADENOCARCINOMA                            11
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 10(5Q12.1) MUTATED   38  1  3  1
  DEL PEAK 10(5Q12.1) WILD-TYPE 85  1  9  3
D34V10, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  R0                          38                            85
  R1                           1                             1
  R2                           3                             9
  RX                           1                             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 10(5Q12.1) MUTATED       0                         4    27
  DEL PEAK 10(5Q12.1) WILD-TYPE     1                         2    54
D34V12, multiclass
                           clus
vv                          DEL PEAK 10(5Q12.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              27
                           clus
vv                          DEL PEAK 10(5Q12.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             2
  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(35) Variable = DEL PEAK 11(5Q22.2) MUTATION ANALYSIS
D35V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(5Q22.2) MUTATED   46 11
  DEL PEAK 11(5Q22.2) WILD-TYPE 92 11
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           57                           103 
  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-AF-A56K TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3611 
       10.39        86.63        65.98        32.02        34.03        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 
       19.99        20.98        29.98        37.02        32.98        19.04 
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-4021 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A01L TCGA-AG-A01W 
       17.03         3.98         6.02        23.01        12.00        70.03 
TCGA-AG-A01Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6903 TCGA-BM-6198 
       64.01         1.94        38.96        41.00         1.81        10.19 
TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       33.17         7.17         5.03        13.97        15.02        27.95 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       10.98         4.01       126.44        41.36        57.24        51.48 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6881 TCGA-F5-6464 
       20.55        19.96        18.28        16.34        16.41         9.96 
TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6233 
       28.57        12.46        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 
       39.48        13.55        19.10        34.49        14.50        16.83 
TCGA-AF-6655 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 
       20.02        11.84        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-3592 
       36.03        20.05        24.00         1.02        46.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03         2.01        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3878 
       15.95        19.99         7.99         0.99         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        14.04         1.02        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       13.94        25.97        37.02        15.95        36.03         9.07 
TCGA-AG-A01J TCGA-AG-A01N TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
        1.02        31.00        10.98        51.98        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       38.04        38.56         1.45         0.69         0.72        26.43 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        12.39        78.12 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 
       21.01        11.01        15.02         8.98        19.99         5.95 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
        5.03         5.29       129.27        24.13        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 
        2.40        20.91        17.00        15.85        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
        8.61        11.51        10.78        13.64        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
        8.45        49.51        31.30         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12         0.76        55.76        47.08 
TCGA-G5-6641 
       26.43 

  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                         1.02                          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 
                        19.99                         15.02 
[1] "1.0 - 126.4 (20.0)" "0.4 - 129.3 (15.0)"
[1] "hr=" "1.2"
D35V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 11(5Q22.2) MUTATED         8        3        16         0         1
  DEL PEAK 11(5Q22.2) WILD-TYPE      22        5        24         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 11(5Q22.2) MUTATED           1          2         12          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
D35V3, 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                           16                            24
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           2                             7
  STAGE IIIB                          12                            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 43  5
  DEL PEAK 11(5Q22.2) WILD-TYPE  8 19 69  9
D35V4, multiclass
    clus
vv   DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  T1                           1                             8
  T2                          10                            19
  T3                          43                            69
  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   28 19 12
  DEL PEAK 11(5Q22.2) WILD-TYPE 57 26 21
D35V5, multiclass
    clus
vv   DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  N0                          28                            57
  N1                          19                            26
  N2                          12                            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"
D35V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q22.2) MUTATED   45  8
  DEL PEAK 11(5Q22.2) WILD-TYPE 81 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED     45    8
  DEL PEAK 11(5Q22.2) WILD-TYPE   81   16
   clus
vv  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  0                          45                            81
  1                           8                            16
[1] 2 2
[1] FALSE
D35V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q22.2) MUTATED   30 29
  DEL PEAK 11(5Q22.2) WILD-TYPE 46 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED     30   29
  DEL PEAK 11(5Q22.2) WILD-TYPE   46   60
        clus
vv       DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  FEMALE                          30                            46
  MALE                            29                            60
[1] 2 2
[1] FALSE
D35V8, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q22.2) MUTATED   36  7
  DEL PEAK 11(5Q22.2) WILD-TYPE 57 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED     36    7
  DEL PEAK 11(5Q22.2) WILD-TYPE   57   12
     clus
vv    DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  NO                           36                            57
  YES                           7                            12
[1] 2 2
[1] FALSE
D35V9, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q22.2) MUTATED   56  2
  DEL PEAK 11(5Q22.2) WILD-TYPE 90 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED     56    2
  DEL PEAK 11(5Q22.2) WILD-TYPE   90   11
                                clus
vv                               DEL PEAK 11(5Q22.2) MUTATED
  RECTAL ADENOCARCINOMA                                   56
  RECTAL MUCINOUS ADENOCARCINOMA                           2
                                clus
vv                               DEL PEAK 11(5Q22.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     90
  RECTAL MUCINOUS ADENOCARCINOMA                            11
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 11(5Q22.2) MUTATED   43  1  4  2
  DEL PEAK 11(5Q22.2) WILD-TYPE 80  1  8  2
D35V10, multiclass
    clus
vv   DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  R0                          43                            80
  R1                           1                             1
  R2                           4                             8
  RX                           2                             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 11(5Q22.2) MUTATED       0                         5    27
  DEL PEAK 11(5Q22.2) WILD-TYPE     1                         1    54
D35V12, multiclass
                           clus
vv                          DEL PEAK 11(5Q22.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              27
                           clus
vv                          DEL PEAK 11(5Q22.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  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(36) Variable = DEL PEAK 12(6P25.3) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6P25.3) MUTATED    18   4
  DEL PEAK 12(6P25.3) WILD-TYPE 120  18
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           22                           138 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                            4                            18 
$`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        34.49        14.50        24.00 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3611 TCGA-AG-4001 
       34.03        34.03        34.03        50.04        13.94        36.03 
TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A011 TCGA-BM-6198 TCGA-DC-4745 TCGA-DC-6682 
        3.98        13.94        37.02        10.19        21.01         4.01 
TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6511 TCGA-EI-6883 
        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        39.48        43.04        37.74        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       36.03        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
       20.05         1.02        46.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        19.99        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        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        46.03 
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        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43         1.81         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        4.73        12.39        78.12         7.17        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       19.99         5.95         5.03       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        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         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        12.46        18.28        55.76        47.08        26.43 

  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                         3.98                          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 
                       18.165                        17.015 
[1] "4.0 - 50.0 (18.2)"  "0.4 - 129.3 (17.0)"
[1] "hr=" "1.9"
D36V2, 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        29         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         21         12
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 12(6P25.3) MUTATED          2         1
  DEL PEAK 12(6P25.3) WILD-TYPE       16         8
D36V3, 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                            29
  STAGE IIB                            0                             2
  STAGE IIC                            1                             1
  STAGE III                            1                             4
  STAGE IIIA                           0                             9
  STAGE IIIB                           3                            21
  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 91 13
D36V4, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  T1                           0                             9
  T2                           2                            27
  T3                          21                            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 12(6P25.3) MUTATED   15  4  5
  DEL PEAK 12(6P25.3) WILD-TYPE 70 41 28
D36V5, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  N0                          15                            70
  N1                           4                            41
  N2                           5                            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"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(6P25.3) MUTATED    18   2
  DEL PEAK 12(6P25.3) WILD-TYPE 108  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     18    2
  DEL PEAK 12(6P25.3) WILD-TYPE  108   22
   clus
vv  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  0                          18                           108
  1                           2                            22
[1] 2 2
[1] FALSE
D36V7, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P25.3) MUTATED   10 14
  DEL PEAK 12(6P25.3) WILD-TYPE 66 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     10   14
  DEL PEAK 12(6P25.3) WILD-TYPE   66   75
        clus
vv       DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  FEMALE                          10                            66
  MALE                            14                            75
[1] 2 2
[1] FALSE
D36V8, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P25.3) MUTATED   15  5
  DEL PEAK 12(6P25.3) WILD-TYPE 78 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     15    5
  DEL PEAK 12(6P25.3) WILD-TYPE   78   14
     clus
vv    DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  NO                           15                            78
  YES                           5                            14
[1] 2 2
[1] FALSE
D36V9, binary
                               cls
clus                              0   1
  DEL PEAK 12(6P25.3) MUTATED    18   3
  DEL PEAK 12(6P25.3) WILD-TYPE 128  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     18    3
  DEL PEAK 12(6P25.3) WILD-TYPE  128   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                                    128
  RECTAL MUCINOUS ADENOCARCINOMA                            10
[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 105   2  10   3
D36V10, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  R0                          18                           105
  R1                           0                             2
  R2                           2                            10
  RX                           1                             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"
D36V11, 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                         6    69
D36V12, 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                             6
  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(37) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D37V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(6Q26) MUTATED    24   4
  DEL PEAK 13(6Q26) WILD-TYPE 114  18
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         28                         132 
  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        34.49        37.74 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
       12.00        32.02        24.00        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-4005 TCGA-AG-4007 
        2.01         6.05        19.99        13.94        14.04         1.02 
TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 TCGA-AH-6644 TCGA-CI-6623 TCGA-DC-6682 
       13.94        37.02        38.56         0.72         9.37         4.01 
TCGA-DT-5265 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
        5.29         0.76        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        39.48        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 
        8.02         7.07        36.03        20.05         1.02        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3612 TCGA-AG-3725 
       50.04        12.03         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 
        0.99        19.04        19.99         1.02        17.95        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-4008 TCGA-AG-4021 
       32.02        19.99        28.04        36.03        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 
       46.03        20.98         6.02        25.97        23.01        15.95 
TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W 
       36.03         9.07         1.02        12.00        31.00        70.03 
TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       64.01        10.98        51.98        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       61.97        41.00        38.04         1.45         0.69        26.43 
TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 
        1.81        10.19         6.05        33.17         6.97         4.73 
TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       12.39        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
        5.03         8.98        13.97        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       19.99         5.95         5.03       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 
       49.51        31.30        28.57         0.39        32.19         0.66 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12        12.46        55.76        47.08 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       0.72                        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 
                     17.755                      17.015 
[1] "0.7 - 46.0 (17.8)"  "0.4 - 129.3 (17.0)"
[1] "hr=" "1.5"
D37V2, 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        31         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         22          9
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK 13(6Q26) MUTATED          3         0
  DEL PEAK 13(6Q26) WILD-TYPE       15         9
D37V3, 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                          31
  STAGE IIB                          0                           2
  STAGE IIC                          1                           1
  STAGE III                          0                           5
  STAGE IIIA                         1                           8
  STAGE IIIB                         2                          22
  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 91 11
D37V4, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  T1                         3                           6
  T2                         3                          26
  T3                        21                          91
  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 69 41 24
D37V5, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  N0                        16                          69
  N1                         4                          41
  N2                         9                          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"
D37V6, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    22   4
  DEL PEAK 13(6Q26) WILD-TYPE 104  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     22    4
  DEL PEAK 13(6Q26) WILD-TYPE  104   20
   clus
vv  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  0                        22                         104
  1                         4                          20
[1] 2 2
[1] FALSE
D37V7, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   10 20
  DEL PEAK 13(6Q26) WILD-TYPE 66 69
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     10   20
  DEL PEAK 13(6Q26) WILD-TYPE   66   69
        clus
vv       DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  FEMALE                        10                          66
  MALE                          20                          69
[1] 2 2
[1] FALSE
D37V8, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   17  6
  DEL PEAK 13(6Q26) WILD-TYPE 76 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     17    6
  DEL PEAK 13(6Q26) WILD-TYPE   76   13
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                         17                          76
  YES                         6                          13
[1] 2 2
[1] FALSE
D37V9, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    22   6
  DEL PEAK 13(6Q26) WILD-TYPE 124   7
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     22    6
  DEL PEAK 13(6Q26) WILD-TYPE  124    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                                  124
  RECTAL MUCINOUS ADENOCARCINOMA                           7
[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 102   2   9   3
D37V10, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  R0                        21                         102
  R1                         0                           2
  R2                         3                           9
  RX                         1                           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"
D37V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(6Q26) MUTATED       1                         0    13
  DEL PEAK 13(6Q26) WILD-TYPE     0                         6    68
D37V12, 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                           6
  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(38) Variable = DEL PEAK 14(7Q31.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(7Q31.1) MUTATED     4   0
  DEL PEAK 14(7Q31.1) WILD-TYPE 134  22
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            4                           156 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            0                            22 
$`DEL PEAK 14(7Q31.1) MUTATED`
TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-A008 TCGA-DC-6682 
       34.03         6.05        13.94         4.01 

$`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        39.48        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 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       12.00        32.02         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 
       24.00         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       19.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       32.98         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        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-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 
       14.04         1.02        17.03         3.98        46.03        20.98 
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-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        38.56         1.45         0.69         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       27.95        10.98        19.99         5.95         5.03         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-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-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19         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        12.46        18.28        55.76        47.08        26.43 

  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                         4.01                          0.39 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                        34.03                        129.27 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                        9.995                        17.130 
[1] "4.0 - 34.0 (10.0)"  "0.4 - 129.3 (17.1)"
[1] "hr="     "9200000"
D38V2, 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        38         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         24         13
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 14(7Q31.1) MUTATED          0         0
  DEL PEAK 14(7Q31.1) WILD-TYPE       18         9
D38V3, 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                            38
  STAGE IIB                            0                             2
  STAGE IIC                            0                             2
  STAGE III                            0                             5
  STAGE IIIA                           0                             9
  STAGE IIIB                           0                            24
  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  28 109  14
D38V4, multiclass
    clus
vv   DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  T1                           0                             9
  T2                           1                            28
  T3                           3                           109
  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 82 45 32
D38V5, multiclass
    clus
vv   DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  N0                           3                            82
  N1                           0                            45
  N2                           1                            32
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(7Q31.1) MUTATED     4   0
  DEL PEAK 14(7Q31.1) WILD-TYPE 122  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      4    0
  DEL PEAK 14(7Q31.1) WILD-TYPE  122   24
   clus
vv  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  0                           4                           122
  1                           0                            24
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(7Q31.1) MUTATED    2  2
  DEL PEAK 14(7Q31.1) WILD-TYPE 74 87
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      2    2
  DEL PEAK 14(7Q31.1) WILD-TYPE   74   87
        clus
vv       DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  FEMALE                           2                            74
  MALE                             2                            87
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                             0  1
  DEL PEAK 14(7Q31.1) MUTATED    1  2
  DEL PEAK 14(7Q31.1) WILD-TYPE 92 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      1    2
  DEL PEAK 14(7Q31.1) WILD-TYPE   92   17
     clus
vv    DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  NO                            1                            92
  YES                           2                            17
[1] 2 2
[1] FALSE
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK 14(7Q31.1) MUTATED     3   1
  DEL PEAK 14(7Q31.1) WILD-TYPE 143  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      3    1
  DEL PEAK 14(7Q31.1) WILD-TYPE  143   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                                    143
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[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 119   2  12   4
D38V10, multiclass
    clus
vv   DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  R0                           4                           119
  R1                           0                             2
  R2                           0                            12
  RX                           0                             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"
D38V11, 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                         6    80
D38V12, 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                            87 
                   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-AF-A56K                    TCGA-AF-A56L 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AF-A56N                    TCGA-AH-6544 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6547                    TCGA-AH-6643 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6644                    TCGA-AH-6897 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-AH-6903                    TCGA-BM-6198 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6619                    TCGA-CI-6620 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6621                    TCGA-CI-6622 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CI-6623                    TCGA-CI-6624 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-CL-5917                    TCGA-CL-5918 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-4745                    TCGA-DC-4749 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-5337                    TCGA-DC-5869 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6154                    TCGA-DC-6155 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6156                    TCGA-DC-6157 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6158                    TCGA-DC-6160 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DC-6681                    TCGA-DC-6683 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DT-5265                    TCGA-DY-A0XA 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DC                    TCGA-DY-A1DD 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DE                    TCGA-DY-A1DF 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-DY-A1DG                    TCGA-DY-A1H8 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EF-5830                    TCGA-EF-5831 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6506                    TCGA-EI-6507 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6508                    TCGA-EI-6509 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6510                    TCGA-EI-6511 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6512                    TCGA-EI-6513 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6514                    TCGA-EI-6881 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6882                    TCGA-EI-6883 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6884                    TCGA-EI-6885 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-6917                    TCGA-EI-7002 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-EI-7004                    TCGA-F5-6464 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6465                    TCGA-F5-6571 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6702                    TCGA-F5-6810 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6811                    TCGA-F5-6812 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6813                    TCGA-F5-6814 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6861                    TCGA-F5-6863 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-F5-6864                    TCGA-G5-6233 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-G5-6235                    TCGA-G5-6572 
"DEL PEAK 14(7Q31.1) WILD-TYPE" "DEL PEAK 14(7Q31.1) WILD-TYPE" 
                   TCGA-G5-6641 
"DEL PEAK 14(7Q31.1) WILD-TYPE" 

Clustering(39) Variable = DEL PEAK 15(8P23.2) MUTATION ANALYSIS
D39V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(8P23.2) MUTATED   82 15
  DEL PEAK 15(8P23.2) WILD-TYPE 56  7
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           97                            63 
  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 
       39.48        17.23        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L 
       37.74        10.39        15.39        20.02        10.39        65.98 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 
       32.02        36.03        24.00         1.02        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3611 
       34.03        34.03         2.01         6.05         0.99        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        29.98        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3902 
       19.04         1.02        17.03        35.01         1.02        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-4021 TCGA-AG-A002 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A014 TCGA-AG-A016 
        3.98        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        12.39        78.12        21.01        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
        5.03        13.97        15.02        27.95        10.98         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.03         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        28.57 
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        12.46        18.28 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 15(8P23.2) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       24.13        14.50        16.83        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3598 TCGA-AG-3599 
       12.00         8.02         7.07        20.05        50.04        12.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 
       15.95        19.99        20.98        37.02         0.99        19.99 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-4022 
       17.95        36.95        13.02        14.01        48.03        46.03 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A025 TCGA-AG-A02N 
       13.94         6.02        37.02        36.03        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       38.04        38.56         0.69        26.43         1.81         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
       33.17         6.97         9.37         7.17        15.02         8.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EI-6506 
       19.99         5.95        24.13        51.48        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
       19.96        20.91        17.00        18.28        17.69        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6814 
       16.41         8.61        17.46        49.51        32.19         0.53 
TCGA-F5-6861 TCGA-G5-6235 TCGA-G5-6572 
        1.12        55.76        47.08 

  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                         0.39                          0.53 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                       129.27                         86.63 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                        15.85                         18.28 
[1] "0.4 - 129.3 (15.8)" "0.5 - 86.6 (18.3)" 
[1] "hr=" "1.6"
D39V2, 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        16         1         0
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 15(8P23.2) MUTATED           4          5         16          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
D39V3, 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                            16
  STAGE IIB                            1                             1
  STAGE IIC                            2                             0
  STAGE III                            4                             1
  STAGE IIIA                           5                             4
  STAGE IIIB                          16                             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 68 11
  DEL PEAK 15(8P23.2) WILD-TYPE  6 11 44  3
D39V4, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  T1                           3                             6
  T2                          18                            11
  T3                          68                            44
  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 22
  DEL PEAK 15(8P23.2) WILD-TYPE 37 16 11
D39V5, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  N0                          48                            37
  N1                          29                            16
  N2                          22                            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"
D39V6, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED   74 16
  DEL PEAK 15(8P23.2) WILD-TYPE 52  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     74   16
  DEL PEAK 15(8P23.2) WILD-TYPE   52    8
   clus
vv  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  0                          74                            52
  1                          16                             8
[1] 2 2
[1] FALSE
D39V7, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED   46 54
  DEL PEAK 15(8P23.2) WILD-TYPE 30 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     46   54
  DEL PEAK 15(8P23.2) WILD-TYPE   30   35
        clus
vv       DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  FEMALE                          46                            30
  MALE                            54                            35
[1] 2 2
[1] FALSE
D39V8, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED   54 11
  DEL PEAK 15(8P23.2) WILD-TYPE 39  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     54   11
  DEL PEAK 15(8P23.2) WILD-TYPE   39    8
     clus
vv    DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  NO                           54                            39
  YES                          11                             8
[1] 2 2
[1] FALSE
D39V9, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED   89  7
  DEL PEAK 15(8P23.2) WILD-TYPE 57  6
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     89    7
  DEL PEAK 15(8P23.2) WILD-TYPE   57    6
                                clus
vv                               DEL PEAK 15(8P23.2) MUTATED
  RECTAL ADENOCARCINOMA                                   89
  RECTAL MUCINOUS ADENOCARCINOMA                           7
                                clus
vv                               DEL PEAK 15(8P23.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     57
  RECTAL MUCINOUS ADENOCARCINOMA                             6
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 15(8P23.2) MUTATED   72  1 10  3
  DEL PEAK 15(8P23.2) WILD-TYPE 51  1  2  1
D39V10, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  R0                          72                            51
  R1                           1                             1
  R2                          10                             2
  RX                           3                             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"
D39V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(8P23.2) MUTATED       1                         4    46
  DEL PEAK 15(8P23.2) WILD-TYPE     0                         2    35
D39V12, multiclass
                           clus
vv                          DEL PEAK 15(8P23.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              46
                           clus
vv                          DEL PEAK 15(8P23.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             2
  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(40) Variable = DEL PEAK 16(8P11.21) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(8P11.21) MUTATED    36   7
  DEL PEAK 16(8P11.21) WILD-TYPE 102  15
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                            43                            117 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                             7                             15 
$`DEL PEAK 16(8P11.21) MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3578 
       39.48        17.23        43.04        13.55        34.49        32.02 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3611 TCGA-AG-3726 TCGA-AG-3727 
        1.02        46.03        34.03        13.94         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3890 TCGA-AG-3999 TCGA-AG-4005 
       29.98         0.99         1.02        17.03        28.04        14.04 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       17.03         3.98        25.97        23.01        37.02         1.02 
TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A026 TCGA-AG-A02G 
       12.00        70.03        10.98        51.98         1.94        38.96 
TCGA-AH-6547 TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-5869 TCGA-DC-6155 TCGA-DY-A0XA 
        1.45        10.19         4.73         5.03        13.97       126.44 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6810 TCGA-F5-6863 
      129.27        51.48        13.64        11.97         0.39         0.76 
TCGA-G5-6641 
       26.43 

$`DEL PEAK 16(8P11.21) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 
       24.13        19.10        37.74        10.39        14.50        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       15.39        20.02        10.39        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00         8.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00        34.03        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-3725 
        6.05         0.99        15.95        19.99        19.99        20.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       37.02        32.98         0.99        19.04        19.99        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       36.95        13.02        35.01        14.01         1.02        48.03 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       32.02        19.99        36.03         1.02        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N 
       13.94         6.02        15.95        36.03         9.07        31.00 
TCGA-AG-A01Y TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       64.01        49.97        61.97        41.00        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72        26.43         1.81         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        6.97         9.37        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       11.01        15.02         8.98        15.02        27.95        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       19.99         5.95         4.01         5.03         5.29        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       57.24        24.13        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-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       17.46         8.45         9.96        49.51        31.30        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       32.19         0.66         0.69         0.53         1.12        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                          0.39                           0.49 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                        129.27                          86.63 
  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE 
                         14.04                          17.69 
[1] "0.4 - 129.3 (14.0)" "0.5 - 86.6 (17.7)" 
[1] "hr=" "1.1"
D40V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 16(8P11.21) MUTATED         7        2        14         0         0
  DEL PEAK 16(8P11.21) WILD-TYPE      23        6        26         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 16(8P11.21) MUTATED           4          2          5          2
  DEL PEAK 16(8P11.21) WILD-TYPE         1          7         19         12
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 16(8P11.21) MUTATED          7         1
  DEL PEAK 16(8P11.21) WILD-TYPE       11         8
D40V3, multiclass
            clus
vv           DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  STAGE I                               7                             23
  STAGE II                              2                              6
  STAGE IIA                            14                             26
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             4                              1
  STAGE IIIA                            2                              7
  STAGE IIIB                            5                             19
  STAGE IIIC                            2                             12
  STAGE IV                              7                             11
  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 16(8P11.21) MUTATED    3  7 32  3
  DEL PEAK 16(8P11.21) WILD-TYPE  6 22 80 11
D40V4, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  T1                            3                              6
  T2                            7                             22
  T3                           32                             80
  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 16(8P11.21) MUTATED   24 13  8
  DEL PEAK 16(8P11.21) WILD-TYPE 61 32 25
D40V5, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  N0                           24                             61
  N1                           13                             32
  N2                            8                             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"
D40V6, binary
                                cls
clus                              0  1
  DEL PEAK 16(8P11.21) MUTATED   33  8
  DEL PEAK 16(8P11.21) WILD-TYPE 93 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     33    8
  DEL PEAK 16(8P11.21) WILD-TYPE   93   16
   clus
vv  DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  0                           33                             93
  1                            8                             16
[1] 2 2
[1] FALSE
D40V7, binary
                                cls
clus                              0  1
  DEL PEAK 16(8P11.21) MUTATED   25 20
  DEL PEAK 16(8P11.21) WILD-TYPE 51 69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     25   20
  DEL PEAK 16(8P11.21) WILD-TYPE   51   69
        clus
vv       DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  FEMALE                           25                             51
  MALE                             20                             69
[1] 2 2
[1] FALSE
D40V8, binary
                                cls
clus                              0  1
  DEL PEAK 16(8P11.21) MUTATED   21  5
  DEL PEAK 16(8P11.21) WILD-TYPE 72 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     21    5
  DEL PEAK 16(8P11.21) WILD-TYPE   72   14
     clus
vv    DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  NO                            21                             72
  YES                            5                             14
[1] 2 2
[1] FALSE
D40V9, binary
                                cls
clus                               0   1
  DEL PEAK 16(8P11.21) MUTATED    39   4
  DEL PEAK 16(8P11.21) WILD-TYPE 107   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(8P11.21) MUTATED     39    4
  DEL PEAK 16(8P11.21) WILD-TYPE  107    9
                                clus
vv                               DEL PEAK 16(8P11.21) MUTATED
  RECTAL ADENOCARCINOMA                                    39
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               DEL PEAK 16(8P11.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     107
  RECTAL MUCINOUS ADENOCARCINOMA                              9
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 16(8P11.21) MUTATED   35  1  3  0
  DEL PEAK 16(8P11.21) WILD-TYPE 88  1  9  4
D40V10, multiclass
    clus
vv   DEL PEAK 16(8P11.21) MUTATED DEL PEAK 16(8P11.21) WILD-TYPE
  R0                           35                             88
  R1                            1                              1
  R2                            3                              9
  RX                            0                              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"
D40V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(8P11.21) MUTATED       0                         1    18
  DEL PEAK 16(8P11.21) WILD-TYPE     1                         5    63
D40V12, multiclass
                           clus
vv                          DEL PEAK 16(8P11.21) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               18
                           clus
vv                          DEL PEAK 16(8P11.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              5
  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(41) Variable = DEL PEAK 17(10Q21.1) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(10Q21.1) MUTATED    36   4
  DEL PEAK 17(10Q21.1) WILD-TYPE 102  18
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            40                            120 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                             4                             18 
$`DEL PEAK 17(10Q21.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56L 
       24.13        13.55        34.49        16.83        10.39        65.98 
TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       32.02        36.03        20.05        46.03        34.03        34.03 
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        12.39        13.97 
TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EI-6509 TCGA-EI-6514 
       27.95         4.01         5.03       129.27        17.00        16.31 
TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
       16.41        28.57        12.46        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 
       39.48        17.23        43.04        19.10        37.74        10.39 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       14.50        15.39        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 
       12.00         8.02         7.07        24.00         1.02         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
       50.04        12.03         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 
       19.99        20.98         7.99         0.99        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3890 
        0.99         0.99        19.04        19.99        17.95        17.03 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 
       13.02        35.01        14.01        48.03        32.02        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        37.02        15.95        36.03         9.07         1.02 
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-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        9.37        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
        5.03         8.98        15.02        10.98        19.99         5.95 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
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-6513 TCGA-EI-6882 TCGA-EI-6883 
       18.28        15.85        17.69        16.34         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-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       49.51        31.30         0.39        32.19         0.66         0.69 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        18.28        55.76        47.08 

  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                          1.02                           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 
                        18.495                         17.030 
[1] "1.0 - 129.3 (18.5)" "0.4 - 126.4 (17.0)"
[1] "hr=" "1.3"
D41V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 17(10Q21.1) MUTATED         8        1        13         1         0
  DEL PEAK 17(10Q21.1) WILD-TYPE      22        7        27         1         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 17(10Q21.1) MUTATED           0          4          6          4
  DEL PEAK 17(10Q21.1) WILD-TYPE         5          5         18         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 17(10Q21.1) MUTATED          3         1
  DEL PEAK 17(10Q21.1) WILD-TYPE       15         8
D41V3, 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                            13                             27
  STAGE IIB                             1                              1
  STAGE IIC                             0                              2
  STAGE III                             0                              5
  STAGE IIIA                            4                              5
  STAGE IIIB                            6                             18
  STAGE IIIC                            4                             10
  STAGE IV                              3                             15
  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 28  3
  DEL PEAK 17(10Q21.1) WILD-TYPE  8 20 84 11
D41V4, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  T1                            1                              8
  T2                            9                             20
  T3                           28                             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
  DEL PEAK 17(10Q21.1) MUTATED   23 11  7
  DEL PEAK 17(10Q21.1) WILD-TYPE 62 34 26
D41V5, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  N0                           23                             62
  N1                           11                             34
  N2                            7                             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"
D41V6, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q21.1) MUTATED   36  3
  DEL PEAK 17(10Q21.1) WILD-TYPE 90 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     36    3
  DEL PEAK 17(10Q21.1) WILD-TYPE   90   21
   clus
vv  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  0                           36                             90
  1                            3                             21
[1] 2 2
[1] FALSE
D41V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q21.1) MUTATED   17 24
  DEL PEAK 17(10Q21.1) WILD-TYPE 59 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     17   24
  DEL PEAK 17(10Q21.1) WILD-TYPE   59   65
        clus
vv       DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  FEMALE                           17                             59
  MALE                             24                             65
[1] 2 2
[1] FALSE
D41V8, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q21.1) MUTATED   19 10
  DEL PEAK 17(10Q21.1) WILD-TYPE 74  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     19   10
  DEL PEAK 17(10Q21.1) WILD-TYPE   74    9
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  NO                            19                             74
  YES                           10                              9
[1] 2 2
[1] FALSE
D41V9, binary
                                cls
clus                               0   1
  DEL PEAK 17(10Q21.1) MUTATED    34   6
  DEL PEAK 17(10Q21.1) WILD-TYPE 112   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     34    6
  DEL PEAK 17(10Q21.1) WILD-TYPE  112    7
                                clus
vv                               DEL PEAK 17(10Q21.1) MUTATED
  RECTAL ADENOCARCINOMA                                    34
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 17(10Q21.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     112
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 17(10Q21.1) MUTATED   32  1  2  1
  DEL PEAK 17(10Q21.1) WILD-TYPE 91  1 10  3
D41V10, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  R0                           32                             91
  R1                            1                              1
  R2                            2                             10
  RX                            1                              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 17(10Q21.1) MUTATED       0                         2    17
  DEL PEAK 17(10Q21.1) WILD-TYPE     1                         4    64
D41V12, multiclass
                           clus
vv                          DEL PEAK 17(10Q21.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               17
                           clus
vv                          DEL PEAK 17(10Q21.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  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(42) Variable = DEL PEAK 18(10Q25.2) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(10Q25.2) MUTATED   41  4
  DEL PEAK 18(10Q25.2) WILD-TYPE 97 18
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            45                            115 
  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-AF-A56L 
       24.13        39.48        13.55        34.49        10.39        65.98 
TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3881 
       32.02        34.03        34.03         6.05        29.98        19.04 
TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4021 
       36.95        17.03         1.02        19.99        36.03         3.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A011 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A020 
       13.94        25.97        37.02        12.00        70.03        10.98 
TCGA-AG-A02X TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 
       41.00        26.43        10.19         4.73        13.97        27.95 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 
       19.99         4.01         5.03       129.27        24.13         2.40 
TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6812 
       17.00        16.31        16.41        11.97        28.57         0.66 
TCGA-F5-6864 TCGA-G5-6572 TCGA-G5-6641 
       12.46        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-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        15.39        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03         2.01        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        7.99         0.99        37.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        17.95        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 
       46.03        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        38.56         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        33.17         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
       15.02         5.03         8.98        15.02        10.98         5.95 
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        49.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 
       32.19         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 
                          0.66                           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 
                         19.99                          16.34 
[1] "0.7 - 129.3 (20.0)" "0.4 - 126.4 (16.3)"
[1] "hr=" "1.9"
D42V2, 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        24         2         2
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 18(10Q25.2) MUTATED           1          3          7          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
D42V3, 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                             24
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             1                              4
  STAGE IIIA                            3                              6
  STAGE IIIB                            7                             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 36  1
  DEL PEAK 18(10Q25.2) WILD-TYPE  8 20 76 13
D42V4, multiclass
    clus
vv   DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  T1                            1                              8
  T2                            9                             20
  T3                           36                             76
  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 11
  DEL PEAK 18(10Q25.2) WILD-TYPE 60 34 22
D42V5, multiclass
    clus
vv   DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  N0                           25                             60
  N1                           11                             34
  N2                           11                             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"
D42V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(10Q25.2) MUTATED   40  4
  DEL PEAK 18(10Q25.2) WILD-TYPE 86 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED     40    4
  DEL PEAK 18(10Q25.2) WILD-TYPE   86   20
   clus
vv  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  0                           40                             86
  1                            4                             20
[1] 2 2
[1] FALSE
D42V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(10Q25.2) MUTATED   23 25
  DEL PEAK 18(10Q25.2) WILD-TYPE 53 64
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED     23   25
  DEL PEAK 18(10Q25.2) WILD-TYPE   53   64
        clus
vv       DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  FEMALE                           23                             53
  MALE                             25                             64
[1] 2 2
[1] FALSE
D42V8, binary
                                cls
clus                              0  1
  DEL PEAK 18(10Q25.2) MUTATED   22  9
  DEL PEAK 18(10Q25.2) WILD-TYPE 71 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED     22    9
  DEL PEAK 18(10Q25.2) WILD-TYPE   71   10
     clus
vv    DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  NO                            22                             71
  YES                            9                             10
[1] 2 2
[1] FALSE
D42V9, binary
                                cls
clus                               0   1
  DEL PEAK 18(10Q25.2) MUTATED    39   7
  DEL PEAK 18(10Q25.2) WILD-TYPE 107   6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED     39    7
  DEL PEAK 18(10Q25.2) WILD-TYPE  107    6
                                clus
vv                               DEL PEAK 18(10Q25.2) MUTATED
  RECTAL ADENOCARCINOMA                                    39
  RECTAL MUCINOUS ADENOCARCINOMA                            7
                                clus
vv                               DEL PEAK 18(10Q25.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     107
  RECTAL MUCINOUS ADENOCARCINOMA                              6
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 18(10Q25.2) MUTATED   40  0  1  1
  DEL PEAK 18(10Q25.2) WILD-TYPE 83  2 11  3
D42V10, multiclass
    clus
vv   DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  R0                           40                             83
  R1                            0                              2
  R2                            1                             11
  RX                            1                              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 18(10Q25.2) MUTATED       0                         2    24
  DEL PEAK 18(10Q25.2) WILD-TYPE     1                         4    57
D42V12, multiclass
                           clus
vv                          DEL PEAK 18(10Q25.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               24
                           clus
vv                          DEL PEAK 18(10Q25.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  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(43) Variable = DEL PEAK 19(11Q22.3) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(11Q22.3) MUTATED    35   3
  DEL PEAK 19(11Q22.3) WILD-TYPE 103  19
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            38                            122 
  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-3591 TCGA-AG-3594 TCGA-AG-3600 
       32.02         7.07        46.03        34.03         2.01         6.05 
TCGA-AG-3611 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3896 
       13.94         0.99        32.98        19.04        17.95         1.02 
TCGA-AG-A008 TCGA-AG-A01L TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A02X 
       13.94        12.00        70.03        64.01        10.98        41.00 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-BM-6198 TCGA-CL-4957 TCGA-DC-6155 
       38.56         0.69         0.72        10.19        12.39        13.97 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6508 TCGA-EI-6509 
       10.98        19.99         5.29        24.13        20.91        17.00 
TCGA-EI-6881 TCGA-EI-7004 
       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        39.48        17.23        34.49        37.74        10.39 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       12.00         8.02        36.03        20.05        24.00         1.02 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
       34.03        34.03        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 
       19.99        19.99        20.98         7.99        29.98        37.02 
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-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-4007 TCGA-AG-4008 TCGA-AG-4021 
       28.04        36.03        14.04         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 
       46.03        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 
       26.43         1.81         6.05        33.17         6.97         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
        4.73        78.12         7.17        21.01        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 
        5.03         8.98        15.02        27.95         5.95         4.01 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
        5.03       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        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       31.30        28.57         0.39        32.19         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        12.46        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 
                          0.69                           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 
                        14.235                         17.985 
[1] "0.7 - 70.0 (14.2)"  "0.4 - 129.3 (18.0)"
[1] "hr=" "1.6"
D43V2, 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        34         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         19         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 19(11Q22.3) MUTATED          1         2
  DEL PEAK 19(11Q22.3) WILD-TYPE       17         7
D43V3, 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                             34
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             2                              3
  STAGE IIIA                            3                              6
  STAGE IIIB                            5                             19
  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 88 11
D43V4, multiclass
    clus
vv   DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  T1                            1                              8
  T2                           10                             19
  T3                           24                             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 19(11Q22.3) MUTATED   19 11  7
  DEL PEAK 19(11Q22.3) WILD-TYPE 66 34 26
D43V5, multiclass
    clus
vv   DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  N0                           19                             66
  N1                           11                             34
  N2                            7                             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"
D43V6, binary
                                cls
clus                              0  1
  DEL PEAK 19(11Q22.3) MUTATED   31  1
  DEL PEAK 19(11Q22.3) WILD-TYPE 95 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED     31    1
  DEL PEAK 19(11Q22.3) WILD-TYPE   95   23
   clus
vv  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  0                           31                             95
  1                            1                             23
[1] 2 2
[1] FALSE
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 19(11Q22.3) MUTATED   19 19
  DEL PEAK 19(11Q22.3) WILD-TYPE 57 70
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED     19   19
  DEL PEAK 19(11Q22.3) WILD-TYPE   57   70
        clus
vv       DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  FEMALE                           19                             57
  MALE                             19                             70
[1] 2 2
[1] FALSE
D43V8, binary
                                cls
clus                              0  1
  DEL PEAK 19(11Q22.3) MUTATED   20  7
  DEL PEAK 19(11Q22.3) WILD-TYPE 73 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED     20    7
  DEL PEAK 19(11Q22.3) WILD-TYPE   73   12
     clus
vv    DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  NO                            20                             73
  YES                            7                             12
[1] 2 2
[1] FALSE
D43V9, binary
                                cls
clus                               0   1
  DEL PEAK 19(11Q22.3) MUTATED    28   6
  DEL PEAK 19(11Q22.3) WILD-TYPE 118   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED     28    6
  DEL PEAK 19(11Q22.3) WILD-TYPE  118    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                                     118
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[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 94  2 12  3
D43V10, multiclass
    clus
vv   DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  R0                           29                             94
  R1                            0                              2
  R2                            0                             12
  RX                            1                              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 19(11Q22.3) MUTATED       1                         0    18
  DEL PEAK 19(11Q22.3) WILD-TYPE     0                         6    63
D43V12, 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                              6
  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(44) Variable = DEL PEAK 20(12P13.1) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(12P13.1) MUTATED    24   7
  DEL PEAK 20(12P13.1) WILD-TYPE 114  15
  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                            31                            129 
  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-3591 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 
       20.02        36.03        34.03        34.03        29.98        37.02 
TCGA-AG-3898 TCGA-AG-4021 TCGA-AG-A00C TCGA-AG-A01W TCGA-AG-A026 TCGA-AH-6544 
       48.03         3.98         6.02        70.03         1.94        38.56 
TCGA-CI-6620 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6158 TCGA-DY-A1DF TCGA-DY-A1DG 
       33.17        11.01        13.97        10.98        24.13        51.48 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       20.91        17.00        16.31        16.41        28.57         0.66 
TCGA-G5-6641 
       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        39.48        17.23        34.49        37.74        16.83 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       10.39        86.63        65.98        11.84        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        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3592 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-3611 TCGA-AG-3612 TCGA-AG-3725 
        0.99        15.95        19.99        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 
        7.99         0.99        32.98         0.99         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        36.95        17.03        13.02 
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-A002 
       36.03        14.04         1.02        17.03        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 
       13.94        25.97        23.01        37.02        15.95        36.03 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 
        9.07         1.02        12.00        31.00        64.01        10.98 
TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 
       51.98        49.97        38.96        61.97        41.00        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
        1.45         0.69         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
        6.05         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
        7.17        21.01        15.02         5.03         8.98        15.02 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       27.95        19.99         5.95         4.01         5.03         5.29 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        57.24       129.27        32.61         0.49 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
        2.40        20.55        19.96        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.34         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-F5-6810 
       11.97         8.45         9.96        49.51        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       32.19         0.69         0.53         1.12         0.76        12.46 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
       18.28        55.76        47.08 

  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE 
                          0.66                           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 
                         20.02                          16.83 
[1] "0.7 - 70.0 (20.0)"  "0.4 - 129.3 (16.8)"
[1] "hr=" "1.9"
D44V2, 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        33         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         20         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 20(12P13.1) MUTATED          3         4
  DEL PEAK 20(12P13.1) WILD-TYPE       15         5
D44V3, 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                             33
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             0                              5
  STAGE IIIA                            4                              5
  STAGE IIIB                            4                             20
  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 88 12
D44V4, multiclass
    clus
vv   DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  T1                            2                              7
  T2                            5                             24
  T3                           24                             88
  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 71 31 28
D44V5, multiclass
    clus
vv   DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  N0                           14                             71
  N1                           14                             31
  N2                            5                             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"
D44V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P13.1) MUTATED    22   7
  DEL PEAK 20(12P13.1) WILD-TYPE 104  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P13.1) MUTATED     22    7
  DEL PEAK 20(12P13.1) WILD-TYPE  104   17
   clus
vv  DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  0                           22                            104
  1                            7                             17
[1] 2 2
[1] FALSE
D44V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(12P13.1) MUTATED   16 17
  DEL PEAK 20(12P13.1) WILD-TYPE 60 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P13.1) MUTATED     16   17
  DEL PEAK 20(12P13.1) WILD-TYPE   60   72
        clus
vv       DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  FEMALE                           16                             60
  MALE                             17                             72
[1] 2 2
[1] FALSE
D44V8, binary
                                cls
clus                              0  1
  DEL PEAK 20(12P13.1) MUTATED   22  4
  DEL PEAK 20(12P13.1) WILD-TYPE 71 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P13.1) MUTATED     22    4
  DEL PEAK 20(12P13.1) WILD-TYPE   71   15
     clus
vv    DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  NO                            22                             71
  YES                            4                             15
[1] 2 2
[1] FALSE
D44V9, binary
                                cls
clus                               0   1
  DEL PEAK 20(12P13.1) MUTATED    29   1
  DEL PEAK 20(12P13.1) WILD-TYPE 117  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12P13.1) MUTATED     29    1
  DEL PEAK 20(12P13.1) WILD-TYPE  117   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                                     117
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[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 99  1 10  4
D44V10, multiclass
    clus
vv   DEL PEAK 20(12P13.1) MUTATED DEL PEAK 20(12P13.1) WILD-TYPE
  R0                           24                             99
  R1                            1                              1
  R2                            2                             10
  RX                            0                              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"
D44V11, 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                         5    61
D44V12, 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                              5
  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(45) Variable = DEL PEAK 21(12Q22) MUTATION ANALYSIS
D45V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 21(12Q22) MUTATED    20   4
  DEL PEAK 21(12Q22) WILD-TYPE 118  18
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                          24                          136 
  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                           4                           18 
$`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        34.49        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 
       38.56        13.97        10.98       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        28.57         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        39.48        17.23        13.55        19.10        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       10.39        16.83        20.02        10.39        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       11.84        12.00        32.02         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       20.05        24.00         1.02        46.03        34.03        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-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       19.99        13.94        19.99        20.98         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
       37.02         0.99         0.99        19.04        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       17.95        36.95        17.03        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
        1.02        32.02        19.99        28.04        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       17.03         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        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-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-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 
        0.69         0.72        26.43         1.81        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       15.02        27.95        19.99         5.95         4.01         5.03 
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-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
        0.49         2.40        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 
       15.85        17.69        16.34         8.61        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        49.51        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19         0.69         0.53         1.12         0.76 
TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        55.76        47.08        26.43 

  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE 
                        0.66                         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 
                      26.350                       16.585 
[1] "0.7 - 129.3 (26.4)" "0.4 - 126.4 (16.6)"
[1] "hr=" "1.1"
D45V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 21(12Q22) MUTATED         4        1         8         0         2
  DEL PEAK 21(12Q22) WILD-TYPE      26        7        32         2         0
                              vv
clus                           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 21(12Q22) MUTATED           0          2          3          3
  DEL PEAK 21(12Q22) WILD-TYPE         5          7         21         11
                              vv
clus                           STAGE IV STAGE IVA
  DEL PEAK 21(12Q22) MUTATED          0         2
  DEL PEAK 21(12Q22) WILD-TYPE       18         7
D45V3, multiclass
            clus
vv           DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  STAGE I                             4                           26
  STAGE II                            1                            7
  STAGE IIA                           8                           32
  STAGE IIB                           0                            2
  STAGE IIC                           2                            0
  STAGE III                           0                            5
  STAGE IIIA                          2                            7
  STAGE IIIB                          3                           21
  STAGE IIIC                          3                           11
  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 20  1
  DEL PEAK 21(12Q22) WILD-TYPE  8 25 92 13
D45V4, multiclass
    clus
vv   DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  T1                          1                            8
  T2                          4                           25
  T3                         20                           92
  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   14  7  5
  DEL PEAK 21(12Q22) WILD-TYPE 71 38 28
D45V5, multiclass
    clus
vv   DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  N0                         14                           71
  N1                          7                           38
  N2                          5                           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"
D45V6, binary
                              cls
clus                             0   1
  DEL PEAK 21(12Q22) MUTATED    22   2
  DEL PEAK 21(12Q22) WILD-TYPE 104  22
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(12Q22) MUTATED     22    2
  DEL PEAK 21(12Q22) WILD-TYPE  104   22
   clus
vv  DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  0                         22                          104
  1                          2                           22
[1] 2 2
[1] FALSE
D45V7, binary
                              cls
clus                            0  1
  DEL PEAK 21(12Q22) MUTATED   12 14
  DEL PEAK 21(12Q22) WILD-TYPE 64 75
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(12Q22) MUTATED     12   14
  DEL PEAK 21(12Q22) WILD-TYPE   64   75
        clus
vv       DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  FEMALE                         12                           64
  MALE                           14                           75
[1] 2 2
[1] FALSE
D45V8, binary
                              cls
clus                            0  1
  DEL PEAK 21(12Q22) MUTATED   16  4
  DEL PEAK 21(12Q22) WILD-TYPE 77 15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(12Q22) MUTATED     16    4
  DEL PEAK 21(12Q22) WILD-TYPE   77   15
     clus
vv    DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  NO                          16                           77
  YES                          4                           15
[1] 2 2
[1] FALSE
D45V9, binary
                              cls
clus                             0   1
  DEL PEAK 21(12Q22) MUTATED    24   1
  DEL PEAK 21(12Q22) WILD-TYPE 122  12
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 21(12Q22) MUTATED     24    1
  DEL PEAK 21(12Q22) WILD-TYPE  122   12
                                clus
vv                               DEL PEAK 21(12Q22) MUTATED
  RECTAL ADENOCARCINOMA                                  24
  RECTAL MUCINOUS ADENOCARCINOMA                          1
                                clus
vv                               DEL PEAK 21(12Q22) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   122
  RECTAL MUCINOUS ADENOCARCINOMA                           12
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 21(12Q22) MUTATED    22   0   0   0
  DEL PEAK 21(12Q22) WILD-TYPE 101   2  12   4
D45V10, multiclass
    clus
vv   DEL PEAK 21(12Q22) MUTATED DEL PEAK 21(12Q22) WILD-TYPE
  R0                         22                          101
  R1                          0                            2
  R2                          0                           12
  RX                          0                            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"
D45V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(12Q22) MUTATED       0                         0    16
  DEL PEAK 21(12Q22) WILD-TYPE     1                         6    65
D45V12, 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                            6
  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(46) Variable = DEL PEAK 22(14Q11.2) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(14Q11.2) MUTATED   59  8
  DEL PEAK 22(14Q11.2) WILD-TYPE 79 14
  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                            67                             93 
  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 
       39.48        13.55        19.10        34.49        37.74        10.39 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3591 TCGA-AG-3592 
       65.98        11.84        36.03         7.07        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 TCGA-AG-3882 
       34.03        50.04         6.05         0.99         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 
        1.02        17.95        17.03        35.01         1.02        28.04 
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-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6619 
        1.94        38.96        38.04        38.56        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 
       33.17         9.37         4.73        12.39         7.17        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
        5.03        13.97        27.95        10.98         4.01         5.03 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 
      129.27        24.13        51.48        20.55        20.91        17.00 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 
       16.34        16.31        16.41        10.78        11.97        31.30 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 
        0.39        32.19         0.66         0.76        18.28        55.76 
TCGA-G5-6641 
       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        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3580 
       15.39        20.02        86.63        12.00        32.02         8.02 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 
       36.03        20.05        24.00         1.02        46.03         2.01 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       12.03         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
       20.98         7.99        29.98        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       19.04        36.95        13.02        14.01        48.03        32.02 
TCGA-AG-3909 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       19.99         1.02         3.98        46.03        20.98        13.94 
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-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       61.97        41.00         1.45         0.69         0.72        26.43 
TCGA-AH-6903 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
        1.81         6.97        78.12        21.01        15.02         8.98 
TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       15.02        19.99         5.95         5.29       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6510 
       57.24        32.61         0.49         2.40        19.96        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 
       15.85        17.69         8.61        11.51        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        49.51        28.57         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
        1.12        12.46        47.08 

  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE 
                          0.39                           0.49 
  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 
                         17.03                          17.23 
[1] "0.4 - 129.3 (17.0)" "0.5 - 126.4 (17.2)"
[1] "hr=" "1"  
D46V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 22(14Q11.2) MUTATED        12        2        21         0         1
  DEL PEAK 22(14Q11.2) WILD-TYPE      18        6        19         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 22(14Q11.2) MUTATED           1          5         12          7
  DEL PEAK 22(14Q11.2) WILD-TYPE         4          4         12          7
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 22(14Q11.2) MUTATED          6         2
  DEL PEAK 22(14Q11.2) WILD-TYPE       12         7
D46V3, 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                            21                             19
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             1                              4
  STAGE IIIA                            5                              4
  STAGE IIIB                           12                             12
  STAGE IIIC                            7                              7
  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 51  4
  DEL PEAK 22(14Q11.2) WILD-TYPE  6 17 61 10
D46V4, multiclass
    clus
vv   DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  T1                            3                              6
  T2                           12                             17
  T3                           51                             61
  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   35 23 12
  DEL PEAK 22(14Q11.2) WILD-TYPE 50 22 21
D46V5, multiclass
    clus
vv   DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  N0                           35                             50
  N1                           23                             22
  N2                           12                             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"
D46V6, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q11.2) MUTATED   55  8
  DEL PEAK 22(14Q11.2) WILD-TYPE 71 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q11.2) MUTATED     55    8
  DEL PEAK 22(14Q11.2) WILD-TYPE   71   16
   clus
vv  DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  0                           55                             71
  1                            8                             16
[1] 2 2
[1] FALSE
D46V7, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q11.2) MUTATED   31 39
  DEL PEAK 22(14Q11.2) WILD-TYPE 45 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q11.2) MUTATED     31   39
  DEL PEAK 22(14Q11.2) WILD-TYPE   45   50
        clus
vv       DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  FEMALE                           31                             45
  MALE                             39                             50
[1] 2 2
[1] FALSE
D46V8, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q11.2) MUTATED   37 12
  DEL PEAK 22(14Q11.2) WILD-TYPE 56  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q11.2) MUTATED     37   12
  DEL PEAK 22(14Q11.2) WILD-TYPE   56    7
     clus
vv    DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  NO                            37                             56
  YES                           12                              7
[1] 2 2
[1] FALSE
D46V9, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q11.2) MUTATED   66  2
  DEL PEAK 22(14Q11.2) WILD-TYPE 80 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q11.2) MUTATED     66    2
  DEL PEAK 22(14Q11.2) WILD-TYPE   80   11
                                clus
vv                               DEL PEAK 22(14Q11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 22(14Q11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      80
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 22(14Q11.2) MUTATED   51  2  2  2
  DEL PEAK 22(14Q11.2) WILD-TYPE 72  0 10  2
D46V10, multiclass
    clus
vv   DEL PEAK 22(14Q11.2) MUTATED DEL PEAK 22(14Q11.2) WILD-TYPE
  R0                           51                             72
  R1                            2                              0
  R2                            2                             10
  RX                            2                              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"
D46V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(14Q11.2) MUTATED       0                         4    37
  DEL PEAK 22(14Q11.2) WILD-TYPE     1                         2    44
D46V12, multiclass
                           clus
vv                          DEL PEAK 22(14Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               37
                           clus
vv                          DEL PEAK 22(14Q11.2) 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(47) Variable = DEL PEAK 23(14Q31.1) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(14Q31.1) MUTATED   60  9
  DEL PEAK 23(14Q31.1) WILD-TYPE 78 13
  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                            69                             91 
  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-AF-A56L TCGA-AF-A56N 
       39.48        17.23        13.55        37.74        65.98        11.84 
TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 
       36.03        46.03        34.03        34.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3881 
       12.03         6.05         0.99        37.02         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        17.95        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        38.56        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 
        6.05        33.17         9.37         4.73        12.39         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       21.01        11.01         5.03        13.97        27.95        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 
        4.01         5.03        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        32.19         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        34.49        10.39        14.50 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 
       16.83        15.39        20.02        10.39        86.63        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        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 
        1.02         2.01         0.99        15.95        19.99        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3878 
       19.99        20.98         7.99        29.98        32.98         0.99 
TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3909 
       19.99        36.95        13.02        14.01        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       28.04         1.02         3.98        46.03        20.98        13.94 
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-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-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       41.00         1.45         0.69         0.72        26.43         1.81 
TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
        6.97        78.12        15.02         8.98        15.02        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
        5.95         5.29       126.44        57.24        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        0.49         2.40        19.96        20.91        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       17.69         8.61        13.64        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       49.51        28.57         0.69         0.53         1.12        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE 
                          0.39                           0.49 
  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 
                         17.03                          16.83 
[1] "0.4 - 129.3 (17.0)" "0.5 - 126.4 (16.8)"
[1] "hr=" "1.2"
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 23(14Q31.1) MUTATED        11        2        23         0         2
  DEL PEAK 23(14Q31.1) WILD-TYPE      19        6        17         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 23(14Q31.1) MUTATED           1          5         12          6
  DEL PEAK 23(14Q31.1) WILD-TYPE         4          4         12          8
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 23(14Q31.1) MUTATED          7         2
  DEL PEAK 23(14Q31.1) WILD-TYPE       11         7
D47V3, 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                            23                             17
  STAGE IIB                             0                              2
  STAGE IIC                             2                              0
  STAGE III                             1                              4
  STAGE IIIA                            5                              4
  STAGE IIIB                           12                             12
  STAGE IIIC                            6                              8
  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 55  3
  DEL PEAK 23(14Q31.1) WILD-TYPE  6 18 57 11
D47V4, multiclass
    clus
vv   DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  T1                            3                              6
  T2                           11                             18
  T3                           55                             57
  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   37 25 10
  DEL PEAK 23(14Q31.1) WILD-TYPE 48 20 23
D47V5, multiclass
    clus
vv   DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  N0                           37                             48
  N1                           25                             20
  N2                           10                             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"
D47V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(14Q31.1) MUTATED   57 10
  DEL PEAK 23(14Q31.1) WILD-TYPE 69 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q31.1) MUTATED     57   10
  DEL PEAK 23(14Q31.1) WILD-TYPE   69   14
   clus
vv  DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  0                           57                             69
  1                           10                             14
[1] 2 2
[1] FALSE
D47V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(14Q31.1) MUTATED   31 41
  DEL PEAK 23(14Q31.1) WILD-TYPE 45 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q31.1) MUTATED     31   41
  DEL PEAK 23(14Q31.1) WILD-TYPE   45   48
        clus
vv       DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  FEMALE                           31                             45
  MALE                             41                             48
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                              0  1
  DEL PEAK 23(14Q31.1) MUTATED   39 11
  DEL PEAK 23(14Q31.1) WILD-TYPE 54  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q31.1) MUTATED     39   11
  DEL PEAK 23(14Q31.1) WILD-TYPE   54    8
     clus
vv    DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  NO                            39                             54
  YES                           11                              8
[1] 2 2
[1] FALSE
D47V9, binary
                                cls
clus                              0  1
  DEL PEAK 23(14Q31.1) MUTATED   68  1
  DEL PEAK 23(14Q31.1) WILD-TYPE 78 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(14Q31.1) MUTATED     68    1
  DEL PEAK 23(14Q31.1) WILD-TYPE   78   12
                                clus
vv                               DEL PEAK 23(14Q31.1) MUTATED
  RECTAL ADENOCARCINOMA                                    68
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 23(14Q31.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      78
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 23(14Q31.1) MUTATED   52  2  4  2
  DEL PEAK 23(14Q31.1) WILD-TYPE 71  0  8  2
D47V10, multiclass
    clus
vv   DEL PEAK 23(14Q31.1) MUTATED DEL PEAK 23(14Q31.1) WILD-TYPE
  R0                           52                             71
  R1                            2                              0
  R2                            4                              8
  RX                            2                              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 23(14Q31.1) MUTATED       0                         4    36
  DEL PEAK 23(14Q31.1) WILD-TYPE     1                         2    45
D47V12, multiclass
                           clus
vv                          DEL PEAK 23(14Q31.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               36
                           clus
vv                          DEL PEAK 23(14Q31.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  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(48) Variable = DEL PEAK 24(15Q21.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 24(15Q21.1) MUTATED   66 10
  DEL PEAK 24(15Q21.1) WILD-TYPE 72 12
  DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE 
                            76                             84 
  DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE 
                            10                             12 
$`DEL PEAK 24(15Q21.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 
       24.13        43.04        13.55        37.74        14.50        10.39 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       65.98        11.84        32.02        36.03        20.05        24.00 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3611 
       46.03        34.03        34.03        34.03         6.05        13.94 
TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
       19.99        20.98         0.99        29.98        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 
       19.04        19.99        17.03        35.01         1.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y 
       28.04        14.04        17.03        13.94        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       37.02         1.02        12.00         1.94        38.96        41.00 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 
       38.04        38.56         0.69        10.19         6.05         9.37 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 
        4.73         7.17         5.03        13.97        27.95         4.01 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
        5.03        41.36        57.24        24.13        51.48         0.49 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
        2.40        15.85        16.31        16.41         8.61        11.51 
TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 
       10.78        13.64        11.97        31.30        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-G5-6233 TCGA-G5-6641 
        0.66         0.69        18.28        26.43 

$`DEL PEAK 24(15Q21.1) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3913 TCGA-AF-5654 
       39.48        17.23        19.10        34.49        10.39        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       15.39        20.02        86.63        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
        7.07         1.02         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 
       15.95        19.99         7.99        37.02         0.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 
       17.95        36.95        13.02        14.01        48.03        32.02 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       36.03         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y 
       15.95        36.03         9.07        31.00        70.03        64.01 
TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 
       10.98        51.98        49.97        61.97         1.45         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5917 
       26.43         1.81        33.17         6.97        12.39        78.12 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       21.01        11.01        15.02         8.98        15.02        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 
       19.99         5.95         5.29       126.44       129.27        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       20.55        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 
       16.34        17.46         8.45         9.96        49.51         0.39 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.53         1.12         0.76        12.46        55.76        47.08 

  DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE 
                          0.49                           0.39 
  DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE 
                         65.98                         129.27 
  DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE 
                        17.655                         16.915 
[1] "0.5 - 66.0 (17.7)"  "0.4 - 129.3 (16.9)"
[1] "hr=" "1.2"
D48V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 24(15Q21.1) MUTATED        12        1        23         1         2
  DEL PEAK 24(15Q21.1) WILD-TYPE      18        7        17         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 24(15Q21.1) MUTATED           3          4         12          8
  DEL PEAK 24(15Q21.1) WILD-TYPE         2          5         12          6
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 24(15Q21.1) MUTATED          9         3
  DEL PEAK 24(15Q21.1) WILD-TYPE        9         6
D48V3, multiclass
            clus
vv           DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE
  STAGE I                              12                             18
  STAGE II                              1                              7
  STAGE IIA                            23                             17
  STAGE IIB                             1                              1
  STAGE IIC                             2                              0
  STAGE III                             3                              2
  STAGE IIIA                            4                              5
  STAGE IIIB                           12                             12
  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(15Q21.1) MUTATED    4 11 59  5
  DEL PEAK 24(15Q21.1) WILD-TYPE  5 18 53  9
D48V4, multiclass
    clus
vv   DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE
  T1                            4                              5
  T2                           11                             18
  T3                           59                             53
  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 24(15Q21.1) MUTATED   38 25 16
  DEL PEAK 24(15Q21.1) WILD-TYPE 47 20 17
D48V5, multiclass
    clus
vv   DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE
  N0                           38                             47
  N1                           25                             20
  N2                           16                             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"
D48V6, binary
                                cls
clus                              0  1
  DEL PEAK 24(15Q21.1) MUTATED   61 11
  DEL PEAK 24(15Q21.1) WILD-TYPE 65 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q21.1) MUTATED     61   11
  DEL PEAK 24(15Q21.1) WILD-TYPE   65   13
   clus
vv  DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE
  0                           61                             65
  1                           11                             13
[1] 2 2
[1] FALSE
D48V7, binary
                                cls
clus                              0  1
  DEL PEAK 24(15Q21.1) MUTATED   32 47
  DEL PEAK 24(15Q21.1) WILD-TYPE 44 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q21.1) MUTATED     32   47
  DEL PEAK 24(15Q21.1) WILD-TYPE   44   42
        clus
vv       DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE
  FEMALE                           32                             44
  MALE                             47                             42
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                              0  1
  DEL PEAK 24(15Q21.1) MUTATED   41 12
  DEL PEAK 24(15Q21.1) WILD-TYPE 52  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q21.1) MUTATED     41   12
  DEL PEAK 24(15Q21.1) WILD-TYPE   52    7
     clus
vv    DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE
  NO                            41                             52
  YES                           12                              7
[1] 2 2
[1] FALSE
D48V9, binary
                                cls
clus                              0  1
  DEL PEAK 24(15Q21.1) MUTATED   70  6
  DEL PEAK 24(15Q21.1) WILD-TYPE 76  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 24(15Q21.1) MUTATED     70    6
  DEL PEAK 24(15Q21.1) WILD-TYPE   76    7
                                clus
vv                               DEL PEAK 24(15Q21.1) MUTATED
  RECTAL ADENOCARCINOMA                                    70
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 24(15Q21.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      76
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 24(15Q21.1) MUTATED   59  1  4  2
  DEL PEAK 24(15Q21.1) WILD-TYPE 64  1  8  2
D48V10, multiclass
    clus
vv   DEL PEAK 24(15Q21.1) MUTATED DEL PEAK 24(15Q21.1) WILD-TYPE
  R0                           59                             64
  R1                            1                              1
  R2                            4                              8
  RX                            2                              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 24(15Q21.1) MUTATED       0                         4    38
  DEL PEAK 24(15Q21.1) WILD-TYPE     1                         2    43
D48V12, multiclass
                           clus
vv                          DEL PEAK 24(15Q21.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               38
                           clus
vv                          DEL PEAK 24(15Q21.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              2
  WHITE                                                 43
[1] 3 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 25(15Q22.33) MUTATION ANALYSIS
D49V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 25(15Q22.33) MUTATED   65  9
  DEL PEAK 25(15Q22.33) WILD-TYPE 73 13
  DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE 
                             74                              86 
  DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE 
                              9                              13 
$`DEL PEAK 25(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        34.49        37.74        14.50 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       10.39        65.98        32.02        36.03        20.05        24.00 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 
       34.03        34.03         6.05        15.95        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3890 
       20.98        29.98         0.99        19.04        19.99        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4008 
       35.01         1.02        19.99        28.04        14.04        17.03 
TCGA-AG-A008 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A01L 
       13.94        25.97        23.01        37.02         1.02        12.00 
TCGA-AG-A01W TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
       70.03        38.96        41.00        38.04        38.56         0.69 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5869 
       10.19         6.05         9.37         7.17        21.01         5.03 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD 
       13.97        27.95         4.01         5.03        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 
      129.27        24.13        51.48         0.49         2.40        15.85 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.31        16.41        11.51        10.78        13.64        11.97 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6864 
       31.30        28.57        32.19         0.66         0.69        12.46 
TCGA-G5-6233 TCGA-G5-6641 
       18.28        26.43 

$`DEL PEAK 25(15Q22.33) WILD-TYPE`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 
       39.48        17.23        19.10        10.39        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3580 
       20.02        86.63        11.84        36.03        12.00         8.02 
TCGA-AG-3581 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
        7.07         1.02        46.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       12.03         0.99        19.99         7.99         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99         1.02        17.95        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 
       14.01        48.03        32.02        36.03         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       46.03        20.98         6.02        15.95        36.03         9.07 
TCGA-AG-A01N TCGA-AG-A01Y TCGA-AG-A020 TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A026 
       31.00        64.01        10.98        51.98        49.97         1.94 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       61.97         1.45         0.72        26.43         1.81        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 
        6.97         4.73        12.39        78.12        11.01        15.02 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
        8.98        15.02        10.98        19.99         5.95         5.29 
TCGA-DY-A0XA TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
      126.44        32.61        20.55        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 
       18.28        17.69        16.34         8.61        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        9.96        49.51         0.39         0.53         1.12         0.76 
TCGA-G5-6235 TCGA-G5-6572 
       55.76        47.08 

  DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE 
                           0.49                            0.39 
  DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE 
                         129.27                          126.44 
  DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE 
                         19.515                          16.145 
[1] "0.5 - 129.3 (19.5)" "0.4 - 126.4 (16.1)"
[1] "hr=" "1.2"
D49V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  DEL PEAK 25(15Q22.33) MUTATED         9        1        23         1
  DEL PEAK 25(15Q22.33) WILD-TYPE      21        7        17         1
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 25(15Q22.33) MUTATED           2         2          4         14
  DEL PEAK 25(15Q22.33) WILD-TYPE         0         3          5         10
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 25(15Q22.33) MUTATED            8        9         3
  DEL PEAK 25(15Q22.33) WILD-TYPE          6        9         6
D49V3, multiclass
            clus
vv           DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE
  STAGE I                                9                              21
  STAGE II                               1                               7
  STAGE IIA                             23                              17
  STAGE IIB                              1                               1
  STAGE IIC                              2                               0
  STAGE III                              2                               3
  STAGE IIIA                             4                               5
  STAGE IIIB                            14                              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 25(15Q22.33) MUTATED    4  8 61  4
  DEL PEAK 25(15Q22.33) WILD-TYPE  5 21 51 10
D49V4, multiclass
    clus
vv   DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE
  T1                             4                               5
  T2                             8                              21
  T3                            61                              51
  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 25(15Q22.33) MUTATED   35 25 17
  DEL PEAK 25(15Q22.33) WILD-TYPE 50 20 16
D49V5, multiclass
    clus
vv   DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE
  N0                            35                              50
  N1                            25                              20
  N2                            17                              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"
D49V6, binary
                                 cls
clus                               0  1
  DEL PEAK 25(15Q22.33) MUTATED   59 11
  DEL PEAK 25(15Q22.33) WILD-TYPE 67 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(15Q22.33) MUTATED     59   11
  DEL PEAK 25(15Q22.33) WILD-TYPE   67   13
   clus
vv  DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE
  0                            59                              67
  1                            11                              13
[1] 2 2
[1] FALSE
D49V7, binary
                                 cls
clus                               0  1
  DEL PEAK 25(15Q22.33) MUTATED   33 44
  DEL PEAK 25(15Q22.33) WILD-TYPE 43 45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(15Q22.33) MUTATED     33   44
  DEL PEAK 25(15Q22.33) WILD-TYPE   43   45
        clus
vv       DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE
  FEMALE                            33                              43
  MALE                              44                              45
[1] 2 2
[1] FALSE
D49V8, binary
                                 cls
clus                               0  1
  DEL PEAK 25(15Q22.33) MUTATED   41 11
  DEL PEAK 25(15Q22.33) WILD-TYPE 52  8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(15Q22.33) MUTATED     41   11
  DEL PEAK 25(15Q22.33) WILD-TYPE   52    8
     clus
vv    DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE
  NO                             41                              52
  YES                            11                               8
[1] 2 2
[1] FALSE
D49V9, binary
                                 cls
clus                               0  1
  DEL PEAK 25(15Q22.33) MUTATED   68  6
  DEL PEAK 25(15Q22.33) WILD-TYPE 78  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 25(15Q22.33) MUTATED     68    6
  DEL PEAK 25(15Q22.33) WILD-TYPE   78    7
                                clus
vv                               DEL PEAK 25(15Q22.33) MUTATED
  RECTAL ADENOCARCINOMA                                     68
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 25(15Q22.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       78
  RECTAL MUCINOUS ADENOCARCINOMA                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 25(15Q22.33) MUTATED   58  0  4  2
  DEL PEAK 25(15Q22.33) WILD-TYPE 65  2  8  2
D49V10, multiclass
    clus
vv   DEL PEAK 25(15Q22.33) MUTATED DEL PEAK 25(15Q22.33) WILD-TYPE
  R0                            58                              65
  R1                             0                               2
  R2                             4                               8
  RX                             2                               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 25(15Q22.33) MUTATED       0                         3    40
  DEL PEAK 25(15Q22.33) WILD-TYPE     1                         3    41
D49V12, multiclass
                           clus
vv                          DEL PEAK 25(15Q22.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                40
                           clus
vv                          DEL PEAK 25(15Q22.33) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               3
  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 26(16P13.3) MUTATION ANALYSIS
D50V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(16P13.3) MUTATED    11   2
  DEL PEAK 26(16P13.3) WILD-TYPE 127  20
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                            13                            147 
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                             2                             20 
$`DEL PEAK 26(16P13.3) MUTATED`
TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3881 
       32.02        34.03         6.05        19.99         7.99        19.04 
TCGA-AG-4005 TCGA-AG-A02G TCGA-DC-6682 TCGA-EI-6882 TCGA-F5-6811 TCGA-F5-6814 
       14.04        38.96         4.01         8.61        32.19         0.53 
TCGA-G5-6233 
       18.28 

$`DEL PEAK 26(16P13.3) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        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 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        10.39        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00         8.02         7.07        36.03        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
        1.02        46.03        34.03        34.03         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
       12.03         0.99        15.95        13.94        19.99        20.98 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
        0.99        29.98        37.02        32.98         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3892 
       19.99         1.02        17.95        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-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03         1.02        17.03         3.98        46.03 
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-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-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
       61.97        41.00        38.04        38.56         1.45         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.72        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        27.95        10.98        19.99         5.95         5.03 
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-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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 
       16.31        16.41        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        49.51        31.30        28.57 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
        0.39         0.66         0.69         1.12         0.76        12.46 
TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       55.76        47.08        26.43 

  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                          0.53                           0.39 
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                         38.96                         129.27 
  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE 
                         18.28                          17.03 
[1] "0.5 - 39.0 (18.3)"  "0.4 - 129.3 (17.0)"
[1] "hr=" "2"  
D50V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 26(16P13.3) MUTATED         1        0         7         0         1
  DEL PEAK 26(16P13.3) WILD-TYPE      29        8        33         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 26(16P13.3) MUTATED           0          0          0          2
  DEL PEAK 26(16P13.3) WILD-TYPE         5          9         24         12
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 26(16P13.3) MUTATED          2         0
  DEL PEAK 26(16P13.3) WILD-TYPE       16         9
D50V3, multiclass
            clus
vv           DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE
  STAGE I                               1                             29
  STAGE II                              0                              8
  STAGE IIA                             7                             33
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             0                              5
  STAGE IIIA                            0                              9
  STAGE IIIB                            0                             24
  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 26(16P13.3) MUTATED     0   3  10   0
  DEL PEAK 26(16P13.3) WILD-TYPE   9  26 102  14
D50V4, multiclass
    clus
vv   DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE
  T1                            0                              9
  T2                            3                             26
  T3                           10                            102
  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 26(16P13.3) MUTATED    8  1  4
  DEL PEAK 26(16P13.3) WILD-TYPE 77 44 29
D50V5, multiclass
    clus
vv   DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE
  N0                            8                             77
  N1                            1                             44
  N2                            4                             29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D50V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(16P13.3) MUTATED    11   2
  DEL PEAK 26(16P13.3) WILD-TYPE 115  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16P13.3) MUTATED     11    2
  DEL PEAK 26(16P13.3) WILD-TYPE  115   22
   clus
vv  DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE
  0                           11                            115
  1                            2                             22
[1] 2 2
[1] FALSE
D50V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(16P13.3) MUTATED    6  7
  DEL PEAK 26(16P13.3) WILD-TYPE 70 82
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16P13.3) MUTATED      6    7
  DEL PEAK 26(16P13.3) WILD-TYPE   70   82
        clus
vv       DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE
  FEMALE                            6                             70
  MALE                              7                             82
[1] 2 2
[1] FALSE
D50V8, binary
                                cls
clus                              0  1
  DEL PEAK 26(16P13.3) MUTATED    9  2
  DEL PEAK 26(16P13.3) WILD-TYPE 84 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16P13.3) MUTATED      9    2
  DEL PEAK 26(16P13.3) WILD-TYPE   84   17
     clus
vv    DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE
  NO                             9                             84
  YES                            2                             17
[1] 2 2
[1] FALSE
D50V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(16P13.3) MUTATED    10   2
  DEL PEAK 26(16P13.3) WILD-TYPE 136  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16P13.3) MUTATED     10    2
  DEL PEAK 26(16P13.3) WILD-TYPE  136   11
                                clus
vv                               DEL PEAK 26(16P13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    10
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 26(16P13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     136
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(16P13.3) MUTATED    10   0   1   0
  DEL PEAK 26(16P13.3) WILD-TYPE 113   2  11   4
D50V10, multiclass
    clus
vv   DEL PEAK 26(16P13.3) MUTATED DEL PEAK 26(16P13.3) WILD-TYPE
  R0                           10                            113
  R1                            0                              2
  R2                            1                             11
  RX                            0                              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"
D50V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(16P13.3) MUTATED       0                         0     5
  DEL PEAK 26(16P13.3) WILD-TYPE     1                         6    76
D50V12, multiclass
                           clus
vv                          DEL PEAK 26(16P13.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                5
                           clus
vv                          DEL PEAK 26(16P13.3) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              6
  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 27(16Q23.1) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 27(16Q23.1) MUTATED    20   3
  DEL PEAK 27(16Q23.1) WILD-TYPE 118  19
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                            23                            137 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                             3                             19 
$`DEL PEAK 27(16Q23.1) MUTATED`
TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 
       10.39        32.02        36.03        34.03         6.05        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-4005 
       20.98         7.99        32.98        19.04         1.02        14.04 
TCGA-AH-6544 TCGA-AH-6644 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6883 TCGA-EI-7002 
       38.56         0.72         4.01       129.27        11.51        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6814 TCGA-G5-6233 
        8.45         9.96        32.19         0.53        18.28 

$`DEL PEAK 27(16Q23.1) WILD-TYPE`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        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 
       34.49        37.74        10.39        14.50        16.83        15.39 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
        8.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 
       34.03        34.03         2.01        50.04        12.03         0.99 
TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        13.94        19.99         0.99        29.98        37.02 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99         0.99        19.99        17.95        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-4021 
       19.99        28.04        36.03         1.02        17.03         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       46.03        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-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 
        1.94        38.96        61.97        41.00        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 
        0.69        26.43         1.81        10.19         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 
        6.97         9.37         4.73        12.39        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        11.01        15.02         5.03         8.98        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       15.02        27.95        10.98        19.99         5.95         5.03 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
        5.29       126.44        41.36        57.24        24.13        51.48 
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-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6465 
       16.41         8.61        10.78        13.64        17.46        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
       31.30        28.57         0.39         0.66         0.69         1.12 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
        0.76        12.46        55.76        47.08        26.43 

  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                          0.53                           0.39 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE 
                         14.04                          17.03 
[1] "0.5 - 129.3 (14.0)" "0.4 - 126.4 (17.0)"
[1] "hr=" "1.3"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 27(16Q23.1) MUTATED         3        0         7         0         2
  DEL PEAK 27(16Q23.1) WILD-TYPE      27        8        33         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 27(16Q23.1) MUTATED           1          0          0          3
  DEL PEAK 27(16Q23.1) WILD-TYPE         4          9         24         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 27(16Q23.1) MUTATED          4         1
  DEL PEAK 27(16Q23.1) WILD-TYPE       14         8
D51V3, multiclass
            clus
vv           DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  STAGE I                               3                             27
  STAGE II                              0                              8
  STAGE IIA                             7                             33
  STAGE IIB                             0                              2
  STAGE IIC                             2                              0
  STAGE III                             1                              4
  STAGE IIIA                            0                              9
  STAGE IIIB                            0                             24
  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 27(16Q23.1) MUTATED    0  4 16  3
  DEL PEAK 27(16Q23.1) WILD-TYPE  9 25 96 11
D51V4, multiclass
    clus
vv   DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  T1                            0                              9
  T2                            4                             25
  T3                           16                             96
  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 27(16Q23.1) MUTATED   11  2  9
  DEL PEAK 27(16Q23.1) WILD-TYPE 74 43 24
D51V5, multiclass
    clus
vv   DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  N0                           11                             74
  N1                            2                             43
  N2                            9                             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"
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 27(16Q23.1) MUTATED    17   4
  DEL PEAK 27(16Q23.1) WILD-TYPE 109  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     17    4
  DEL PEAK 27(16Q23.1) WILD-TYPE  109   20
   clus
vv  DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  0                           17                            109
  1                            4                             20
[1] 2 2
[1] FALSE
D51V7, binary
                                cls
clus                              0  1
  DEL PEAK 27(16Q23.1) MUTATED   11 12
  DEL PEAK 27(16Q23.1) WILD-TYPE 65 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     11   12
  DEL PEAK 27(16Q23.1) WILD-TYPE   65   77
        clus
vv       DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  FEMALE                           11                             65
  MALE                             12                             77
[1] 2 2
[1] FALSE
D51V8, binary
                                cls
clus                              0  1
  DEL PEAK 27(16Q23.1) MUTATED   15  3
  DEL PEAK 27(16Q23.1) WILD-TYPE 78 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     15    3
  DEL PEAK 27(16Q23.1) WILD-TYPE   78   16
     clus
vv    DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  NO                            15                             78
  YES                            3                             16
[1] 2 2
[1] FALSE
D51V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(16Q23.1) MUTATED    20   2
  DEL PEAK 27(16Q23.1) WILD-TYPE 126  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(16Q23.1) MUTATED     20    2
  DEL PEAK 27(16Q23.1) WILD-TYPE  126   11
                                clus
vv                               DEL PEAK 27(16Q23.1) MUTATED
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 27(16Q23.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     126
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 27(16Q23.1) MUTATED    16   0   1   0
  DEL PEAK 27(16Q23.1) WILD-TYPE 107   2  11   4
D51V10, multiclass
    clus
vv   DEL PEAK 27(16Q23.1) MUTATED DEL PEAK 27(16Q23.1) WILD-TYPE
  R0                           16                            107
  R1                            0                              2
  R2                            1                             11
  RX                            0                              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"
D51V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(16Q23.1) MUTATED       0                         0    12
  DEL PEAK 27(16Q23.1) WILD-TYPE     1                         6    69
D51V12, multiclass
                           clus
vv                          DEL PEAK 27(16Q23.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               12
                           clus
vv                          DEL PEAK 27(16Q23.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              6
  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 28(17P11.2) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(17P11.2) MUTATED   95 14
  DEL PEAK 28(17P11.2) WILD-TYPE 43  8
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                           109                             51 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                            14                              8 
$`DEL PEAK 28(17P11.2) MUTATED`
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       39.48        17.23        43.04        13.55        19.10        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        14.50        15.39        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 
       11.84        12.00        32.02         7.07        36.03        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 
        1.02        46.03        34.03        34.03         2.01         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       15.95        19.99        13.94        20.98         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 
       37.02        32.98         0.99        19.04         1.02        17.95 
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-4021 
       28.04        36.03        14.04         1.02        17.03         3.98 
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-A01J TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A023 
        1.02        12.00        31.00        70.03        64.01        51.98 
TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
        1.94        41.00        38.56         0.69         0.72        26.43 
TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-4957 TCGA-CL-5918 
       10.19         6.05        33.17         6.97        12.39         7.17 
TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       11.01        13.97        15.02        10.98        19.99         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
        5.03         5.29       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 
       24.13        51.48         0.49         2.40        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       18.28        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        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
       28.57         0.39         0.69         0.53         0.76        12.46 
TCGA-G5-6235 
       55.76 

$`DEL PEAK 28(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        16.83        10.39        36.03         8.02 
TCGA-AG-3583 TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3612 
       20.05        34.03        50.04        12.03         6.05        19.99 
TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
       29.98         0.99        19.99        36.95        13.02        14.01 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 
       46.03        20.98        36.03         9.07        10.98        49.97 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 
       38.96        61.97        38.04         1.45         1.81         9.37 
TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        4.73        78.12        21.01        15.02         5.03         8.98 
TCGA-DC-6157 TCGA-DC-6681 TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 
       27.95         5.95        32.61        20.55        19.96        15.85 
TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 
        8.61        13.64        17.46        32.19         0.66         1.12 
TCGA-G5-6233 TCGA-G5-6572 TCGA-G5-6641 
       18.28        47.08        26.43 

  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                          0.39                           0.66 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                        129.27                          78.12 
  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE 
                         17.00                          18.28 
[1] "0.4 - 129.3 (17.0)" "0.7 - 78.1 (18.3)" 
[1] "hr=" "1.3"
D52V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 28(17P11.2) MUTATED        17        5        31         2         1
  DEL PEAK 28(17P11.2) WILD-TYPE      13        3         9         0         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 28(17P11.2) MUTATED           4          5         16         11
  DEL PEAK 28(17P11.2) WILD-TYPE         1          4          8          3
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 28(17P11.2) MUTATED         12         7
  DEL PEAK 28(17P11.2) WILD-TYPE        6         2
D52V3, multiclass
            clus
vv           DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  STAGE I                              17                             13
  STAGE II                              5                              3
  STAGE IIA                            31                              9
  STAGE IIB                             2                              0
  STAGE IIC                             1                              1
  STAGE III                             4                              1
  STAGE IIIA                            5                              4
  STAGE IIIB                           16                              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 28(17P11.2) MUTATED    2 20 79 12
  DEL PEAK 28(17P11.2) WILD-TYPE  7  9 33  2
D52V4, multiclass
    clus
vv   DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  T1                            2                              7
  T2                           20                              9
  T3                           79                             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 28(17P11.2) MUTATED   58 30 24
  DEL PEAK 28(17P11.2) WILD-TYPE 27 15  9
D52V5, multiclass
    clus
vv   DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  N0                           58                             27
  N1                           30                             15
  N2                           24                              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"
D52V6, binary
                                cls
clus                              0  1
  DEL PEAK 28(17P11.2) MUTATED   86 17
  DEL PEAK 28(17P11.2) WILD-TYPE 40  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED     86   17
  DEL PEAK 28(17P11.2) WILD-TYPE   40    7
   clus
vv  DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  0                           86                             40
  1                           17                              7
[1] 2 2
[1] FALSE
D52V7, binary
                                cls
clus                              0  1
  DEL PEAK 28(17P11.2) MUTATED   54 59
  DEL PEAK 28(17P11.2) WILD-TYPE 22 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED     54   59
  DEL PEAK 28(17P11.2) WILD-TYPE   22   30
        clus
vv       DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  FEMALE                           54                             22
  MALE                             59                             30
[1] 2 2
[1] FALSE
D52V8, binary
                                cls
clus                              0  1
  DEL PEAK 28(17P11.2) MUTATED   65 11
  DEL PEAK 28(17P11.2) WILD-TYPE 28  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED     65   11
  DEL PEAK 28(17P11.2) WILD-TYPE   28    8
     clus
vv    DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  NO                            65                             28
  YES                           11                              8
[1] 2 2
[1] FALSE
D52V9, binary
                                cls
clus                               0   1
  DEL PEAK 28(17P11.2) MUTATED   102   6
  DEL PEAK 28(17P11.2) WILD-TYPE  44   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(17P11.2) MUTATED    102    6
  DEL PEAK 28(17P11.2) WILD-TYPE   44    7
                                clus
vv                               DEL PEAK 28(17P11.2) MUTATED
  RECTAL ADENOCARCINOMA                                   102
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 28(17P11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      44
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 28(17P11.2) MUTATED   82  2  9  3
  DEL PEAK 28(17P11.2) WILD-TYPE 41  0  3  1
D52V10, multiclass
    clus
vv   DEL PEAK 28(17P11.2) MUTATED DEL PEAK 28(17P11.2) WILD-TYPE
  R0                           82                             41
  R1                            2                              0
  R2                            9                              3
  RX                            3                              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 28(17P11.2) MUTATED       1                         3    56
  DEL PEAK 28(17P11.2) WILD-TYPE     0                         3    25
D52V12, multiclass
                           clus
vv                          DEL PEAK 28(17P11.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               56
                           clus
vv                          DEL PEAK 28(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 29(18Q21.2) MUTATION ANALYSIS
D53V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(18Q21.2) MUTATED   121  19
  DEL PEAK 29(18Q21.2) WILD-TYPE  17   3
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                           140                             20 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                            19                              3 
$`DEL PEAK 29(18Q21.2) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        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 
       34.49        37.74        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       32.02         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 
       46.03        34.03        34.03        34.03         2.01        50.04 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 
        6.05         0.99        15.95        13.94        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
       19.04        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       35.01         1.02        48.03        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       36.03        14.04         1.02        17.03         3.98        46.03 
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 
       38.56         0.69         0.72        26.43        10.19         6.05 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 
       33.17         6.97         9.37         4.73        12.39        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        11.01        15.02         5.03         8.98 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        15.02        27.95        10.98        19.99         5.95 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        4.01         5.03         5.29       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        51.48         0.49         2.40        20.55 
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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.31        16.41        11.51        10.78        13.64        11.97 
TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45        49.51        31.30        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 
        0.66         0.69         0.76        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

$`DEL PEAK 29(18Q21.2) WILD-TYPE`
TCGA-AF-5654 TCGA-AG-3580 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 TCGA-AG-3892 
       16.83         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-AH-6903 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 
        1.81        32.61        19.96         8.61        17.46         9.96 
TCGA-F5-6814 TCGA-F5-6861 
        0.53         1.12 

  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                          0.39                           0.53 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                        129.27                          61.97 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                        17.460                         13.515 
[1] "0.4 - 129.3 (17.5)" "0.5 - 62.0 (13.5)" 
[1] "hr=" "1.5"
D53V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 29(18Q21.2) MUTATED        22        7        36         2         2
  DEL PEAK 29(18Q21.2) WILD-TYPE       8        1         4         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 29(18Q21.2) MUTATED           5          6         23         12
  DEL PEAK 29(18Q21.2) WILD-TYPE         0          3          1          2
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 29(18Q21.2) MUTATED         18         9
  DEL PEAK 29(18Q21.2) WILD-TYPE        0         0
D53V3, multiclass
            clus
vv           DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  STAGE I                              22                              8
  STAGE II                              7                              1
  STAGE IIA                            36                              4
  STAGE IIB                             2                              0
  STAGE IIC                             2                              0
  STAGE III                             5                              0
  STAGE IIIA                            6                              3
  STAGE IIIB                           23                              1
  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 29(18Q21.2) MUTATED     5  23 103  13
  DEL PEAK 29(18Q21.2) WILD-TYPE   4   6   9   1
D53V4, multiclass
    clus
vv   DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  T1                            5                              4
  T2                           23                              6
  T3                          103                              9
  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(18Q21.2) MUTATED   70 42 31
  DEL PEAK 29(18Q21.2) WILD-TYPE 15  3  2
D53V5, multiclass
    clus
vv   DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  N0                           70                             15
  N1                           42                              3
  N2                           31                              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"
D53V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q21.2) MUTATED   107  24
  DEL PEAK 29(18Q21.2) WILD-TYPE  19   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED    107   24
  DEL PEAK 29(18Q21.2) WILD-TYPE   19    0
   clus
vv  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  0                          107                             19
  1                           24                              0
[1] 2 2
[1] FALSE
D53V7, binary
                                cls
clus                              0  1
  DEL PEAK 29(18Q21.2) MUTATED   67 78
  DEL PEAK 29(18Q21.2) WILD-TYPE  9 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED     67   78
  DEL PEAK 29(18Q21.2) WILD-TYPE    9   11
        clus
vv       DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  FEMALE                           67                              9
  MALE                             78                             11
[1] 2 2
[1] FALSE
D53V8, binary
                                cls
clus                              0  1
  DEL PEAK 29(18Q21.2) MUTATED   82 18
  DEL PEAK 29(18Q21.2) WILD-TYPE 11  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED     82   18
  DEL PEAK 29(18Q21.2) WILD-TYPE   11    1
     clus
vv    DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  NO                            82                             11
  YES                           18                              1
[1] 2 2
[1] FALSE
D53V9, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q21.2) MUTATED   129  11
  DEL PEAK 29(18Q21.2) WILD-TYPE  17   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED    129   11
  DEL PEAK 29(18Q21.2) WILD-TYPE   17    2
                                clus
vv                               DEL PEAK 29(18Q21.2) MUTATED
  RECTAL ADENOCARCINOMA                                   129
  RECTAL MUCINOUS ADENOCARCINOMA                           11
                                clus
vv                               DEL PEAK 29(18Q21.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      17
  RECTAL MUCINOUS ADENOCARCINOMA                              2
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 29(18Q21.2) MUTATED   105   2  12   4
  DEL PEAK 29(18Q21.2) WILD-TYPE  18   0   0   0
D53V10, multiclass
    clus
vv   DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  R0                          105                             18
  R1                            2                              0
  R2                           12                              0
  RX                            4                              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 29(18Q21.2) MUTATED       1                         6    71
  DEL PEAK 29(18Q21.2) WILD-TYPE     0                         0    10
D53V12, multiclass
                           clus
vv                          DEL PEAK 29(18Q21.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               71
                           clus
vv                          DEL PEAK 29(18Q21.2) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              0
  WHITE                                                 10
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(54) Variable = DEL PEAK 30(18Q22.1) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(18Q22.1) MUTATED   118  19
  DEL PEAK 30(18Q22.1) WILD-TYPE  20   3
  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                           137                             23 
  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                            19                              3 
$`DEL PEAK 30(18Q22.1) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       24.13        39.48        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 
       34.49        37.74        10.39        14.50        15.39        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       10.39        86.63        65.98        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
       32.02         7.07        36.03        20.05        24.00        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 
       34.03        34.03        34.03         2.01        50.04         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 
        0.99        15.95        13.94        19.99        20.98         7.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 
        0.99        29.98        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 TCGA-AG-3893 TCGA-AG-3896 
        1.02        17.95        36.95        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-4007 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C 
        1.02        17.03         3.98        46.03        13.94         6.02 
TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01J 
       25.97        23.01        37.02        15.95         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-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
        1.94        38.96        41.00        38.04        38.56         0.69 
TCGA-AH-6644 TCGA-AH-6897 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        0.72        26.43        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
        9.37         4.73        12.39        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       11.01        15.02         5.03         8.98        13.97        15.02 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       27.95        10.98        19.99         5.95         4.01         5.03 
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        49.51        31.30 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       28.57         0.39        32.19         0.66         0.69         0.76 
TCGA-F5-6864 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 TCGA-G5-6641 
       12.46        18.28        55.76        47.08        26.43 

$`DEL PEAK 30(18Q22.1) WILD-TYPE`
TCGA-AF-5654 TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3731 
       16.83         8.02         1.02        12.03        19.99        37.02 
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 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                          0.39                           0.53 
  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                        129.27                          61.97 
  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                         17.69                          13.02 
[1] "0.4 - 129.3 (17.7)" "0.5 - 62.0 (13.0)" 
[1] "hr=" "1.3"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 30(18Q22.1) MUTATED        22        6        36         2         2
  DEL PEAK 30(18Q22.1) WILD-TYPE       8        2         4         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 30(18Q22.1) MUTATED           3          6         23         12
  DEL PEAK 30(18Q22.1) WILD-TYPE         2          3          1          2
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 30(18Q22.1) MUTATED         17         9
  DEL PEAK 30(18Q22.1) WILD-TYPE        1         0
D54V3, multiclass
            clus
vv           DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  STAGE I                              22                              8
  STAGE II                              6                              2
  STAGE IIA                            36                              4
  STAGE IIB                             2                              0
  STAGE IIC                             2                              0
  STAGE III                             3                              2
  STAGE IIIA                            6                              3
  STAGE IIIB                           23                              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 30(18Q22.1) MUTATED    5 23 99 13
  DEL PEAK 30(18Q22.1) WILD-TYPE  4  6 13  1
D54V4, multiclass
    clus
vv   DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  T1                            5                              4
  T2                           23                              6
  T3                           99                             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 30(18Q22.1) MUTATED   69 40 30
  DEL PEAK 30(18Q22.1) WILD-TYPE 16  5  3
D54V5, multiclass
    clus
vv   DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  N0                           69                             16
  N1                           40                              5
  N2                           30                              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"
D54V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(18Q22.1) MUTATED   105  23
  DEL PEAK 30(18Q22.1) WILD-TYPE  21   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q22.1) MUTATED    105   23
  DEL PEAK 30(18Q22.1) WILD-TYPE   21    1
   clus
vv  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  0                          105                             21
  1                           23                              1
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q22.1) MUTATED   66 75
  DEL PEAK 30(18Q22.1) WILD-TYPE 10 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q22.1) MUTATED     66   75
  DEL PEAK 30(18Q22.1) WILD-TYPE   10   14
        clus
vv       DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  FEMALE                           66                             10
  MALE                             75                             14
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q22.1) MUTATED   80 18
  DEL PEAK 30(18Q22.1) WILD-TYPE 13  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q22.1) MUTATED     80   18
  DEL PEAK 30(18Q22.1) WILD-TYPE   13    1
     clus
vv    DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  NO                            80                             13
  YES                           18                              1
[1] 2 2
[1] FALSE
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 30(18Q22.1) MUTATED   127  10
  DEL PEAK 30(18Q22.1) WILD-TYPE  19   3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q22.1) MUTATED    127   10
  DEL PEAK 30(18Q22.1) WILD-TYPE   19    3
                                clus
vv                               DEL PEAK 30(18Q22.1) MUTATED
  RECTAL ADENOCARCINOMA                                   127
  RECTAL MUCINOUS ADENOCARCINOMA                           10
                                clus
vv                               DEL PEAK 30(18Q22.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      19
  RECTAL MUCINOUS ADENOCARCINOMA                              3
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 30(18Q22.1) MUTATED   104   2  11   3
  DEL PEAK 30(18Q22.1) WILD-TYPE  19   0   1   1
D54V10, multiclass
    clus
vv   DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  R0                          104                             19
  R1                            2                              0
  R2                           11                              1
  RX                            3                              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 30(18Q22.1) MUTATED       0                         6    70
  DEL PEAK 30(18Q22.1) WILD-TYPE     1                         0    11
D54V12, multiclass
                           clus
vv                          DEL PEAK 30(18Q22.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            6
  WHITE                                               70
                           clus
vv                          DEL PEAK 30(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 31(19P13.3) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 31(19P13.3) MUTATED    29   6
  DEL PEAK 31(19P13.3) WILD-TYPE 109  16
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                            35                            125 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                             6                             16 
$`DEL PEAK 31(19P13.3) MUTATED`
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-4110 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3587 
       24.13        39.48        14.50        12.00        36.03        46.03 
TCGA-AG-3608 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3893 
       15.95        13.94        20.98        32.98        19.04        35.01 
TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A016 TCGA-AG-A01Y TCGA-CI-6619 TCGA-CI-6620 
       17.03        15.95         9.07        64.01         6.05        33.17 
TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 
        4.73        12.39        11.01         5.03        13.97        10.98 
TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6513 
        5.29       129.27        24.13        51.48        17.00        16.34 
TCGA-EI-6885 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-G5-6233 
       13.64        31.30        28.57         0.39        18.28 

$`DEL PEAK 31(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        34.49        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       10.39        16.83        15.39        20.02        10.39        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3581 
       65.98        11.84        36.03        32.02         8.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 
        2.01        50.04        12.03         6.05         0.99        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        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04         1.02         3.98        46.03 
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-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        38.56         1.45         0.69         0.72        26.43 
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        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       21.01        15.02         8.98        15.02        27.95        19.99 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
        5.95         4.01         5.03       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 
       49.51        32.19         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        12.46        55.76        47.08        26.43 

  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                          0.39                           0.49 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE 
                         17.00                          17.23 
[1] "0.4 - 129.3 (17.0)" "0.5 - 126.4 (17.2)"
[1] "hr=" "1.3"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 31(19P13.3) MUTATED         6        3         8         0         1
  DEL PEAK 31(19P13.3) WILD-TYPE      24        5        32         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 31(19P13.3) MUTATED           1          2          4          3
  DEL PEAK 31(19P13.3) WILD-TYPE         4          7         20         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 31(19P13.3) MUTATED          5         4
  DEL PEAK 31(19P13.3) WILD-TYPE       13         5
D55V3, multiclass
            clus
vv           DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  STAGE I                               6                             24
  STAGE II                              3                              5
  STAGE IIA                             8                             32
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             1                              4
  STAGE IIIA                            2                              7
  STAGE IIIB                            4                             20
  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 31(19P13.3) MUTATED    0  7 28  2
  DEL PEAK 31(19P13.3) WILD-TYPE  9 22 84 12
D55V4, multiclass
    clus
vv   DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  T1                            0                              9
  T2                            7                             22
  T3                           28                             84
  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 31(19P13.3) MUTATED   17 12  8
  DEL PEAK 31(19P13.3) WILD-TYPE 68 33 25
D55V5, multiclass
    clus
vv   DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  N0                           17                             68
  N1                           12                             33
  N2                            8                             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"
D55V6, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   28  8
  DEL PEAK 31(19P13.3) WILD-TYPE 98 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     28    8
  DEL PEAK 31(19P13.3) WILD-TYPE   98   16
   clus
vv  DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  0                           28                             98
  1                            8                             16
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   16 21
  DEL PEAK 31(19P13.3) WILD-TYPE 60 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     16   21
  DEL PEAK 31(19P13.3) WILD-TYPE   60   68
        clus
vv       DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  FEMALE                           16                             60
  MALE                             21                             68
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                              0  1
  DEL PEAK 31(19P13.3) MUTATED   24  2
  DEL PEAK 31(19P13.3) WILD-TYPE 69 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     24    2
  DEL PEAK 31(19P13.3) WILD-TYPE   69   17
     clus
vv    DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  NO                            24                             69
  YES                            2                             17
[1] 2 2
[1] FALSE
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 31(19P13.3) MUTATED    34   1
  DEL PEAK 31(19P13.3) WILD-TYPE 112  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 31(19P13.3) MUTATED     34    1
  DEL PEAK 31(19P13.3) WILD-TYPE  112   12
                                clus
vv                               DEL PEAK 31(19P13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    34
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 31(19P13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     112
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 31(19P13.3) MUTATED   25  0  3  1
  DEL PEAK 31(19P13.3) WILD-TYPE 98  2  9  3
D55V10, multiclass
    clus
vv   DEL PEAK 31(19P13.3) MUTATED DEL PEAK 31(19P13.3) WILD-TYPE
  R0                           25                             98
  R1                            0                              2
  R2                            3                              9
  RX                            1                              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"
D55V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 31(19P13.3) MUTATED       1                         1    19
  DEL PEAK 31(19P13.3) WILD-TYPE     0                         5    62
D55V12, multiclass
                           clus
vv                          DEL PEAK 31(19P13.3) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               19
                           clus
vv                          DEL PEAK 31(19P13.3) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              5
  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 32(20P12.1) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(20P12.1) MUTATED    35  12
  DEL PEAK 32(20P12.1) WILD-TYPE 103  10
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                            47                            113 
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                            12                             10 
$`DEL PEAK 32(20P12.1) MUTATED`
TCGA-AF-2689 TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       39.48        10.39        14.50        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3600 
       36.03        32.02         7.07        20.05        24.00         6.05 
TCGA-AG-3608 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3902 TCGA-AG-4022 TCGA-AG-A008 
       15.95         0.99         1.02        32.02        46.03        13.94 
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-DC-6154 TCGA-DC-6158 
       38.96         1.45         0.69         4.73         8.98        10.98 
TCGA-DC-6160 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       19.99         5.03        41.36        57.24        24.13        32.61 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        2.40        15.85        17.69        16.41        11.51        10.78 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6864 TCGA-G5-6641 
        8.45        31.30        28.57        12.46        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        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       37.74        16.83        15.39        20.02        10.39        12.00 
TCGA-AG-3580 TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
        8.02        36.03         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 
       34.03         2.01        50.04        12.03         0.99        19.99 
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       13.94        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 
       37.02        32.98         0.99        19.04        19.99        17.95 
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-4001 TCGA-AG-4005 TCGA-AG-4007 
       48.03        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A00Y 
       17.03         3.98        20.98         6.02        25.97        23.01 
TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A023 
       37.02        15.95        36.03         9.07        10.98        51.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6644 
       49.97        61.97        41.00        38.04        38.56         0.72 
TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       26.43         1.81        10.19         6.05        33.17         6.97 
TCGA-CI-6623 TCGA-CL-4957 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
        9.37        12.39        78.12         7.17        21.01        11.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 
       15.02         5.03        13.97        15.02        27.95         5.95 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 
        4.01         5.29       126.44       129.27        51.48         0.49 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 
       20.55        19.96        20.91        17.00        18.28        16.34 
TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 
       16.31         8.61        13.64        17.46        11.97         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       49.51         0.39        32.19         0.66         0.69         0.53 
TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6572 
        1.12         0.76        18.28        55.76        47.08 

  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                          0.69                           0.39 
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                         86.63                         129.27 
  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE 
                         15.95                          17.23 
[1] "0.7 - 86.6 (15.9)"  "0.4 - 129.3 (17.2)"
[1] "hr=" "2.5"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 32(20P12.1) MUTATED         7        5         9         0         1
  DEL PEAK 32(20P12.1) WILD-TYPE      23        3        31         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 32(20P12.1) MUTATED           0          4          7          5
  DEL PEAK 32(20P12.1) WILD-TYPE         5          5         17          9
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 32(20P12.1) MUTATED          6         4
  DEL PEAK 32(20P12.1) WILD-TYPE       12         5
D56V3, multiclass
            clus
vv           DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  STAGE I                               7                             23
  STAGE II                              5                              3
  STAGE IIA                             9                             31
  STAGE IIB                             0                              2
  STAGE IIC                             1                              1
  STAGE III                             0                              5
  STAGE IIIA                            4                              5
  STAGE IIIB                            7                             17
  STAGE IIIC                            5                              9
  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 32(20P12.1) MUTATED    2  9 33  5
  DEL PEAK 32(20P12.1) WILD-TYPE  7 20 79  9
D56V4, multiclass
    clus
vv   DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  T1                            2                              7
  T2                            9                             20
  T3                           33                             79
  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   24 13 12
  DEL PEAK 32(20P12.1) WILD-TYPE 61 32 21
D56V5, multiclass
    clus
vv   DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  N0                           24                             61
  N1                           13                             32
  N2                           12                             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"
D56V6, binary
                                cls
clus                              0  1
  DEL PEAK 32(20P12.1) MUTATED   38  8
  DEL PEAK 32(20P12.1) WILD-TYPE 88 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(20P12.1) MUTATED     38    8
  DEL PEAK 32(20P12.1) WILD-TYPE   88   16
   clus
vv  DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  0                           38                             88
  1                            8                             16
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                              0  1
  DEL PEAK 32(20P12.1) MUTATED   25 24
  DEL PEAK 32(20P12.1) WILD-TYPE 51 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(20P12.1) MUTATED     25   24
  DEL PEAK 32(20P12.1) WILD-TYPE   51   65
        clus
vv       DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  FEMALE                           25                             51
  MALE                             24                             65
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                              0  1
  DEL PEAK 32(20P12.1) MUTATED   25  4
  DEL PEAK 32(20P12.1) WILD-TYPE 68 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(20P12.1) MUTATED     25    4
  DEL PEAK 32(20P12.1) WILD-TYPE   68   15
     clus
vv    DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  NO                            25                             68
  YES                            4                             15
[1] 2 2
[1] FALSE
D56V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(20P12.1) MUTATED    43   5
  DEL PEAK 32(20P12.1) WILD-TYPE 103   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(20P12.1) MUTATED     43    5
  DEL PEAK 32(20P12.1) WILD-TYPE  103    8
                                clus
vv                               DEL PEAK 32(20P12.1) MUTATED
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 32(20P12.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     103
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 32(20P12.1) MUTATED   36  1  5  1
  DEL PEAK 32(20P12.1) WILD-TYPE 87  1  7  3
D56V10, multiclass
    clus
vv   DEL PEAK 32(20P12.1) MUTATED DEL PEAK 32(20P12.1) WILD-TYPE
  R0                           36                             87
  R1                            1                              1
  R2                            5                              7
  RX                            1                              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"
D56V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 32(20P12.1) MUTATED       0                         4    24
  DEL PEAK 32(20P12.1) WILD-TYPE     1                         2    57
D56V12, multiclass
                           clus
vv                          DEL PEAK 32(20P12.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            4
  WHITE                                               24
                           clus
vv                          DEL PEAK 32(20P12.1) 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(57) Variable = DEL PEAK 33(21Q11.2) MUTATION ANALYSIS
D57V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 33(21Q11.2) MUTATED   60 12
  DEL PEAK 33(21Q11.2) WILD-TYPE 78 10
  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                            72                             88 
  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        39.48        17.23        19.10        14.50        15.39 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       20.02        10.39        86.63        11.84        36.03        12.00 
TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 
        7.07        36.03        24.00        46.03        34.03        34.03 
TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3881 TCGA-AG-3882 
       12.03        19.99        20.98        29.98        19.04        19.99 
TCGA-AG-3890 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       17.03         1.02        48.03        19.99        36.03        14.04 
TCGA-AG-4008 TCGA-AG-A01L TCGA-AG-A01N TCGA-AG-A01W TCGA-AG-A01Y TCGA-AG-A020 
       17.03        12.00        31.00        70.03        64.01        10.98 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 
        1.94        38.96        61.97        41.00        38.56         0.69 
TCGA-CI-6624 TCGA-CL-4957 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        4.73        12.39        21.01        13.97        27.95        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 
        4.01         5.03       126.44        57.24        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 
        0.49         2.40        20.55        20.91        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 
       16.34        16.41        11.97         8.45        31.30         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 TCGA-G5-6233 TCGA-G5-6641 
       32.19         0.66         0.53         0.76        18.28        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        34.49        37.74        10.39        16.83 
TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3580 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 
       65.98        32.02         8.02        20.05         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3611 
        2.01        50.04         6.05         0.99        15.95        13.94 
TCGA-AG-3612 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       19.99         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
        0.99         1.02        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       14.01        32.02        28.04         1.02         3.98        46.03 
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-A014 TCGA-AG-A015 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A023 TCGA-AG-A025 
       15.95        36.03         9.07         1.02        51.98        49.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-BM-6198 
       38.04         1.45         0.72        26.43         1.81        10.19 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
        6.05        33.17         6.97         9.37        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
       11.01        15.02         5.03         8.98        15.02        19.99 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6507 
        5.95         5.29        41.36       129.27        24.13        19.96 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       17.00        18.28        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 
       13.64        17.46         9.96        49.51        28.57         0.69 
TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        1.12        12.46        55.76        47.08 

  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE 
                          0.39                           0.69 
  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 
                        19.070                         15.485 
[1] "0.4 - 126.4 (19.1)" "0.7 - 129.3 (15.5)"
[1] "hr=" "1.2"
D57V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 33(21Q11.2) MUTATED        11        6        17         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         12         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 33(21Q11.2) MUTATED          8         3
  DEL PEAK 33(21Q11.2) WILD-TYPE       10         6
D57V3, 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                            17                             23
  STAGE IIB                             1                              1
  STAGE IIC                             1                              1
  STAGE III                             3                              2
  STAGE IIIA                            6                              3
  STAGE IIIB                           12                             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
  DEL PEAK 33(21Q11.2) MUTATED    1 17 49  6
  DEL PEAK 33(21Q11.2) WILD-TYPE  8 12 63  8
D57V4, multiclass
    clus
vv   DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  T1                            1                              8
  T2                           17                             12
  T3                           49                             63
  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   36 24 13
  DEL PEAK 33(21Q11.2) WILD-TYPE 49 21 20
D57V5, multiclass
    clus
vv   DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  N0                           36                             49
  N1                           24                             21
  N2                           13                             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"
D57V6, binary
                                cls
clus                              0  1
  DEL PEAK 33(21Q11.2) MUTATED   58  9
  DEL PEAK 33(21Q11.2) WILD-TYPE 68 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(21Q11.2) MUTATED     58    9
  DEL PEAK 33(21Q11.2) WILD-TYPE   68   15
   clus
vv  DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  0                           58                             68
  1                            9                             15
[1] 2 2
[1] FALSE
D57V7, binary
                                cls
clus                              0  1
  DEL PEAK 33(21Q11.2) MUTATED   32 41
  DEL PEAK 33(21Q11.2) WILD-TYPE 44 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(21Q11.2) MUTATED     32   41
  DEL PEAK 33(21Q11.2) WILD-TYPE   44   48
        clus
vv       DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  FEMALE                           32                             44
  MALE                             41                             48
[1] 2 2
[1] FALSE
D57V8, binary
                                cls
clus                              0  1
  DEL PEAK 33(21Q11.2) MUTATED   41  8
  DEL PEAK 33(21Q11.2) WILD-TYPE 52 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(21Q11.2) MUTATED     41    8
  DEL PEAK 33(21Q11.2) WILD-TYPE   52   11
     clus
vv    DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  NO                            41                             52
  YES                            8                             11
[1] 2 2
[1] FALSE
D57V9, binary
                                cls
clus                              0  1
  DEL PEAK 33(21Q11.2) MUTATED   66  3
  DEL PEAK 33(21Q11.2) WILD-TYPE 80 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(21Q11.2) MUTATED     66    3
  DEL PEAK 33(21Q11.2) WILD-TYPE   80   10
                                clus
vv                               DEL PEAK 33(21Q11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 33(21Q11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      80
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 33(21Q11.2) MUTATED   55  1  4  0
  DEL PEAK 33(21Q11.2) WILD-TYPE 68  1  8  4
D57V10, multiclass
    clus
vv   DEL PEAK 33(21Q11.2) MUTATED DEL PEAK 33(21Q11.2) WILD-TYPE
  R0                           55                             68
  R1                            1                              1
  R2                            4                              8
  RX                            0                              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"
D57V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 33(21Q11.2) MUTATED       0                         3    39
  DEL PEAK 33(21Q11.2) WILD-TYPE     1                         3    42
D57V12, multiclass
                           clus
vv                          DEL PEAK 33(21Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               39
                           clus
vv                          DEL PEAK 33(21Q11.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              3
  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(58) Variable = DEL PEAK 34(22Q13.31) MUTATION ANALYSIS
D58V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 34(22Q13.31) MUTATED   53 11
  DEL PEAK 34(22Q13.31) WILD-TYPE 85 11
  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                             64                              96 
  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-AF-A56L 
       13.55        19.10        14.50        15.39        10.39        65.98 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       12.00        32.02         7.07        36.03        20.05        24.00 
TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3611 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 
       34.03        34.03        13.94        20.98        29.98        37.02 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 
       19.99         1.02        17.95         1.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A00H TCGA-AG-A00Y TCGA-AG-A01L 
       36.03        14.04         3.98        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        38.56         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        12.39        21.01        11.01 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 
        5.03        13.97        10.98        19.99         4.01         5.03 
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        28.57         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        39.48        17.23        43.04        34.49        37.74 
TCGA-AF-3913 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       10.39        16.83        20.02        86.63        11.84        36.03 
TCGA-AG-3580 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 
        8.02         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-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-3881 
        7.99         0.99        32.98         0.99         0.99        19.04 
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-4007 TCGA-AG-4008 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       32.02         1.02        17.03        46.03        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-A01W TCGA-AG-A01Y TCGA-AG-A023 TCGA-AG-A025 TCGA-AG-A02N 
       31.00        70.03        64.01        51.98        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       38.04         1.45         0.69        26.43         1.81        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
        6.97         9.37        78.12         7.17        15.02         8.98 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       15.02        27.95         5.95         5.29       126.44        57.24 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       24.13         0.49        19.96        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6811 
       17.46         8.45         9.96        49.51        31.30        32.19 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6235 TCGA-G5-6572 
        0.69         0.53         1.12        12.46        55.76        47.08 

  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE 
                           0.39                            0.49 
  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 
                         17.820                          17.015 
[1] "0.4 - 129.3 (17.8)" "0.5 - 126.4 (17.0)"
[1] "hr=" "2.1"
D58V2, 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        24         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         11
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 34(22Q13.31) MUTATED            3       10         3
  DEL PEAK 34(22Q13.31) WILD-TYPE         11        8         6
D58V3, 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                              24
  STAGE IIB                              0                               2
  STAGE IIC                              1                               1
  STAGE III                              3                               2
  STAGE IIIA                             5                               4
  STAGE IIIB                            13                              11
  STAGE IIIC                             3                              11
  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 49  5
  DEL PEAK 34(22Q13.31) WILD-TYPE  8 16 63  9
D58V4, multiclass
    clus
vv   DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  T1                             1                               8
  T2                            13                              16
  T3                            49                              63
  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 12
  DEL PEAK 34(22Q13.31) WILD-TYPE 57 18 21
D58V5, multiclass
    clus
vv   DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  N0                            28                              57
  N1                            27                              18
  N2                            12                              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"
D58V6, binary
                                 cls
clus                               0  1
  DEL PEAK 34(22Q13.31) MUTATED   48 12
  DEL PEAK 34(22Q13.31) WILD-TYPE 78 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.31) MUTATED     48   12
  DEL PEAK 34(22Q13.31) WILD-TYPE   78   12
   clus
vv  DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  0                            48                              78
  1                            12                              12
[1] 2 2
[1] FALSE
D58V7, binary
                                 cls
clus                               0  1
  DEL PEAK 34(22Q13.31) MUTATED   29 39
  DEL PEAK 34(22Q13.31) WILD-TYPE 47 50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.31) MUTATED     29   39
  DEL PEAK 34(22Q13.31) WILD-TYPE   47   50
        clus
vv       DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  FEMALE                            29                              47
  MALE                              39                              50
[1] 2 2
[1] FALSE
D58V8, binary
                                 cls
clus                               0  1
  DEL PEAK 34(22Q13.31) MUTATED   36  7
  DEL PEAK 34(22Q13.31) WILD-TYPE 57 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.31) MUTATED     36    7
  DEL PEAK 34(22Q13.31) WILD-TYPE   57   12
     clus
vv    DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  NO                             36                              57
  YES                             7                              12
[1] 2 2
[1] FALSE
D58V9, binary
                                 cls
clus                               0  1
  DEL PEAK 34(22Q13.31) MUTATED   61  4
  DEL PEAK 34(22Q13.31) WILD-TYPE 85  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 34(22Q13.31) MUTATED     61    4
  DEL PEAK 34(22Q13.31) WILD-TYPE   85    9
                                clus
vv                               DEL PEAK 34(22Q13.31) MUTATED
  RECTAL ADENOCARCINOMA                                     61
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               DEL PEAK 34(22Q13.31) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       85
  RECTAL MUCINOUS ADENOCARCINOMA                               9
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 34(22Q13.31) MUTATED   46  1  7  1
  DEL PEAK 34(22Q13.31) WILD-TYPE 77  1  5  3
D58V10, multiclass
    clus
vv   DEL PEAK 34(22Q13.31) MUTATED DEL PEAK 34(22Q13.31) WILD-TYPE
  R0                            46                              77
  R1                             1                               1
  R2                             7                               5
  RX                             1                               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 34(22Q13.31) MUTATED       0                         2    34
  DEL PEAK 34(22Q13.31) WILD-TYPE     1                         4    47
D58V12, multiclass
                           clus
vv                          DEL PEAK 34(22Q13.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             2
  WHITE                                                34
                           clus
vv                          DEL PEAK 34(22Q13.31) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               4
  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(59) Variable = DEL PEAK 35(XP22.33) MUTATION ANALYSIS
D59V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 35(XP22.33) MUTATED    28   4
  DEL PEAK 35(XP22.33) WILD-TYPE 110  18
  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                            32                            128 
  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-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 
       13.55        19.10        11.84        12.00        32.02        24.00 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3893 
       34.03         2.01         6.05        32.98        19.04        35.01 
TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00H TCGA-AG-A02G TCGA-AG-A02X 
        1.02        13.94         6.02        25.97        38.96        41.00 
TCGA-AH-6544 TCGA-BM-6198 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6155 
       38.56        10.19         9.37        78.12        21.01        13.97 
TCGA-DC-6156 TCGA-DC-6160 TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-7002 TCGA-F5-6465 
       15.02        19.99       129.27        32.61        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6810 
       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        39.48        17.23        43.04        34.49        37.74 
TCGA-AF-3913 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       10.39        14.50        16.83        15.39        20.02        10.39 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3580 TCGA-AG-3581 TCGA-AG-3582 
       86.63        65.98        36.03         8.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3598 
       20.05         1.02        46.03        34.03        34.03        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3611 TCGA-AG-3612 
       12.03         0.99        15.95        19.99        13.94        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 
       20.98         7.99         0.99        29.98        37.02         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3890 
        0.99        19.99         1.02        17.95        36.95        17.03 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       13.02        14.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4008 TCGA-AG-4021 TCGA-AG-4022 
       28.04        36.03        14.04        17.03         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A016 
       20.98        23.01        37.02        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-A02N TCGA-AG-A032 TCGA-AH-6547 
       51.98        49.97         1.94        61.97        38.04         1.45 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        0.69         0.72        26.43         1.81         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-4957 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
        6.97         4.73        12.39         7.17        11.01        15.02 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 
        5.03         8.98        27.95        10.98         5.95         4.01 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
        5.03         5.29       126.44        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       51.48         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-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
        8.45         9.96        28.57        32.19         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        12.46        18.28        55.76 
TCGA-G5-6572 TCGA-G5-6641 
       47.08        26.43 

  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE 
                          0.39                           0.49 
  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 
                        19.545                         16.915 
[1] "0.4 - 129.3 (19.5)" "0.5 - 126.4 (16.9)"
[1] "hr=" "1.2"
D59V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 35(XP22.33) MUTATED         6        1        12         0         0
  DEL PEAK 35(XP22.33) WILD-TYPE      24        7        28         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         20         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 35(XP22.33) MUTATED          4         1
  DEL PEAK 35(XP22.33) WILD-TYPE       14         8
D59V3, 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                            12                             28
  STAGE IIB                             0                              2
  STAGE IIC                             0                              2
  STAGE III                             0                              5
  STAGE IIIA                            2                              7
  STAGE IIIB                            4                             20
  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 23  2
  DEL PEAK 35(XP22.33) WILD-TYPE  8 21 89 12
D59V4, multiclass
    clus
vv   DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  T1                            1                              8
  T2                            8                             21
  T3                           23                             89
  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   19  8  7
  DEL PEAK 35(XP22.33) WILD-TYPE 66 37 26
D59V5, multiclass
    clus
vv   DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  N0                           19                             66
  N1                            8                             37
  N2                            7                             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"
D59V6, binary
                                cls
clus                               0   1
  DEL PEAK 35(XP22.33) MUTATED    25   6
  DEL PEAK 35(XP22.33) WILD-TYPE 101  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XP22.33) MUTATED     25    6
  DEL PEAK 35(XP22.33) WILD-TYPE  101   18
   clus
vv  DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  0                           25                            101
  1                            6                             18
[1] 2 2
[1] FALSE
D59V7, binary
                                cls
clus                              0  1
  DEL PEAK 35(XP22.33) MUTATED   17 17
  DEL PEAK 35(XP22.33) WILD-TYPE 59 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XP22.33) MUTATED     17   17
  DEL PEAK 35(XP22.33) WILD-TYPE   59   72
        clus
vv       DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  FEMALE                           17                             59
  MALE                             17                             72
[1] 2 2
[1] FALSE
D59V8, binary
                                cls
clus                              0  1
  DEL PEAK 35(XP22.33) MUTATED   19  6
  DEL PEAK 35(XP22.33) WILD-TYPE 74 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XP22.33) MUTATED     19    6
  DEL PEAK 35(XP22.33) WILD-TYPE   74   13
     clus
vv    DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  NO                            19                             74
  YES                            6                             13
[1] 2 2
[1] FALSE
D59V9, binary
                                cls
clus                               0   1
  DEL PEAK 35(XP22.33) MUTATED    28   3
  DEL PEAK 35(XP22.33) WILD-TYPE 118  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 35(XP22.33) MUTATED     28    3
  DEL PEAK 35(XP22.33) WILD-TYPE  118   10
                                clus
vv                               DEL PEAK 35(XP22.33) MUTATED
  RECTAL ADENOCARCINOMA                                    28
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 35(XP22.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     118
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 35(XP22.33) MUTATED   24  0  3  1
  DEL PEAK 35(XP22.33) WILD-TYPE 99  2  9  3
D59V10, multiclass
    clus
vv   DEL PEAK 35(XP22.33) MUTATED DEL PEAK 35(XP22.33) WILD-TYPE
  R0                           24                             99
  R1                            0                              2
  R2                            3                              9
  RX                            1                              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 35(XP22.33) MUTATED       0                         1    16
  DEL PEAK 35(XP22.33) WILD-TYPE     1                         5    65
D59V12, multiclass
                           clus
vv                          DEL PEAK 35(XP22.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               16
                           clus
vv                          DEL PEAK 35(XP22.33) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              5
  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"
