[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/22507018/READ-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/READ-TP/22532761/transformed.cor.cli.txt"

nPatients in clinical file=171, in cluster file=165, common to both=165
[1]  58 165
[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(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           49                           116 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           49                           116 
[1] "AMP PEAK  3(6P21.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                           54                           111 
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                           54                           111 
[1] "AMP PEAK  4(8P11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                            53                            112 
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                            53                            112 
[1] "AMP PEAK  5(8P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                            70                             95 
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                            70                             95 
[1] "AMP PEAK  6(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                           109                             56 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                           109                             56 
[1] "AMP PEAK  7(10Q22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE 
                            11                            154 
  AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE 
                            11                            154 
[1] "AMP PEAK  8(11P15.5) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE 
                            45                            120 
  AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE 
                            45                            120 
[1] "AMP PEAK  9(11Q13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE 
                            28                            137 
  AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE 
                            28                            137 
[1] "AMP PEAK 10(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                             41                             124 
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                             41                             124 
[1] "AMP PEAK 11(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                            40                            125 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                            40                            125 
[1] "AMP PEAK 12(13Q12.13) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            126                              39 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            126                              39 
[1] "AMP PEAK 13(13Q12.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                           125                             40 
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                           125                             40 
[1] "AMP PEAK 14(13Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                           120                             45 
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                           120                             45 
[1] "AMP PEAK 15(16P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE 
                            47                            118 
  AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE 
                            47                            118 
[1] "AMP PEAK 16(17Q12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                          46                          119 
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                          46                          119 
[1] "AMP PEAK 17(17Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                            39                            126 
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                            39                            126 
[1] "AMP PEAK 18(20Q11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE 
                            146                              19 
  AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE 
                            146                              19 
[1] "AMP PEAK 19(20Q11.23) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE 
                            147                              18 
  AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE 
                            147                              18 
[1] "AMP PEAK 20(20Q13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE 
                            146                              19 
  AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE 
                            146                              19 
[1] "AMP PEAK 21(XP22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE 
                           32                           133 
  AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE 
                           32                           133 
[1] "AMP PEAK 22(XQ27.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE 
                           37                           128 
  AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE 
                           37                           128 
[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(8Q11.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE 
                           17                           148 
  DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE 
                           17                           148 
[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(12Q13.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE 
                            20                            145 
  DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE 
                            20                            145 
[1] "DEL PEAK 21(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE 
                            70                             95 
  DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE 
                            70                             95 
[1] "DEL PEAK 22(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                            72                             93 
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                            72                             93 
[1] "DEL PEAK 23(15Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            79                             86 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            79                             86 
[1] "DEL PEAK 24(15Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             77                              88 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             77                              88 
[1] "DEL PEAK 25(16P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                            14                            151 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                            14                            151 
[1] "DEL PEAK 26(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            23                            142 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            23                            142 
[1] "DEL PEAK 27(17P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           113                             52 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           113                             52 
[1] "DEL PEAK 28(18P11.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE 
                            125                              40 
  DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE 
                            125                              40 
[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(18Q23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                         141                           24 
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                         141                           24 
[1] "DEL PEAK 32(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            36                            129 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            36                            129 
[1] "DEL PEAK 33(20P12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            49                            116 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            49                            116 
[1] "DEL PEAK 34(21Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                            73                             92 
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                            73                             92 
[1] "DEL PEAK 35(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                             68                              97 
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                             68                              97 
[1] "DEL PEAK 36(XP22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE 
                            34                            131 
  DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(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] "TUMOR_STAGE"                         
[16] "RESIDUAL_TUMOR"                      
[17] "NUMBER_OF_LYMPH_NODES"               
[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=26,	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=102,	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=8,	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:'TUMOR_STAGE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_STAGE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 16:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=18,	numeric=TRUE,	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 10 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"
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  28 112  14 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
  9  28 112  14 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
  9  28 112  14 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
  9  28 112  14 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
84 45 33 
[1] "table(vv)"
vv
N0 N1 N2 
84 45 33 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
84 45 33 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
84 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

Clustering(1) Variable = AMP PEAK  1(1Q21.3) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1Q21.3) MUTATED   36  9
  AMP PEAK  1(1Q21.3) WILD-TYPE 95 18
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                           45                           113 
  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                            9                            18 
$`AMP PEAK  1(1Q21.3) MUTATED`
TCGA-AG-3611 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 
       13.94        36.03        31.00        21.24        18.28        26.43 
TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 
       46.92        13.55        37.97        29.98        24.36        24.59 
TCGA-AG-3578 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3881 
       32.02        46.03        34.03        34.03        19.99        19.04 
TCGA-AG-3882 TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A026 TCGA-AG-A02G 
       19.99        28.04        23.01        37.02         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 
       38.04        43.20        27.55        13.78        47.44        48.20 
TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EI-6506 
       25.05        13.97        31.00       129.27        24.13        20.55 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6810 
        8.61        10.78        13.64        11.97         9.96         0.39 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
       19.66        11.87        47.08 

$`AMP PEAK  1(1Q21.3) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A023 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       15.95        51.98        55.76        39.48        17.23        43.04 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L 
       34.49        37.74        16.83        20.02        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03        12.00         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       24.00         1.02        34.03         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        9.07         1.02         1.02        49.97        61.97        41.00 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       38.56         2.50        26.43        19.46         6.05        33.17 
TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 
       44.78        78.12         7.17        21.01        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       12.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       25.05        12.62       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         3.48         4.18        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        42.35        28.57 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       32.19        36.49        37.18        38.14        12.46 

  AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE 
                         0.39                          0.99 
  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 
                        24.59                         20.02 
[1] "0.4 - 129.3 (24.6)" "1.0 - 126.4 (20.0)"
[1] "hr=" "1.3"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  1(1Q21.3) MUTATED         7        3        11         0         0
  AMP PEAK  1(1Q21.3) WILD-TYPE      23        5        29         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  1(1Q21.3) MUTATED           0          3          6          7
  AMP PEAK  1(1Q21.3) WILD-TYPE         4          4         19          7
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK  1(1Q21.3) MUTATED          5         2
  AMP PEAK  1(1Q21.3) WILD-TYPE       13         5
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                           11                            29
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            0                             4
  STAGE IIIA                           3                             4
  STAGE IIIB                           6                            19
  STAGE IIIC                           7                             7
  STAGE IV                             5                            13
  STAGE IVA                            2                             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
  AMP PEAK  1(1Q21.3) MUTATED    3  8 27  8
  AMP PEAK  1(1Q21.3) WILD-TYPE  6 20 85  6
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  T1                           3                             6
  T2                           8                            20
  T3                          27                            85
  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   22 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                          22                            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   33  5
  AMP PEAK  1(1Q21.3) WILD-TYPE 92 19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     33    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                          33                            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   31  7
  AMP PEAK  1(1Q21.3) WILD-TYPE 81 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q21.3) MUTATED     31    7
  AMP PEAK  1(1Q21.3) WILD-TYPE   81   13
     clus
vv    AMP PEAK  1(1Q21.3) MUTATED AMP PEAK  1(1Q21.3) WILD-TYPE
  NO                           31                            81
  YES                           7                            13
[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

Clustering(2) Variable = AMP PEAK  2(1Q32.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  2(1Q32.1) MUTATED   37 11
  AMP PEAK  2(1Q32.1) WILD-TYPE 94 16
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           48                           110 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           11                            16 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-AG-3611 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       13.94        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6641 TCGA-AF-2692 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 
       26.43        13.55        29.98        24.36        24.59        32.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3881 
       46.03        34.03        34.03         6.05         0.99        19.04 
TCGA-AG-3882 TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G 
       19.99        48.03        28.04        23.01         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6621 TCGA-CI-6623 
       38.04        38.56        43.20        27.55        13.78        47.44 
TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-6155 TCGA-DC-6156 TCGA-DY-A1DE TCGA-DY-A1DF 
       48.20        25.05        13.97        31.00       129.27        24.13 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       32.61        20.55         8.61        10.78        13.64        11.97 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6810 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
        8.45         9.96         0.39        19.66        11.87        47.08 

$`AMP PEAK  2(1Q32.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       15.95        55.76        46.92        39.48        17.23        43.04 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K 
       37.97        34.49        37.74        16.83        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        36.03        12.00         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-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
       12.03        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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
        3.98        46.03        20.98        13.94         6.02        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        9.07         1.02         1.02        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
        2.50        26.43        19.46         6.05        33.17        44.78 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        21.01        26.04        31.00        12.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EF-5830 
       12.62       126.44        41.36        57.24        51.48         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        4.18        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6917 
       17.69        16.34        16.31        16.41        11.51        17.46 
TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       49.51        42.35        28.57        32.19        36.49        37.18 
TCGA-F5-6861 TCGA-F5-6864 
       38.14        12.46 

  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         0.39                          0.99 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                       129.27                        126.44 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                       24.475                        20.035 
[1] "0.4 - 129.3 (24.5)" "1.0 - 126.4 (20.0)"
[1] "hr=" "1.6"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  2(1Q32.1) MUTATED         6        2        11         0         0
  AMP PEAK  2(1Q32.1) WILD-TYPE      24        6        29         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  2(1Q32.1) MUTATED           0          4          5          6
  AMP PEAK  2(1Q32.1) WILD-TYPE         4          3         20          8
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK  2(1Q32.1) MUTATED          7         2
  AMP PEAK  2(1Q32.1) WILD-TYPE       11         5
D2V3, multiclass
            clus
vv           AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  STAGE I                              6                            24
  STAGE II                             2                             6
  STAGE IIA                           11                            29
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            0                             4
  STAGE IIIA                           4                             3
  STAGE IIIB                           5                            20
  STAGE IIIC                           6                             8
  STAGE IV                             7                            11
  STAGE IVA                            2                             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
  AMP PEAK  2(1Q32.1) MUTATED    3  8 27  9
  AMP PEAK  2(1Q32.1) WILD-TYPE  6 20 85  5
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  T1                           3                             6
  T2                           8                            20
  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(1Q32.1) MUTATED   20 13 13
  AMP PEAK  2(1Q32.1) WILD-TYPE 64 32 20
D2V5, multiclass
    clus
vv   AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  N0                          20                            64
  N1                          13                            32
  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(1Q32.1) MUTATED   32  8
  AMP PEAK  2(1Q32.1) WILD-TYPE 93 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     32    8
  AMP PEAK  2(1Q32.1) WILD-TYPE   93   16
   clus
vv  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  0                          32                            93
  1                           8                            16
[1] 2 2
[1] FALSE
D2V7, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q32.1) MUTATED   23 26
  AMP PEAK  2(1Q32.1) WILD-TYPE 53 63
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     23   26
  AMP PEAK  2(1Q32.1) WILD-TYPE   53   63
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          23                            53
  MALE                            26                            63
[1] 2 2
[1] FALSE
D2V8, binary
                               cls
clus                             0  1
  AMP PEAK  2(1Q32.1) MUTATED   32  7
  AMP PEAK  2(1Q32.1) WILD-TYPE 80 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     32    7
  AMP PEAK  2(1Q32.1) WILD-TYPE   80   13
     clus
vv    AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  NO                           32                            80
  YES                           7                            13
[1] 2 2
[1] FALSE
D2V9, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    42   4
  AMP PEAK  2(1Q32.1) WILD-TYPE 104   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     42    4
  AMP PEAK  2(1Q32.1) WILD-TYPE  104    9
                                clus
vv                               AMP PEAK  2(1Q32.1) MUTATED
  RECTAL ADENOCARCINOMA                                   42
  RECTAL MUCINOUS ADENOCARCINOMA                           4
                                clus
vv                               AMP PEAK  2(1Q32.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    104
  RECTAL MUCINOUS ADENOCARCINOMA                             9
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  2(1Q32.1) MUTATED   32  1  4  0
  AMP PEAK  2(1Q32.1) WILD-TYPE 91  1  8  4
D2V10, multiclass
    clus
vv   AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  R0                          32                            91
  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"
D2V11, continuous

Clustering(3) Variable = AMP PEAK  3(6P21.1) MUTATION ANALYSIS
D3V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  3(6P21.1) MUTATED   42  8
  AMP PEAK  3(6P21.1) WILD-TYPE 89 19
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                           50                           108 
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                            8                            19 
$`AMP PEAK  3(6P21.1) MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A015 TCGA-AG-A01N TCGA-BM-6198 TCGA-G5-6233 
       10.39        19.99        36.03        31.00        21.24        18.28 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 
       26.43        46.92        43.04        37.97        37.74        29.98 
TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 
       24.36        65.98        36.03        24.00        46.03        34.03 
TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3883 
       34.03         6.05        19.99        20.98        29.98         1.02 
TCGA-AG-3896 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A016 
        1.02        14.04         1.02         3.98        46.03         9.07 
TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-DC-4745 TCGA-DC-5869 
       27.55         6.05        13.78        47.44        21.01        31.00 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6682 TCGA-DY-A1DE TCGA-DY-A1DF 
       12.00        31.00        51.98        25.05       129.27        24.13 
TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-6512 TCGA-F5-6465 TCGA-F5-6702 
       51.48        20.55        15.85        17.69        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6812 
        0.39        36.49 

$`AMP PEAK  3(6P21.1) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
        8.02        13.94        17.03        17.03        25.97        15.95 
TCGA-AG-A023 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3400 
       51.98        55.76        39.48        17.23        13.55        34.49 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       16.83        20.02        24.59        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3593 
       12.00        32.02         7.07        20.05         1.02        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3726 
        2.01        50.04        12.03         0.99        15.95         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-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       20.98        13.94         6.02        23.01        37.02         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X 
        1.02        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         2.50        43.20        26.43        19.46 
TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 
       33.17        44.78        48.20        78.12         7.17        25.05 
TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       26.04        13.97        10.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 
       12.62       126.44        41.36        57.24        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 
        4.18        19.96        20.91        17.00        18.28        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6811 
       17.46        11.97         8.45         9.96        42.35        32.19 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                         0.39                          0.99 
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                       129.27                        126.44 
  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE 
                       25.740                        19.975 
[1] "0.4 - 129.3 (25.7)" "1.0 - 126.4 (20.0)"
[1] "hr=" "1.2"
D3V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  3(6P21.1) MUTATED         8        1         8         0         0
  AMP PEAK  3(6P21.1) WILD-TYPE      22        7        32         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  3(6P21.1) MUTATED           1          1         11          7
  AMP PEAK  3(6P21.1) WILD-TYPE         3          6         14          7
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK  3(6P21.1) MUTATED          9         5
  AMP PEAK  3(6P21.1) WILD-TYPE        9         2
D3V3, multiclass
            clus
vv           AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  STAGE I                              8                            22
  STAGE II                             1                             7
  STAGE IIA                            8                            32
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            1                             3
  STAGE IIIA                           1                             6
  STAGE IIIB                          11                            14
  STAGE IIIC                           7                             7
  STAGE IV                             9                             9
  STAGE IVA                            5                             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  3(6P21.1) MUTATED    4  6 38  5
  AMP PEAK  3(6P21.1) WILD-TYPE  5 22 74  9
D3V4, multiclass
    clus
vv   AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  T1                           4                             5
  T2                           6                            22
  T3                          38                            74
  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  3(6P21.1) MUTATED   18 17 17
  AMP PEAK  3(6P21.1) WILD-TYPE 66 28 16
D3V5, multiclass
    clus
vv   AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  N0                          18                            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"
D3V6, binary
                               cls
clus                             0  1
  AMP PEAK  3(6P21.1) MUTATED   32 13
  AMP PEAK  3(6P21.1) WILD-TYPE 93 11
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED     32   13
  AMP PEAK  3(6P21.1) WILD-TYPE   93   11
   clus
vv  AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  0                          32                            93
  1                          13                            11
[1] 2 2
[1] FALSE
D3V7, binary
                               cls
clus                             0  1
  AMP PEAK  3(6P21.1) MUTATED   22 32
  AMP PEAK  3(6P21.1) WILD-TYPE 54 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED     22   32
  AMP PEAK  3(6P21.1) WILD-TYPE   54   57
        clus
vv       AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  FEMALE                          22                            54
  MALE                            32                            57
[1] 2 2
[1] FALSE
D3V8, binary
                               cls
clus                             0  1
  AMP PEAK  3(6P21.1) MUTATED   32  8
  AMP PEAK  3(6P21.1) WILD-TYPE 80 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED     32    8
  AMP PEAK  3(6P21.1) WILD-TYPE   80   12
     clus
vv    AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(6P21.1) WILD-TYPE
  NO                           32                            80
  YES                           8                            12
[1] 2 2
[1] FALSE
D3V9, binary
                               cls
clus                             0  1
  AMP PEAK  3(6P21.1) MUTATED   51  1
  AMP PEAK  3(6P21.1) WILD-TYPE 95 12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  3(6P21.1) MUTATED     51    1
  AMP PEAK  3(6P21.1) WILD-TYPE   95   12
                                clus
vv                               AMP PEAK  3(6P21.1) MUTATED
  RECTAL ADENOCARCINOMA                                   51
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK  3(6P21.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     95
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  3(6P21.1) MUTATED   36  0  7  1
  AMP PEAK  3(6P21.1) WILD-TYPE 87  2  5  3
D3V10, multiclass
    clus
vv   AMP PEAK  3(6P21.1) MUTATED AMP PEAK  3(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"
D3V11, continuous

Clustering(4) Variable = AMP PEAK  4(8P11.23) MUTATION ANALYSIS
D4V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  4(8P11.23) MUTATED   37 15
  AMP PEAK  4(8P11.23) WILD-TYPE 94 12
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                            52                            106 
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                            15                             12 
$`AMP PEAK  4(8P11.23) MUTATED`
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-AF-3911 TCGA-AF-6655 
       15.95        31.00        51.98        18.28        37.74        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3591 
       24.59        65.98        36.03        36.03        24.00        34.03 
TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 
       34.03         2.01         0.99        36.95        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A032 
       48.03        32.02        36.03         1.02        46.03        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 
       38.56        43.20        27.55         6.05        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       78.12         7.17        31.00        51.98        10.98        25.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6509 
       41.36        57.24        24.13        51.48         3.48        17.00 
TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-F5-6465 TCGA-F5-6702 
       15.85        16.31        11.51        10.78        49.51        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 
       32.19        19.66        12.46        47.08 

$`AMP PEAK  4(8P11.23) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       25.97        36.03        21.24        55.76        26.43        46.92 
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        37.97        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 
       29.98        16.83        24.36        86.63        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3593 
       32.02         7.07        20.05         1.02        46.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       50.04        12.03         6.05        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-3892 
        0.99        19.04        19.99         1.02        17.95        13.02 
TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 
       14.01        25.02        19.99        28.04        14.04         3.98 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        49.97         1.94        38.96        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 
       41.00         2.50        26.43        19.46        33.17        13.78 
TCGA-CI-6622 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       44.78        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       13.97        44.02        25.97        25.05        12.62       126.44 
TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      129.27        32.61         4.18        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        42.35         0.39 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       36.49        37.18        38.14        11.87 

  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                          0.99                           0.39 
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                         78.12                         129.27 
  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE 
                         31.51                          19.99 
[1] "1.0 - 78.1 (31.5)"  "0.4 - 129.3 (20.0)"
[1] "hr=" "1.7"
D4V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  4(8P11.23) MUTATED         6        2        13         1         1
  AMP PEAK  4(8P11.23) WILD-TYPE      24        6        27         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  4(8P11.23) MUTATED           0          2          6          7
  AMP PEAK  4(8P11.23) WILD-TYPE         4          5         19          7
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  4(8P11.23) MUTATED          8         3
  AMP PEAK  4(8P11.23) WILD-TYPE       10         4
D4V3, multiclass
            clus
vv           AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  STAGE I                               6                             24
  STAGE II                              2                              6
  STAGE IIA                            13                             27
  STAGE IIB                             1                              1
  STAGE IIC                             1                              0
  STAGE III                             0                              4
  STAGE IIIA                            2                              5
  STAGE IIIB                            6                             19
  STAGE IIIC                            7                              7
  STAGE IV                              8                             10
  STAGE IVA                             3                              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(8P11.23) MUTATED    1  7 37  7
  AMP PEAK  4(8P11.23) WILD-TYPE  8 21 75  7
D4V4, multiclass
    clus
vv   AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  T1                            1                              8
  T2                            7                             21
  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  4(8P11.23) MUTATED   24 13 14
  AMP PEAK  4(8P11.23) WILD-TYPE 60 32 19
D4V5, multiclass
    clus
vv   AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  N0                           24                             60
  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"
D4V6, binary
                                cls
clus                              0  1
  AMP PEAK  4(8P11.23) MUTATED   36 11
  AMP PEAK  4(8P11.23) WILD-TYPE 89 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED     36   11
  AMP PEAK  4(8P11.23) WILD-TYPE   89   13
   clus
vv  AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  0                           36                             89
  1                           11                             13
[1] 2 2
[1] FALSE
D4V7, binary
                                cls
clus                              0  1
  AMP PEAK  4(8P11.23) MUTATED   19 34
  AMP PEAK  4(8P11.23) WILD-TYPE 57 55
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED     19   34
  AMP PEAK  4(8P11.23) WILD-TYPE   57   55
        clus
vv       AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  FEMALE                           19                             57
  MALE                             34                             55
[1] 2 2
[1] FALSE
D4V8, binary
                                cls
clus                              0  1
  AMP PEAK  4(8P11.23) MUTATED   34  7
  AMP PEAK  4(8P11.23) WILD-TYPE 78 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED     34    7
  AMP PEAK  4(8P11.23) WILD-TYPE   78   13
     clus
vv    AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(8P11.23) WILD-TYPE
  NO                            34                             78
  YES                            7                             13
[1] 2 2
[1] FALSE
D4V9, binary
                                cls
clus                              0  1
  AMP PEAK  4(8P11.23) MUTATED   51  2
  AMP PEAK  4(8P11.23) WILD-TYPE 95 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  4(8P11.23) MUTATED     51    2
  AMP PEAK  4(8P11.23) WILD-TYPE   95   11
                                clus
vv                               AMP PEAK  4(8P11.23) MUTATED
  RECTAL ADENOCARCINOMA                                    51
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               AMP PEAK  4(8P11.23) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      95
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  4(8P11.23) MUTATED   30  0  7  3
  AMP PEAK  4(8P11.23) WILD-TYPE 93  2  5  1
D4V10, multiclass
    clus
vv   AMP PEAK  4(8P11.23) MUTATED AMP PEAK  4(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"
D4V11, continuous

Clustering(5) Variable = AMP PEAK  5(8P11.21) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  5(8P11.21) MUTATED   50 17
  AMP PEAK  5(8P11.21) WILD-TYPE 81 10
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                            67                             91 
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                            17                             10 
$`AMP PEAK  5(8P11.21) MUTATED`
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       15.95        31.00        51.98        18.28        55.76        26.43 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3582 TCGA-AG-3584 
       20.02        24.59        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-A016 
       28.04        14.04         1.02        46.03        23.01         9.07 
TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.02         1.94        38.96        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       43.20        27.55         6.05        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
        7.17        13.97        31.00        51.98        10.98        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       25.05       126.44        41.36        57.24       129.27        24.13 
TCGA-EF-5830 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 
        3.48        17.00        15.85        16.31        11.51        10.78 
TCGA-EI-6885 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6863 TCGA-F5-6864 
       13.64        49.51        28.57        32.19        11.87        12.46 
TCGA-G5-6572 
       47.08 

$`AMP PEAK  5(8P11.21) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-BM-6198 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       25.97        36.03        21.24        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       16.83        24.36        86.63        11.84        12.00        32.02 
TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
        7.07        20.05        46.03        34.03        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 
        6.05        15.95        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-3885 
       29.98        37.02         0.99         0.99        19.99        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-4001 
       13.02        35.01        14.01        25.02        19.99        36.03 
TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A020 
        3.98        20.98        13.94         6.02        37.02         1.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       49.97        61.97        41.00        26.43        19.46        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       13.78        44.78        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DG TCGA-DY-A1H8 
       12.00        44.02        25.97        12.62        51.48        32.61 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 
        4.18        20.55        19.96        20.91        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
       16.34        16.41         8.61        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
        9.96        42.35         0.39        36.49        19.66        37.18 
TCGA-F5-6861 
       38.14 

  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                          0.99                           0.39 
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                        129.27                          86.63 
  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE 
                         25.05                          19.99 
[1] "1.0 - 129.3 (25.1)" "0.4 - 86.6 (20.0)" 
[1] "hr=" "1.7"
D5V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  5(8P11.21) MUTATED         8        4        18         1         1
  AMP PEAK  5(8P11.21) WILD-TYPE      22        4        22         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  5(8P11.21) MUTATED           1          4          8          6
  AMP PEAK  5(8P11.21) WILD-TYPE         3          3         17          8
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  5(8P11.21) MUTATED         12         2
  AMP PEAK  5(8P11.21) WILD-TYPE        6         5
D5V3, multiclass
            clus
vv           AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  STAGE I                               8                             22
  STAGE II                              4                              4
  STAGE IIA                            18                             22
  STAGE IIB                             1                              1
  STAGE IIC                             1                              0
  STAGE III                             1                              3
  STAGE IIIA                            4                              3
  STAGE IIIB                            8                             17
  STAGE IIIC                            6                              8
  STAGE IV                             12                              6
  STAGE IVA                             2                              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
  AMP PEAK  5(8P11.21) MUTATED    2 11 48  8
  AMP PEAK  5(8P11.21) WILD-TYPE  7 17 64  6
D5V4, multiclass
    clus
vv   AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  T1                            2                              7
  T2                           11                             17
  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  5(8P11.21) MUTATED   34 18 16
  AMP PEAK  5(8P11.21) WILD-TYPE 50 27 17
D5V5, multiclass
    clus
vv   AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  N0                           34                             50
  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"
D5V6, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.21) MUTATED   48 14
  AMP PEAK  5(8P11.21) WILD-TYPE 77 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED     48   14
  AMP PEAK  5(8P11.21) WILD-TYPE   77   10
   clus
vv  AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  0                           48                             77
  1                           14                             10
[1] 2 2
[1] FALSE
D5V7, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.21) MUTATED   31 39
  AMP PEAK  5(8P11.21) WILD-TYPE 45 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED     31   39
  AMP PEAK  5(8P11.21) WILD-TYPE   45   50
        clus
vv       AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  FEMALE                           31                             45
  MALE                             39                             50
[1] 2 2
[1] FALSE
D5V8, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.21) MUTATED   45  6
  AMP PEAK  5(8P11.21) WILD-TYPE 67 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED     45    6
  AMP PEAK  5(8P11.21) WILD-TYPE   67   14
     clus
vv    AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(8P11.21) WILD-TYPE
  NO                            45                             67
  YES                            6                             14
[1] 2 2
[1] FALSE
D5V9, binary
                                cls
clus                              0  1
  AMP PEAK  5(8P11.21) MUTATED   65  3
  AMP PEAK  5(8P11.21) WILD-TYPE 81 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8P11.21) MUTATED     65    3
  AMP PEAK  5(8P11.21) WILD-TYPE   81   10
                                clus
vv                               AMP PEAK  5(8P11.21) MUTATED
  RECTAL ADENOCARCINOMA                                    65
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               AMP PEAK  5(8P11.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      81
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  5(8P11.21) MUTATED   41  2  9  3
  AMP PEAK  5(8P11.21) WILD-TYPE 82  0  3  1
D5V10, multiclass
    clus
vv   AMP PEAK  5(8P11.21) MUTATED AMP PEAK  5(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"
D5V11, continuous

Clustering(6) Variable = AMP PEAK  6(8Q24.21) MUTATION ANALYSIS
D6V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  6(8Q24.21) MUTATED   82 23
  AMP PEAK  6(8Q24.21) WILD-TYPE 49  4
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                           105                             53 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                            23                              4 
$`AMP PEAK  6(8Q24.21) MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       10.39        19.99        17.03        17.03        25.97        15.95 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       31.00        51.98        21.24        18.28        55.76        26.43 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       46.92        39.48        17.23        43.04        13.55        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       37.74        16.83        20.02        24.59        86.63        65.98 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       36.03        32.02        36.03        24.00         1.02        46.03 
TCGA-AG-3591 TCGA-AG-3592 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-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
        1.02        36.95         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-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02N 
       23.01        37.02         9.07         1.02         1.94        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         2.50        43.20        27.55 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
        6.05        13.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       21.01        25.05        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       51.98        10.98        25.05        25.05       126.44        41.36 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6509 
       57.24        24.13        32.61         3.48         4.18        17.00 
TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       15.85        16.34        16.31        11.51        10.78        13.64 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6814 
        9.96        49.51        28.57         0.39        32.19        37.18 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

$`AMP PEAK  6(8Q24.21) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-A015 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 
        8.02        13.94        36.03        37.97        29.98        24.36 
TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3593 TCGA-AG-3599 
       11.84        12.00         7.07        20.05        34.03        12.03 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 
       15.95        19.99        20.98        29.98         0.99        19.99 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-A002 
       17.95        13.02        35.01        14.01        25.02        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AH-6897 
       13.94         6.02         1.02        49.97        38.96        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-DC-5337 TCGA-DC-6160 TCGA-DC-6681 
       19.46        33.17        44.78        26.04        44.02        25.97 
TCGA-DT-5265 TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
       12.62       129.27        51.48        20.55        19.96        20.91 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7002 
       18.28        17.69        16.41         8.61        17.46        11.97 
TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 
        8.45        42.35        36.49        19.66        38.14 

  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                          0.39                           0.99 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                        126.44                         129.27 
  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE 
                         24.59                          19.99 
[1] "0.4 - 126.4 (24.6)" "1.0 - 129.3 (20.0)"
[1] "hr=" "2.3"
D6V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  6(8Q24.21) MUTATED        16        6        28         1         1
  AMP PEAK  6(8Q24.21) WILD-TYPE      14        2        12         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  6(8Q24.21) MUTATED           2          5         15         11
  AMP PEAK  6(8Q24.21) WILD-TYPE         2          2         10          3
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  6(8Q24.21) MUTATED         15         3
  AMP PEAK  6(8Q24.21) WILD-TYPE        3         4
D6V3, multiclass
            clus
vv           AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  STAGE I                              16                             14
  STAGE II                              6                              2
  STAGE IIA                            28                             12
  STAGE IIB                             1                              1
  STAGE IIC                             1                              0
  STAGE III                             2                              2
  STAGE IIIA                            5                              2
  STAGE IIIB                           15                             10
  STAGE IIIC                           11                              3
  STAGE IV                             15                              3
  STAGE IVA                             3                              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  6(8Q24.21) MUTATED    4 17 76 10
  AMP PEAK  6(8Q24.21) WILD-TYPE  5 11 36  4
D6V4, multiclass
    clus
vv   AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  T1                            4                              5
  T2                           17                             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  6(8Q24.21) MUTATED   54 28 24
  AMP PEAK  6(8Q24.21) WILD-TYPE 30 17  9
D6V5, multiclass
    clus
vv   AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  N0                           54                             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"
D6V6, binary
                                cls
clus                              0  1
  AMP PEAK  6(8Q24.21) MUTATED   79 18
  AMP PEAK  6(8Q24.21) WILD-TYPE 46  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED     79   18
  AMP PEAK  6(8Q24.21) WILD-TYPE   46    6
   clus
vv  AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  0                           79                             46
  1                           18                              6
[1] 2 2
[1] FALSE
D6V7, binary
                                cls
clus                              0  1
  AMP PEAK  6(8Q24.21) MUTATED   49 60
  AMP PEAK  6(8Q24.21) WILD-TYPE 27 29
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED     49   60
  AMP PEAK  6(8Q24.21) WILD-TYPE   27   29
        clus
vv       AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  FEMALE                           49                             27
  MALE                             60                             29
[1] 2 2
[1] FALSE
D6V8, binary
                                cls
clus                              0  1
  AMP PEAK  6(8Q24.21) MUTATED   71 12
  AMP PEAK  6(8Q24.21) WILD-TYPE 41  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED     71   12
  AMP PEAK  6(8Q24.21) WILD-TYPE   41    8
     clus
vv    AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(8Q24.21) WILD-TYPE
  NO                            71                             41
  YES                           12                              8
[1] 2 2
[1] FALSE
D6V9, binary
                                cls
clus                               0   1
  AMP PEAK  6(8Q24.21) MUTATED   101   5
  AMP PEAK  6(8Q24.21) WILD-TYPE  45   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  6(8Q24.21) MUTATED    101    5
  AMP PEAK  6(8Q24.21) WILD-TYPE   45    8
                                clus
vv                               AMP PEAK  6(8Q24.21) MUTATED
  RECTAL ADENOCARCINOMA                                   101
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK  6(8Q24.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      45
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  6(8Q24.21) MUTATED   77  2 10  3
  AMP PEAK  6(8Q24.21) WILD-TYPE 46  0  2  1
D6V10, multiclass
    clus
vv   AMP PEAK  6(8Q24.21) MUTATED AMP PEAK  6(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"
D6V11, continuous

Clustering(7) Variable = AMP PEAK  7(10Q22.2) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(10Q22.2) MUTATED     9   1
  AMP PEAK  7(10Q22.2) WILD-TYPE 122  26
  AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE 
                            10                            148 
  AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE 
                             1                             26 
$`AMP PEAK  7(10Q22.2) MUTATED`
TCGA-AG-A014 TCGA-BM-6198 TCGA-AF-2689 TCGA-AG-3587 TCGA-AG-3598 TCGA-AG-3881 
       15.95        21.24        39.48        46.03        50.04        19.04 
TCGA-AG-3999 TCGA-AG-A020 TCGA-CI-6619 TCGA-DC-4745 
       28.04         1.02         6.05        21.01 

$`AMP PEAK  7(10Q22.2) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       25.97        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       26.43        46.92        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        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-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03        34.03         2.01        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 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-3892 TCGA-AG-3893 TCGA-AG-3894 
        1.02        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 
        1.02        48.03        25.02        32.02        19.99        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       14.04         1.02         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 
        6.02        23.01        37.02         9.07         1.02        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-6897 TCGA-AH-6903 TCGA-CI-6620 
        2.50        43.20        27.55        26.43        19.46        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       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         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE 
                          1.02                           0.39 
  AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE 
                         50.04                         129.27 
  AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE 
                        21.125                         20.980 
[1] "1.0 - 50.0 (21.1)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.7"
D7V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  7(10Q22.2) MUTATED         2        1         2         0         0
  AMP PEAK  7(10Q22.2) WILD-TYPE      28        7        38         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  7(10Q22.2) MUTATED           1          0          2          1
  AMP PEAK  7(10Q22.2) WILD-TYPE         3          7         23         13
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  7(10Q22.2) MUTATED          2         0
  AMP PEAK  7(10Q22.2) WILD-TYPE       16         7
D7V3, multiclass
            clus
vv           AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE
  STAGE I                               2                             28
  STAGE II                              1                              7
  STAGE IIA                             2                             38
  STAGE IIB                             0                              2
  STAGE IIC                             0                              1
  STAGE III                             1                              3
  STAGE IIIA                            0                              7
  STAGE IIIB                            2                             23
  STAGE IIIC                            1                             13
  STAGE IV                              2                             16
  STAGE IVA                             0                              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  7(10Q22.2) MUTATED     0   2   9   0
  AMP PEAK  7(10Q22.2) WILD-TYPE   9  26 103  14
D7V4, multiclass
    clus
vv   AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE
  T1                            0                              9
  T2                            2                             26
  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  7(10Q22.2) MUTATED    5  4  2
  AMP PEAK  7(10Q22.2) WILD-TYPE 79 41 31
D7V5, multiclass
    clus
vv   AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE
  N0                            5                             79
  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"
D7V6, binary
                                cls
clus                               0   1
  AMP PEAK  7(10Q22.2) MUTATED     8   2
  AMP PEAK  7(10Q22.2) WILD-TYPE 117  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(10Q22.2) MUTATED      8    2
  AMP PEAK  7(10Q22.2) WILD-TYPE  117   22
   clus
vv  AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE
  0                            8                            117
  1                            2                             22
[1] 2 2
[1] FALSE
D7V7, binary
                                cls
clus                              0  1
  AMP PEAK  7(10Q22.2) MUTATED    6  5
  AMP PEAK  7(10Q22.2) WILD-TYPE 70 84
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(10Q22.2) MUTATED      6    5
  AMP PEAK  7(10Q22.2) WILD-TYPE   70   84
        clus
vv       AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE
  FEMALE                            6                             70
  MALE                              5                             84
[1] 2 2
[1] FALSE
D7V8, binary
                                cls
clus                               0   1
  AMP PEAK  7(10Q22.2) MUTATED     6   1
  AMP PEAK  7(10Q22.2) WILD-TYPE 106  19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(10Q22.2) MUTATED      6    1
  AMP PEAK  7(10Q22.2) WILD-TYPE  106   19
     clus
vv    AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(10Q22.2) WILD-TYPE
  NO                             6                            106
  YES                            1                             19
[1] 2 2
[1] FALSE
D7V9, binary
                                cls
clus                               0   1
  AMP PEAK  7(10Q22.2) MUTATED     9   1
  AMP PEAK  7(10Q22.2) WILD-TYPE 137  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(10Q22.2) MUTATED      9    1
  AMP PEAK  7(10Q22.2) WILD-TYPE  137   12
                                clus
vv                               AMP PEAK  7(10Q22.2) MUTATED
  RECTAL ADENOCARCINOMA                                     9
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK  7(10Q22.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     137
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  7(10Q22.2) MUTATED     9   0   0   0
  AMP PEAK  7(10Q22.2) WILD-TYPE 114   2  12   4
D7V10, multiclass
    clus
vv   AMP PEAK  7(10Q22.2) MUTATED AMP PEAK  7(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"
D7V11, continuous

Clustering(8) Variable = AMP PEAK  8(11P15.5) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  8(11P15.5) MUTATED   37  7
  AMP PEAK  8(11P15.5) WILD-TYPE 94 20
  AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE 
                            44                            114 
  AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE 
                             7                             20 
$`AMP PEAK  8(11P15.5) MUTATED`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A01N 
       10.39         8.02        13.94        19.99        25.97        31.00 
TCGA-BM-6198 TCGA-G5-6233 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-5654 
       21.24        18.28        39.48        17.23        13.55        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3583 
       20.02        24.59        65.98        36.03        12.00        20.05 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3609 TCGA-AG-3727 
       46.03        34.03        34.03        34.03        19.99         0.99 
TCGA-AG-3894 TCGA-AG-4001 TCGA-AG-4007 TCGA-AH-6897 TCGA-CI-6621 TCGA-CI-6623 
       14.01        36.03         1.02        26.43        13.78        47.44 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6160 
       25.05        26.04        31.00        12.00        51.98        44.02 
TCGA-DY-A0XA TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6514 TCGA-F5-6810 
      126.44         3.48         4.18        20.55        16.31         0.39 
TCGA-F5-6811 TCGA-F5-6861 
       32.19        38.14 

$`AMP PEAK  8(11P15.5) WILD-TYPE`
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6235 
       17.03        17.03        15.95        36.03        51.98        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       26.43        46.92        43.04        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3581 
       29.98        24.36        86.63        11.84        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       36.03        24.00         1.02         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 
        6.05         0.99        15.95        20.98         7.99        29.98 
TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3896 
        1.02        17.95        36.95        13.02        35.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       48.03        25.02        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-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        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         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       43.20        27.55        19.46         6.05        33.17        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6156 
       48.20        78.12         7.17        21.01        13.97        31.00 
TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC 
       10.98        25.97        25.05        25.05        12.62        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        42.35        28.57 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        37.18        11.87        12.46        47.08 

  AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE 
                          0.39                           0.99 
  AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE 
                        126.44                         129.27 
  AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE 
                        20.895                         20.995 
[1] "0.4 - 126.4 (20.9)" "1.0 - 129.3 (21.0)"
[1] "hr=" "1.1"
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  8(11P15.5) MUTATED         9        2        14         1         0
  AMP PEAK  8(11P15.5) WILD-TYPE      21        6        26         1         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  8(11P15.5) MUTATED           1          1          4          3
  AMP PEAK  8(11P15.5) WILD-TYPE         3          6         21         11
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  8(11P15.5) MUTATED          6         1
  AMP PEAK  8(11P15.5) WILD-TYPE       12         6
D8V3, multiclass
            clus
vv           AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE
  STAGE I                               9                             21
  STAGE II                              2                              6
  STAGE IIA                            14                             26
  STAGE IIB                             1                              1
  STAGE IIC                             0                              1
  STAGE III                             1                              3
  STAGE IIIA                            1                              6
  STAGE IIIB                            4                             21
  STAGE IIIC                            3                             11
  STAGE IV                              6                             12
  STAGE IVA                             1                              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  8(11P15.5) MUTATED    3  8 29  4
  AMP PEAK  8(11P15.5) WILD-TYPE  6 20 83 10
D8V4, multiclass
    clus
vv   AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE
  T1                            3                              6
  T2                            8                             20
  T3                           29                             83
  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  8(11P15.5) MUTATED   27  8  9
  AMP PEAK  8(11P15.5) WILD-TYPE 57 37 24
D8V5, multiclass
    clus
vv   AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE
  N0                           27                             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"
D8V6, binary
                                cls
clus                              0  1
  AMP PEAK  8(11P15.5) MUTATED   35  6
  AMP PEAK  8(11P15.5) WILD-TYPE 90 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11P15.5) MUTATED     35    6
  AMP PEAK  8(11P15.5) WILD-TYPE   90   18
   clus
vv  AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE
  0                           35                             90
  1                            6                             18
[1] 2 2
[1] FALSE
D8V7, binary
                                cls
clus                              0  1
  AMP PEAK  8(11P15.5) MUTATED   21 24
  AMP PEAK  8(11P15.5) WILD-TYPE 55 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11P15.5) MUTATED     21   24
  AMP PEAK  8(11P15.5) WILD-TYPE   55   65
        clus
vv       AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE
  FEMALE                           21                             55
  MALE                             24                             65
[1] 2 2
[1] FALSE
D8V8, binary
                                cls
clus                              0  1
  AMP PEAK  8(11P15.5) MUTATED   33  6
  AMP PEAK  8(11P15.5) WILD-TYPE 79 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11P15.5) MUTATED     33    6
  AMP PEAK  8(11P15.5) WILD-TYPE   79   14
     clus
vv    AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(11P15.5) WILD-TYPE
  NO                            33                             79
  YES                            6                             14
[1] 2 2
[1] FALSE
D8V9, binary
                                cls
clus                               0   1
  AMP PEAK  8(11P15.5) MUTATED    43   1
  AMP PEAK  8(11P15.5) WILD-TYPE 103  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  8(11P15.5) MUTATED     43    1
  AMP PEAK  8(11P15.5) WILD-TYPE  103   12
                                clus
vv                               AMP PEAK  8(11P15.5) MUTATED
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK  8(11P15.5) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     103
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  8(11P15.5) MUTATED   35  0  3  1
  AMP PEAK  8(11P15.5) WILD-TYPE 88  2  9  3
D8V10, multiclass
    clus
vv   AMP PEAK  8(11P15.5) MUTATED AMP PEAK  8(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"
D8V11, continuous

Clustering(9) Variable = AMP PEAK  9(11Q13.3) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  9(11Q13.3) MUTATED    24   3
  AMP PEAK  9(11Q13.3) WILD-TYPE 107  24
  AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE 
                            27                            131 
  AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE 
                             3                             24 
$`AMP PEAK  9(11Q13.3) MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A01N TCGA-AF-2690 TCGA-AF-A56L 
       10.39        19.99        25.97        31.00        17.23        65.98 
TCGA-AG-3575 TCGA-AG-3592 TCGA-AG-3883 TCGA-AG-4001 TCGA-AG-4007 TCGA-AH-6897 
       12.00        34.03         1.02        36.03         1.02        26.43 
TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       13.78        47.44        48.20        25.05        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE TCGA-EI-6514 
       31.00        51.98        10.98        12.62       129.27        16.31 
TCGA-EI-6885 TCGA-F5-6810 TCGA-F5-6811 
       13.64         0.39        32.19 

$`AMP PEAK  9(11Q13.3) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
        8.02        13.94        17.03        17.03        15.95        36.03 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       51.98        21.24        18.28        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       39.48        43.04        13.55        37.97        34.49        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       11.84        36.03        32.02         7.07        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        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-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 
        0.99         0.99        19.04        19.99        17.95        36.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       13.02        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 
       32.02        19.99        28.04        14.04         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       20.98        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N 
        1.02         1.02        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         2.50        43.20        27.55 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-CL-5918 
       19.46         6.05        33.17        44.78        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 
       21.01        26.04        13.97        44.02        25.97        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05       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         3.48         4.18        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6881 
       17.00        18.28        15.85        17.69        16.34        16.41 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 
        8.61        11.51        10.78        17.46        11.97         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6812 TCGA-F5-6813 
        9.96        49.51        42.35        28.57        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE 
                          0.39                           0.99 
  AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE 
                        129.27                         126.44 
  AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE 
                         25.05                          20.98 
[1] "0.4 - 129.3 (25.1)" "1.0 - 126.4 (21.0)"
[1] "hr=" "1.8"
D9V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK  9(11Q13.3) MUTATED         7        3         6         0         0
  AMP PEAK  9(11Q13.3) WILD-TYPE      23        5        34         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK  9(11Q13.3) MUTATED           0          0          3          2
  AMP PEAK  9(11Q13.3) WILD-TYPE         4          7         22         12
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK  9(11Q13.3) MUTATED          4         2
  AMP PEAK  9(11Q13.3) WILD-TYPE       14         5
D9V3, multiclass
            clus
vv           AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE
  STAGE I                               7                             23
  STAGE II                              3                              5
  STAGE IIA                             6                             34
  STAGE IIB                             0                              2
  STAGE IIC                             0                              1
  STAGE III                             0                              4
  STAGE IIIA                            0                              7
  STAGE IIIB                            3                             22
  STAGE IIIC                            2                             12
  STAGE IV                              4                             14
  STAGE IVA                             2                              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
  AMP PEAK  9(11Q13.3) MUTATED    1  7 16  3
  AMP PEAK  9(11Q13.3) WILD-TYPE  8 21 96 11
D9V4, multiclass
    clus
vv   AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE
  T1                            1                              8
  T2                            7                             21
  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
  AMP PEAK  9(11Q13.3) MUTATED   17  5  5
  AMP PEAK  9(11Q13.3) WILD-TYPE 67 40 28
D9V5, multiclass
    clus
vv   AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE
  N0                           17                             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"
D9V6, binary
                                cls
clus                               0   1
  AMP PEAK  9(11Q13.3) MUTATED    20   6
  AMP PEAK  9(11Q13.3) WILD-TYPE 105  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11Q13.3) MUTATED     20    6
  AMP PEAK  9(11Q13.3) WILD-TYPE  105   18
   clus
vv  AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE
  0                           20                            105
  1                            6                             18
[1] 2 2
[1] FALSE
D9V7, binary
                                cls
clus                              0  1
  AMP PEAK  9(11Q13.3) MUTATED   13 15
  AMP PEAK  9(11Q13.3) WILD-TYPE 63 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11Q13.3) MUTATED     13   15
  AMP PEAK  9(11Q13.3) WILD-TYPE   63   74
        clus
vv       AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE
  FEMALE                           13                             63
  MALE                             15                             74
[1] 2 2
[1] FALSE
D9V8, binary
                                cls
clus                              0  1
  AMP PEAK  9(11Q13.3) MUTATED   18  2
  AMP PEAK  9(11Q13.3) WILD-TYPE 94 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11Q13.3) MUTATED     18    2
  AMP PEAK  9(11Q13.3) WILD-TYPE   94   18
     clus
vv    AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(11Q13.3) WILD-TYPE
  NO                            18                             94
  YES                            2                             18
[1] 2 2
[1] FALSE
D9V9, binary
                                cls
clus                               0   1
  AMP PEAK  9(11Q13.3) MUTATED    27   1
  AMP PEAK  9(11Q13.3) WILD-TYPE 119  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(11Q13.3) MUTATED     27    1
  AMP PEAK  9(11Q13.3) WILD-TYPE  119   12
                                clus
vv                               AMP PEAK  9(11Q13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    27
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               AMP PEAK  9(11Q13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     119
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  AMP PEAK  9(11Q13.3) MUTATED    19   0   2   2
  AMP PEAK  9(11Q13.3) WILD-TYPE 104   2  10   2
D9V10, multiclass
    clus
vv   AMP PEAK  9(11Q13.3) MUTATED AMP PEAK  9(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"
D9V11, continuous

Clustering(10) Variable = AMP PEAK 10(12P13.33) MUTATION ANALYSIS
D10V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 10(12P13.33) MUTATED   33  7
  AMP PEAK 10(12P13.33) WILD-TYPE 98 20
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                             40                             118 
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                              7                              20 
$`AMP PEAK 10(12P13.33) MUTATED`
TCGA-AG-3611 TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2693 
       13.94        15.95        36.03        18.28        26.43        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 
       34.49        37.74        29.98        16.83        24.59        36.03 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 
       46.03         2.01         6.05        19.99         7.99        37.02 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-4001 TCGA-AG-4022 
       19.04         1.02        36.95         1.02        36.03        46.03 
TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-6682 TCGA-DC-6683 
       38.96        61.97        48.20        78.12        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 
       12.62       126.44        57.24        32.61        19.96        18.28 
TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6812 
       17.69        13.64        11.97        36.49 

$`AMP PEAK 10(12P13.33) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 
       31.00        51.98        21.24        55.76        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       17.23        43.04        13.55        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        12.00        32.02         7.07        36.03 
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-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 
       50.04        12.03         0.99        15.95        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       29.98        32.98         0.99         0.99        19.99        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 
       19.99        28.04        14.04         1.02         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.02        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-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 
       33.17        13.78        44.78        47.44         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DC TCGA-DY-A1DE 
       51.98        10.98        44.02        25.97        41.36       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         3.48         4.18        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 
       42.35        28.57         0.39        32.19        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                           1.02                            0.39 
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                         126.44                          129.27 
  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE 
                          25.74                           20.73 
[1] "1.0 - 126.4 (25.7)" "0.4 - 129.3 (20.7)"
[1] "hr=" "1.3"
D10V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 10(12P13.33) MUTATED         9        4        10         0
  AMP PEAK 10(12P13.33) WILD-TYPE      21        4        30         2
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 10(12P13.33) MUTATED           0         0          2          4
  AMP PEAK 10(12P13.33) WILD-TYPE         1         4          5         21
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 10(12P13.33) MUTATED            4        5         1
  AMP PEAK 10(12P13.33) WILD-TYPE         10       13         6
D10V3, multiclass
            clus
vv           AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  STAGE I                                9                              21
  STAGE II                               4                               4
  STAGE IIA                             10                              30
  STAGE IIB                              0                               2
  STAGE IIC                              0                               1
  STAGE III                              0                               4
  STAGE IIIA                             2                               5
  STAGE IIIB                             4                              21
  STAGE IIIC                             4                              10
  STAGE IV                               5                              13
  STAGE IVA                              1                               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 10(12P13.33) MUTATED    2 11 25  3
  AMP PEAK 10(12P13.33) WILD-TYPE  7 17 87 11
D10V4, multiclass
    clus
vv   AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  T1                             2                               7
  T2                            11                              17
  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 10(12P13.33) MUTATED   24  9  8
  AMP PEAK 10(12P13.33) WILD-TYPE 60 36 25
D10V5, multiclass
    clus
vv   AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  N0                            24                              60
  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"
D10V6, binary
                                 cls
clus                               0  1
  AMP PEAK 10(12P13.33) MUTATED   30  4
  AMP PEAK 10(12P13.33) WILD-TYPE 95 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P13.33) MUTATED     30    4
  AMP PEAK 10(12P13.33) WILD-TYPE   95   20
   clus
vv  AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  0                            30                              95
  1                             4                              20
[1] 2 2
[1] FALSE
D10V7, binary
                                 cls
clus                               0  1
  AMP PEAK 10(12P13.33) MUTATED   17 24
  AMP PEAK 10(12P13.33) WILD-TYPE 59 65
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P13.33) MUTATED     17   24
  AMP PEAK 10(12P13.33) WILD-TYPE   59   65
        clus
vv       AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  FEMALE                            17                              59
  MALE                              24                              65
[1] 2 2
[1] FALSE
D10V8, binary
                                 cls
clus                               0  1
  AMP PEAK 10(12P13.33) MUTATED   24  8
  AMP PEAK 10(12P13.33) WILD-TYPE 88 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P13.33) MUTATED     24    8
  AMP PEAK 10(12P13.33) WILD-TYPE   88   12
     clus
vv    AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(12P13.33) WILD-TYPE
  NO                             24                              88
  YES                             8                              12
[1] 2 2
[1] FALSE
D10V9, binary
                                 cls
clus                                0   1
  AMP PEAK 10(12P13.33) MUTATED    33   5
  AMP PEAK 10(12P13.33) WILD-TYPE 113   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P13.33) MUTATED     33    5
  AMP PEAK 10(12P13.33) WILD-TYPE  113    8
                                clus
vv                               AMP PEAK 10(12P13.33) MUTATED
  RECTAL ADENOCARCINOMA                                     33
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 10(12P13.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      113
  RECTAL MUCINOUS ADENOCARCINOMA                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 10(12P13.33) MUTATED   28  0  3  2
  AMP PEAK 10(12P13.33) WILD-TYPE 95  2  9  2
D10V10, multiclass
    clus
vv   AMP PEAK 10(12P13.33) MUTATED AMP PEAK 10(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"
D10V11, continuous

Clustering(11) Variable = AMP PEAK 11(12P12.1) MUTATION ANALYSIS
D11V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 11(12P12.1) MUTATED   32  7
  AMP PEAK 11(12P12.1) WILD-TYPE 99 20
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                            39                            119 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                             7                             20 
$`AMP PEAK 11(12P12.1) MUTATED`
TCGA-AG-3611 TCGA-AG-A014 TCGA-AG-A015 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2693 
       13.94        15.95        36.03        18.28        26.43        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 
       34.49        37.74        29.98        16.83        24.59        36.03 
TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 
       46.03         2.01         6.05        19.99         7.99        37.02 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-4001 
       19.04         1.02        36.95         1.02        28.04        36.03 
TCGA-AG-4021 TCGA-AG-A02G TCGA-AG-A02N TCGA-CI-6620 TCGA-CI-6624 TCGA-CL-5917 
        3.98        38.96        61.97        33.17        48.20        78.12 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6510 
       25.05        25.05        12.62        32.61        19.96        18.28 
TCGA-EI-6512 TCGA-EI-6885 TCGA-EI-7002 
       17.69        13.64        11.97 

$`AMP PEAK 11(12P12.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 
       31.00        51.98        21.24        55.76        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       17.23        43.04        13.55        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       65.98        11.84        12.00        32.02         7.07        36.03 
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-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 
       50.04        12.03         0.99        15.95        20.98         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 
       29.98        32.98         0.99         0.99        19.99        17.95 
TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       13.02        35.01        14.01        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       19.99        14.04         1.02        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
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         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 
       43.20        27.55        26.43        19.46         6.05        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       44.78        47.44         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       44.02        25.97       126.44        41.36        57.24       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 
       24.13        51.48         3.48         4.18        20.55        20.91 
TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       17.00        15.85        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                          1.02                           0.39 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                         78.12                         129.27 
  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE 
                         25.05                          20.98 
[1] "1.0 - 78.1 (25.1)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.1"
D11V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 11(12P12.1) MUTATED         9        3         8         0         0
  AMP PEAK 11(12P12.1) WILD-TYPE      21        5        32         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 11(12P12.1) MUTATED           0          2          3          5
  AMP PEAK 11(12P12.1) WILD-TYPE         4          5         22          9
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 11(12P12.1) MUTATED          6         2
  AMP PEAK 11(12P12.1) WILD-TYPE       12         5
D11V3, multiclass
            clus
vv           AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  STAGE I                               9                             21
  STAGE II                              3                              5
  STAGE IIA                             8                             32
  STAGE IIB                             0                              2
  STAGE IIC                             0                              1
  STAGE III                             0                              4
  STAGE IIIA                            2                              5
  STAGE IIIB                            3                             22
  STAGE IIIC                            5                              9
  STAGE IV                              6                             12
  STAGE IVA                             2                              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
  AMP PEAK 11(12P12.1) MUTATED    2 11 24  3
  AMP PEAK 11(12P12.1) WILD-TYPE  7 17 88 11
D11V4, multiclass
    clus
vv   AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  T1                            2                              7
  T2                           11                             17
  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 11(12P12.1) MUTATED   21  9 10
  AMP PEAK 11(12P12.1) WILD-TYPE 63 36 23
D11V5, multiclass
    clus
vv   AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  N0                           21                             63
  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"
D11V6, binary
                                cls
clus                              0  1
  AMP PEAK 11(12P12.1) MUTATED   27  6
  AMP PEAK 11(12P12.1) WILD-TYPE 98 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED     27    6
  AMP PEAK 11(12P12.1) WILD-TYPE   98   18
   clus
vv  AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  0                           27                             98
  1                            6                             18
[1] 2 2
[1] FALSE
D11V7, binary
                                cls
clus                              0  1
  AMP PEAK 11(12P12.1) MUTATED   17 23
  AMP PEAK 11(12P12.1) WILD-TYPE 59 66
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED     17   23
  AMP PEAK 11(12P12.1) WILD-TYPE   59   66
        clus
vv       AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  FEMALE                           17                             59
  MALE                             23                             66
[1] 2 2
[1] FALSE
D11V8, binary
                                cls
clus                              0  1
  AMP PEAK 11(12P12.1) MUTATED   26  7
  AMP PEAK 11(12P12.1) WILD-TYPE 86 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED     26    7
  AMP PEAK 11(12P12.1) WILD-TYPE   86   13
     clus
vv    AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(12P12.1) WILD-TYPE
  NO                            26                             86
  YES                            7                             13
[1] 2 2
[1] FALSE
D11V9, binary
                                cls
clus                               0   1
  AMP PEAK 11(12P12.1) MUTATED    32   5
  AMP PEAK 11(12P12.1) WILD-TYPE 114   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 11(12P12.1) MUTATED     32    5
  AMP PEAK 11(12P12.1) WILD-TYPE  114    8
                                clus
vv                               AMP PEAK 11(12P12.1) MUTATED
  RECTAL ADENOCARCINOMA                                    32
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 11(12P12.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     114
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 11(12P12.1) MUTATED   27  0  4  2
  AMP PEAK 11(12P12.1) WILD-TYPE 96  2  8  2
D11V10, multiclass
    clus
vv   AMP PEAK 11(12P12.1) MUTATED AMP PEAK 11(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"
D11V11, continuous

Clustering(12) Variable = AMP PEAK 12(13Q12.13) MUTATION ANALYSIS
D12V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 12(13Q12.13) MUTATED   97 24
  AMP PEAK 12(13Q12.13) WILD-TYPE 34  3
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                            121                              37 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                             24                               3 
$`AMP PEAK 12(13Q12.13) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       15.95        36.03        51.98        18.28        55.76        26.43 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
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-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 
        0.99        19.99        20.98         0.99        29.98         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        17.95        36.95        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02         3.98        46.03         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 
        9.07        49.97         1.94        38.96        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       43.20        27.55        26.43         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        12.00        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC 
       10.98        44.02        25.05        25.05       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         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
        4.18        20.55        20.91        17.00        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
       17.69        16.34        16.31        16.41        11.51        10.78 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 
       11.97         8.45         9.96        49.51        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
        0.39        32.19        36.49        19.66        11.87        12.46 
TCGA-G5-6572 
       47.08 

$`AMP PEAK 12(13Q12.13) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-3400 TCGA-AG-3574 TCGA-AG-3575 
        8.02        31.00        21.24        34.49        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3608 
       32.02        24.00        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-3901 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A020 
       48.03        25.02        20.98        13.94         1.02         1.02 
TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6903 TCGA-DC-6155 TCGA-DC-6681 
       61.97        41.00         2.50        19.46        13.97        25.97 
TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6814 
       12.62        19.96         8.61        13.64        17.46        37.18 
TCGA-F5-6861 
       38.14 

  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                           0.39                            0.99 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                         129.27                           61.97 
  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE 
                          24.13                           19.46 
[1] "0.4 - 129.3 (24.1)" "1.0 - 62.0 (19.5)" 
[1] "hr=" "1.8"
D12V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 12(13Q12.13) MUTATED        21        2        29         2
  AMP PEAK 12(13Q12.13) WILD-TYPE       9        6        11         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 12(13Q12.13) MUTATED           1         3          5         22
  AMP PEAK 12(13Q12.13) WILD-TYPE         0         1          2          3
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 12(13Q12.13) MUTATED           13       14         6
  AMP PEAK 12(13Q12.13) WILD-TYPE          1        4         1
D12V3, multiclass
            clus
vv           AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  STAGE I                               21                               9
  STAGE II                               2                               6
  STAGE IIA                             29                              11
  STAGE IIB                              2                               0
  STAGE IIC                              1                               0
  STAGE III                              3                               1
  STAGE IIIA                             5                               2
  STAGE IIIB                            22                               3
  STAGE IIIC                            13                               1
  STAGE IV                              14                               4
  STAGE IVA                              6                               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 12(13Q12.13) MUTATED    7 19 84 14
  AMP PEAK 12(13Q12.13) WILD-TYPE  2  9 28  0
D12V4, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  T1                             7                               2
  T2                            19                               9
  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 12(13Q12.13) MUTATED   56 37 30
  AMP PEAK 12(13Q12.13) WILD-TYPE 28  8  3
D12V5, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  N0                            56                              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"
D12V6, binary
                                 cls
clus                               0  1
  AMP PEAK 12(13Q12.13) MUTATED   93 19
  AMP PEAK 12(13Q12.13) WILD-TYPE 32  5
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED     93   19
  AMP PEAK 12(13Q12.13) WILD-TYPE   32    5
   clus
vv  AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  0                            93                              32
  1                            19                               5
[1] 2 2
[1] FALSE
D12V7, binary
                                 cls
clus                               0  1
  AMP PEAK 12(13Q12.13) MUTATED   57 69
  AMP PEAK 12(13Q12.13) WILD-TYPE 19 20
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED     57   69
  AMP PEAK 12(13Q12.13) WILD-TYPE   19   20
        clus
vv       AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  FEMALE                            57                              19
  MALE                              69                              20
[1] 2 2
[1] FALSE
D12V8, binary
                                 cls
clus                               0  1
  AMP PEAK 12(13Q12.13) MUTATED   83 17
  AMP PEAK 12(13Q12.13) WILD-TYPE 29  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED     83   17
  AMP PEAK 12(13Q12.13) WILD-TYPE   29    3
     clus
vv    AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(13Q12.13) WILD-TYPE
  NO                             83                              29
  YES                            17                               3
[1] 2 2
[1] FALSE
D12V9, binary
                                 cls
clus                                0   1
  AMP PEAK 12(13Q12.13) MUTATED   117   5
  AMP PEAK 12(13Q12.13) WILD-TYPE  29   8
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 12(13Q12.13) MUTATED    117    5
  AMP PEAK 12(13Q12.13) WILD-TYPE   29    8
                                clus
vv                               AMP PEAK 12(13Q12.13) MUTATED
  RECTAL ADENOCARCINOMA                                    117
  RECTAL MUCINOUS ADENOCARCINOMA                             5
                                clus
vv                               AMP PEAK 12(13Q12.13) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       29
  RECTAL MUCINOUS ADENOCARCINOMA                               8
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 12(13Q12.13) MUTATED   90  2  9  3
  AMP PEAK 12(13Q12.13) WILD-TYPE 33  0  3  1
D12V10, multiclass
    clus
vv   AMP PEAK 12(13Q12.13) MUTATED AMP PEAK 12(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"
D12V11, continuous

Clustering(13) Variable = AMP PEAK 13(13Q12.2) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 13(13Q12.2) MUTATED   97 23
  AMP PEAK 13(13Q12.2) WILD-TYPE 34  4
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                           120                             38 
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                            23                              4 
$`AMP PEAK 13(13Q12.2) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       15.95        36.03        51.98        18.28        55.76        26.43 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        29.98        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       65.98        11.84         7.07        36.03        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3605 
       46.03        34.03        34.03        34.03         2.01         0.99 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 
       19.99        20.98         0.99        29.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        17.95        36.95        35.01        14.01         1.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
        3.98        46.03         6.02        23.01        37.02         9.07 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        41.00        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 
       43.20        27.55        26.43         6.05        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       26.04        31.00        12.00        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.05        25.05       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         3.48         4.18 
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-7002 
       16.34        16.31        16.41        11.51        10.78        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        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       32.19        36.49        19.66        11.87        12.46        47.08 

$`AMP PEAK 13(13Q12.2) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 
        8.02        31.00        21.24        34.49        16.83        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       12.00        32.02        24.00        50.04        12.03         6.05 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 
       15.95         7.99        37.02        32.98         0.99        19.04 
TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A01J 
       13.02        48.03        25.02        20.98        13.94         1.02 
TCGA-AG-A020 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-DC-6155 
        1.02        61.97         2.50        19.46        33.17        13.97 
TCGA-DC-6681 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       25.97        12.62        19.96         8.61        13.64        17.46 
TCGA-F5-6814 TCGA-F5-6861 
       37.18        38.14 

  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                          0.39                           0.99 
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                        129.27                          61.97 
  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE 
                        24.245                         19.250 
[1] "0.4 - 129.3 (24.2)" "1.0 - 62.0 (19.2)" 
[1] "hr=" "1.3"
D13V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 13(13Q12.2) MUTATED        21        2        29         2         1
  AMP PEAK 13(13Q12.2) WILD-TYPE       9        6        11         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 13(13Q12.2) MUTATED           3          5         22         13
  AMP PEAK 13(13Q12.2) WILD-TYPE         1          2          3          1
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 13(13Q12.2) MUTATED         14         5
  AMP PEAK 13(13Q12.2) WILD-TYPE        4         2
D13V3, multiclass
            clus
vv           AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  STAGE I                              21                              9
  STAGE II                              2                              6
  STAGE IIA                            29                             11
  STAGE IIB                             2                              0
  STAGE IIC                             1                              0
  STAGE III                             3                              1
  STAGE IIIA                            5                              2
  STAGE IIIB                           22                              3
  STAGE IIIC                           13                              1
  STAGE IV                             14                              4
  STAGE IVA                             5                              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 13(13Q12.2) MUTATED    7 19 83 14
  AMP PEAK 13(13Q12.2) WILD-TYPE  2  9 29  0
D13V4, multiclass
    clus
vv   AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  T1                            7                              2
  T2                           19                              9
  T3                           83                             29
  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(13Q12.2) MUTATED   56 36 30
  AMP PEAK 13(13Q12.2) WILD-TYPE 28  9  3
D13V5, multiclass
    clus
vv   AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  N0                           56                             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"
D13V6, binary
                                cls
clus                              0  1
  AMP PEAK 13(13Q12.2) MUTATED   93 18
  AMP PEAK 13(13Q12.2) WILD-TYPE 32  6
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED     93   18
  AMP PEAK 13(13Q12.2) WILD-TYPE   32    6
   clus
vv  AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  0                           93                             32
  1                           18                              6
[1] 2 2
[1] FALSE
D13V7, binary
                                cls
clus                              0  1
  AMP PEAK 13(13Q12.2) MUTATED   55 70
  AMP PEAK 13(13Q12.2) WILD-TYPE 21 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED     55   70
  AMP PEAK 13(13Q12.2) WILD-TYPE   21   19
        clus
vv       AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  FEMALE                           55                             21
  MALE                             70                             19
[1] 2 2
[1] FALSE
D13V8, binary
                                cls
clus                              0  1
  AMP PEAK 13(13Q12.2) MUTATED   81 17
  AMP PEAK 13(13Q12.2) WILD-TYPE 31  3
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED     81   17
  AMP PEAK 13(13Q12.2) WILD-TYPE   31    3
     clus
vv    AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(13Q12.2) WILD-TYPE
  NO                            81                             31
  YES                           17                              3
[1] 2 2
[1] FALSE
D13V9, binary
                                cls
clus                               0   1
  AMP PEAK 13(13Q12.2) MUTATED   116   5
  AMP PEAK 13(13Q12.2) WILD-TYPE  30   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 13(13Q12.2) MUTATED    116    5
  AMP PEAK 13(13Q12.2) WILD-TYPE   30    8
                                clus
vv                               AMP PEAK 13(13Q12.2) MUTATED
  RECTAL ADENOCARCINOMA                                   116
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               AMP PEAK 13(13Q12.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      30
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 13(13Q12.2) MUTATED   90  2  9  3
  AMP PEAK 13(13Q12.2) WILD-TYPE 33  0  3  1
D13V10, multiclass
    clus
vv   AMP PEAK 13(13Q12.2) MUTATED AMP PEAK 13(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"
D13V11, continuous

Clustering(14) Variable = AMP PEAK 14(13Q22.1) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(13Q22.1) MUTATED   92 21
  AMP PEAK 14(13Q22.1) WILD-TYPE 39  6
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                           113                             45 
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                            21                              6 
$`AMP PEAK 14(13Q22.1) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 
       15.95        36.03        51.98        18.28        55.76        26.43 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       46.92        39.48        17.23        43.04        13.55        37.97 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.74        29.98        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 
       65.98        11.84         7.07        36.03        20.05         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3605 TCGA-AG-3609 
       46.03        34.03        34.03        34.03         0.99        19.99 
TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3882 TCGA-AG-3883 
       20.98         0.99        29.98         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3902 
       17.95        36.95        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-4022 
       19.99        28.04        36.03        14.04         1.02        46.03 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        6.02        23.01         9.07        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        43.20        27.55        26.43         6.05 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 
       21.01        25.05        26.04        31.00        12.00        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       51.98        10.98        44.02        25.05        25.05        12.62 
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         3.48        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        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
       32.19        36.49        19.66        11.87        47.08 

$`AMP PEAK 14(13Q22.1) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A01N TCGA-BM-6198 TCGA-AF-3400 TCGA-AF-5654 TCGA-AG-3574 
        8.02        31.00        21.24        34.49        16.83        36.03 
TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 
       12.00        32.02        24.00         2.01        50.04        12.03 
TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
        6.05        15.95         7.99        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3892 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-4021 TCGA-AG-A002 
       19.04        13.02        48.03        25.02         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A02N TCGA-AG-A02X 
       13.94        37.02         1.02         1.02        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6620 TCGA-DC-6155 TCGA-DC-6681 TCGA-EF-5831 
        2.50        19.46        33.17        13.97        25.97         4.18 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       19.96        20.91         8.61        13.64        17.46         8.45 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       37.18        38.14        12.46 

  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                          0.39                           0.99 
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                        129.27                          61.97 
  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE 
                         24.59                          19.04 
[1] "0.4 - 129.3 (24.6)" "1.0 - 62.0 (19.0)" 
[1] "hr=" "1.1"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 14(13Q22.1) MUTATED        20        5        26         2         1
  AMP PEAK 14(13Q22.1) WILD-TYPE      10        3        14         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 14(13Q22.1) MUTATED           3          5         20         13
  AMP PEAK 14(13Q22.1) WILD-TYPE         1          2          5          1
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 14(13Q22.1) MUTATED         13         5
  AMP PEAK 14(13Q22.1) WILD-TYPE        5         2
D14V3, multiclass
            clus
vv           AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  STAGE I                              20                             10
  STAGE II                              5                              3
  STAGE IIA                            26                             14
  STAGE IIB                             2                              0
  STAGE IIC                             1                              0
  STAGE III                             3                              1
  STAGE IIIA                            5                              2
  STAGE IIIB                           20                              5
  STAGE IIIC                           13                              1
  STAGE IV                             13                              5
  STAGE IVA                             5                              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(13Q22.1) MUTATED    7 18 80 13
  AMP PEAK 14(13Q22.1) WILD-TYPE  2 10 32  1
D14V4, multiclass
    clus
vv   AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  T1                            7                              2
  T2                           18                             10
  T3                           80                             32
  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 14(13Q22.1) MUTATED   55 35 27
  AMP PEAK 14(13Q22.1) WILD-TYPE 29 10  6
D14V5, multiclass
    clus
vv   AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  N0                           55                             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"
D14V6, binary
                                cls
clus                              0  1
  AMP PEAK 14(13Q22.1) MUTATED   89 17
  AMP PEAK 14(13Q22.1) WILD-TYPE 36  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED     89   17
  AMP PEAK 14(13Q22.1) WILD-TYPE   36    7
   clus
vv  AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  0                           89                             36
  1                           17                              7
[1] 2 2
[1] FALSE
D14V7, binary
                                cls
clus                              0  1
  AMP PEAK 14(13Q22.1) MUTATED   53 67
  AMP PEAK 14(13Q22.1) WILD-TYPE 23 22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED     53   67
  AMP PEAK 14(13Q22.1) WILD-TYPE   23   22
        clus
vv       AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  FEMALE                           53                             23
  MALE                             67                             22
[1] 2 2
[1] FALSE
D14V8, binary
                                cls
clus                              0  1
  AMP PEAK 14(13Q22.1) MUTATED   74 18
  AMP PEAK 14(13Q22.1) WILD-TYPE 38  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED     74   18
  AMP PEAK 14(13Q22.1) WILD-TYPE   38    2
     clus
vv    AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(13Q22.1) WILD-TYPE
  NO                            74                             38
  YES                           18                              2
[1] 2 2
[1] FALSE
D14V9, binary
                                cls
clus                               0   1
  AMP PEAK 14(13Q22.1) MUTATED   112   4
  AMP PEAK 14(13Q22.1) WILD-TYPE  34   9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(13Q22.1) MUTATED    112    4
  AMP PEAK 14(13Q22.1) WILD-TYPE   34    9
                                clus
vv                               AMP PEAK 14(13Q22.1) MUTATED
  RECTAL ADENOCARCINOMA                                   112
  RECTAL MUCINOUS ADENOCARCINOMA                            4
                                clus
vv                               AMP PEAK 14(13Q22.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      34
  RECTAL MUCINOUS ADENOCARCINOMA                              9
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 14(13Q22.1) MUTATED   85  2  8  4
  AMP PEAK 14(13Q22.1) WILD-TYPE 38  0  4  0
D14V10, multiclass
    clus
vv   AMP PEAK 14(13Q22.1) MUTATED AMP PEAK 14(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"
D14V11, continuous

Clustering(15) Variable = AMP PEAK 15(16P11.2) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(16P11.2) MUTATED   37  8
  AMP PEAK 15(16P11.2) WILD-TYPE 94 19
  AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE 
                            45                            113 
  AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE 
                             8                             19 
$`AMP PEAK 15(16P11.2) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       10.39        13.94        17.03        15.95        36.03        31.00 
TCGA-BM-6198 TCGA-AF-2689 TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K 
       21.24        39.48        37.74        24.36        20.02        86.63 
TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3726 
       65.98        36.03        34.03         6.05        20.98         7.99 
TCGA-AG-3731 TCGA-AG-3885 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4022 
       37.02        17.95        19.99        36.03         1.02        46.03 
TCGA-AG-A016 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6644 TCGA-CI-6622 TCGA-CI-6623 
        9.07        38.96        38.04        27.55        44.78        47.44 
TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6683 TCGA-DY-A1DF 
       78.12        25.05        31.00        12.00        25.05        24.13 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6512 TCGA-EI-6514 TCGA-F5-6465 TCGA-F5-6702 
       51.48         3.48        17.69        16.31        49.51        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6863 
        0.39        32.19        11.87 

$`AMP PEAK 15(16P11.2) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A023 TCGA-G5-6233 
        8.02        19.99        17.03        25.97        51.98        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       55.76        26.43        46.92        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6672 TCGA-AF-A56N 
       37.97        34.49        29.98        16.83        24.59        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00        32.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 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-3609 TCGA-AG-3727 TCGA-AG-3728 
       12.03         0.99        15.95        19.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-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-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 
       25.02        32.02        28.04        14.04         3.98        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        23.01        37.02         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6547 
       49.97         1.94        61.97        41.00        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       43.20        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6155 TCGA-DC-6156 
       48.20         7.17        21.01        26.04        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5831 
      126.44        41.36        57.24       129.27        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       20.55        19.96        20.91        17.00        18.28        15.85 
TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.34        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6812 
       17.46        11.97         8.45         9.96        42.35        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        12.46        47.08 

  AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE 
                          0.39                           0.99 
  AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE 
                         86.63                         129.27 
  AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE 
                         25.05                          19.99 
[1] "0.4 - 86.6 (25.1)"  "1.0 - 129.3 (20.0)"
[1] "hr=" "1.1"
D15V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 15(16P11.2) MUTATED         6        1         7         2         0
  AMP PEAK 15(16P11.2) WILD-TYPE      24        7        33         0         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 15(16P11.2) MUTATED           1          1         11          5
  AMP PEAK 15(16P11.2) WILD-TYPE         3          6         14          9
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 15(16P11.2) MUTATED          8         3
  AMP PEAK 15(16P11.2) WILD-TYPE       10         4
D15V3, multiclass
            clus
vv           AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE
  STAGE I                               6                             24
  STAGE II                              1                              7
  STAGE IIA                             7                             33
  STAGE IIB                             2                              0
  STAGE IIC                             0                              1
  STAGE III                             1                              3
  STAGE IIIA                            1                              6
  STAGE IIIB                           11                             14
  STAGE IIIC                            5                              9
  STAGE IV                              8                             10
  STAGE IVA                             3                              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 15(16P11.2) MUTATED    2  7 31  6
  AMP PEAK 15(16P11.2) WILD-TYPE  7 21 81  8
D15V4, multiclass
    clus
vv   AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE
  T1                            2                              7
  T2                            7                             21
  T3                           31                             81
  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 15(16P11.2) MUTATED   17 18 10
  AMP PEAK 15(16P11.2) WILD-TYPE 67 27 23
D15V5, multiclass
    clus
vv   AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE
  N0                           17                             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"
D15V6, binary
                                cls
clus                              0  1
  AMP PEAK 15(16P11.2) MUTATED   30 11
  AMP PEAK 15(16P11.2) WILD-TYPE 95 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16P11.2) MUTATED     30   11
  AMP PEAK 15(16P11.2) WILD-TYPE   95   13
   clus
vv  AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE
  0                           30                             95
  1                           11                             13
[1] 2 2
[1] FALSE
D15V7, binary
                                cls
clus                              0  1
  AMP PEAK 15(16P11.2) MUTATED   20 27
  AMP PEAK 15(16P11.2) WILD-TYPE 56 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16P11.2) MUTATED     20   27
  AMP PEAK 15(16P11.2) WILD-TYPE   56   62
        clus
vv       AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE
  FEMALE                           20                             56
  MALE                             27                             62
[1] 2 2
[1] FALSE
D15V8, binary
                                cls
clus                              0  1
  AMP PEAK 15(16P11.2) MUTATED   32  7
  AMP PEAK 15(16P11.2) WILD-TYPE 80 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16P11.2) MUTATED     32    7
  AMP PEAK 15(16P11.2) WILD-TYPE   80   13
     clus
vv    AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(16P11.2) WILD-TYPE
  NO                            32                             80
  YES                            7                             13
[1] 2 2
[1] FALSE
D15V9, binary
                                cls
clus                              0  1
  AMP PEAK 15(16P11.2) MUTATED   47  0
  AMP PEAK 15(16P11.2) WILD-TYPE 99 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(16P11.2) MUTATED     47    0
  AMP PEAK 15(16P11.2) WILD-TYPE   99   13
                                clus
vv                               AMP PEAK 15(16P11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    47
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 15(16P11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      99
  RECTAL MUCINOUS ADENOCARCINOMA                             13
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 15(16P11.2) MUTATED   30  0  7  2
  AMP PEAK 15(16P11.2) WILD-TYPE 93  2  5  2
D15V10, multiclass
    clus
vv   AMP PEAK 15(16P11.2) MUTATED AMP PEAK 15(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"
D15V11, continuous

Clustering(16) Variable = AMP PEAK 16(17Q12) MUTATION ANALYSIS
D16V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 16(17Q12) MUTATED   38  6
  AMP PEAK 16(17Q12) WILD-TYPE 93 21
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                          44                          114 
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                           6                           21 
$`AMP PEAK 16(17Q12) MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 
       13.94        19.99        17.03        15.95        31.00        51.98 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2690 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       55.76        26.43        17.23        86.63        65.98        11.84 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3608 
       12.00         7.07        36.03        46.03        34.03        15.95 
TCGA-AG-3609 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-A016 TCGA-AH-6643 TCGA-AH-6897 TCGA-CI-6619 
       36.03         1.02         9.07        43.20        26.43         6.05 
TCGA-CI-6621 TCGA-CI-6623 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       13.78        47.44        12.00        25.05        25.05        12.62 
TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 TCGA-F5-6811 
       51.48        17.00        18.28        16.31        11.97        32.19 
TCGA-F5-6813 TCGA-F5-6864 
       19.66        12.46 

$`AMP PEAK 16(17Q12) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A015 TCGA-BM-6198 
       10.39         8.02        17.03        25.97        36.03        21.24 
TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       18.28        46.92        39.48        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       24.59        36.03        32.02        20.05        24.00         1.02 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
        0.99        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 
       32.98         0.99        19.04        17.95        36.95        13.02 
TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 
       35.01        14.01         1.02        25.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        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         2.50 
TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 
       27.55        19.46        33.17        44.78        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.17        21.01        25.05        26.04        31.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A0XA 
       31.00        51.98        10.98        44.02        25.97       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        24.13        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 
        4.18        20.55        19.96        20.91        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        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
        0.39        36.49        37.18        38.14        11.87        47.08 

  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                        0.99                         0.39 
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                       86.63                       129.27 
  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE 
                      19.825                       23.505 
[1] "1.0 - 86.6 (19.8)"  "0.4 - 129.3 (23.5)"
[1] "hr=" "1.4"
D16V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 16(17Q12) MUTATED         8        3        12         0         0
  AMP PEAK 16(17Q12) WILD-TYPE      22        5        28         2         1
                              vv
clus                           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 16(17Q12) MUTATED           0          1          6          6
  AMP PEAK 16(17Q12) WILD-TYPE         4          6         19          8
                              vv
clus                           STAGE IV STAGE IVA
  AMP PEAK 16(17Q12) MUTATED          7         2
  AMP PEAK 16(17Q12) WILD-TYPE       11         5
D16V3, multiclass
            clus
vv           AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  STAGE I                             8                           22
  STAGE II                            3                            5
  STAGE IIA                          12                           28
  STAGE IIB                           0                            2
  STAGE IIC                           0                            1
  STAGE III                           0                            4
  STAGE IIIA                          1                            6
  STAGE IIIB                          6                           19
  STAGE IIIC                          6                            8
  STAGE IV                            7                           11
  STAGE IVA                           2                            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
  AMP PEAK 16(17Q12) MUTATED    3  8 30  5
  AMP PEAK 16(17Q12) WILD-TYPE  6 20 82  9
D16V4, multiclass
    clus
vv   AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  T1                          3                            6
  T2                          8                           20
  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 16(17Q12) MUTATED   25  9 12
  AMP PEAK 16(17Q12) WILD-TYPE 59 36 21
D16V5, multiclass
    clus
vv   AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  N0                         25                           59
  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"
D16V6, binary
                              cls
clus                            0  1
  AMP PEAK 16(17Q12) MUTATED   33  9
  AMP PEAK 16(17Q12) WILD-TYPE 92 15
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(17Q12) MUTATED     33    9
  AMP PEAK 16(17Q12) WILD-TYPE   92   15
   clus
vv  AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  0                         33                           92
  1                          9                           15
[1] 2 2
[1] FALSE
D16V7, binary
                              cls
clus                            0  1
  AMP PEAK 16(17Q12) MUTATED   18 28
  AMP PEAK 16(17Q12) WILD-TYPE 58 61
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(17Q12) MUTATED     18   28
  AMP PEAK 16(17Q12) WILD-TYPE   58   61
        clus
vv       AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  FEMALE                         18                           58
  MALE                           28                           61
[1] 2 2
[1] FALSE
D16V8, binary
                              cls
clus                            0  1
  AMP PEAK 16(17Q12) MUTATED   32  4
  AMP PEAK 16(17Q12) WILD-TYPE 80 16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(17Q12) MUTATED     32    4
  AMP PEAK 16(17Q12) WILD-TYPE   80   16
     clus
vv    AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(17Q12) WILD-TYPE
  NO                          32                           80
  YES                          4                           16
[1] 2 2
[1] FALSE
D16V9, binary
                              cls
clus                             0   1
  AMP PEAK 16(17Q12) MUTATED    44   2
  AMP PEAK 16(17Q12) WILD-TYPE 102  11
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 16(17Q12) MUTATED     44    2
  AMP PEAK 16(17Q12) WILD-TYPE  102   11
                                clus
vv                               AMP PEAK 16(17Q12) MUTATED
  RECTAL ADENOCARCINOMA                                  44
  RECTAL MUCINOUS ADENOCARCINOMA                          2
                                clus
vv                               AMP PEAK 16(17Q12) WILD-TYPE
  RECTAL ADENOCARCINOMA                                   102
  RECTAL MUCINOUS ADENOCARCINOMA                           11
[1] 2 2
[1] FALSE
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 16(17Q12) MUTATED   32  1  6  2
  AMP PEAK 16(17Q12) WILD-TYPE 91  1  6  2
D16V10, multiclass
    clus
vv   AMP PEAK 16(17Q12) MUTATED AMP PEAK 16(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"
D16V11, continuous

Clustering(17) Variable = AMP PEAK 17(17Q24.1) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(17Q24.1) MUTATED   33  5
  AMP PEAK 17(17Q24.1) WILD-TYPE 98 22
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                            38                            120 
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                             5                             22 
$`AMP PEAK 17(17Q24.1) MUTATED`
TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 
       19.99        17.03        15.95        31.00        51.98        55.76 
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-3882 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-A016 TCGA-AH-6643 TCGA-AH-6897 
       19.99        36.03         1.02         9.07        43.20        26.43 
TCGA-CI-6619 TCGA-CI-6621 TCGA-DC-6154 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE 
        6.05        13.78        12.00        25.05        25.05       129.27 
TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-7002 
       51.48         3.48         4.18        18.28        16.31        11.97 
TCGA-F5-6811 TCGA-F5-6864 
       32.19        12.46 

$`AMP PEAK 17(17Q24.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A015 
       10.39         8.02        13.94        17.03        25.97        36.03 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 
       21.24        18.28        26.43        46.92        43.04        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       34.49        37.74        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 
       24.59        65.98        36.03        32.02        36.03        20.05 
TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3599 
       24.00         1.02        34.03        34.03         2.01        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-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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 
       48.03        25.02        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-A00Y 
        3.98        46.03        20.98        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         1.02         1.02        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         2.50        27.55 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
       19.46        33.17        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.17        21.01        25.05        26.04        31.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 
       31.00        51.98        10.98        44.02        25.97        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EI-6506 
      126.44        41.36        57.24        24.13        32.61        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        17.00        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-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
        8.45         9.96        49.51        42.35        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       36.49        19.66        37.18        38.14        11.87        47.08 

  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                          1.02                           0.39 
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                        129.27                         126.44 
  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE 
                        19.135                         23.505 
[1] "1.0 - 129.3 (19.1)" "0.4 - 126.4 (23.5)"
[1] "hr=" "1.6"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 17(17Q24.1) MUTATED         5        1        13         1         0
  AMP PEAK 17(17Q24.1) WILD-TYPE      25        7        27         1         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 17(17Q24.1) MUTATED           0          0          6          3
  AMP PEAK 17(17Q24.1) WILD-TYPE         4          7         19         11
                                vv
clus                             STAGE IV STAGE IVA
  AMP PEAK 17(17Q24.1) MUTATED          7         2
  AMP PEAK 17(17Q24.1) WILD-TYPE       11         5
D17V3, multiclass
            clus
vv           AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  STAGE I                               5                             25
  STAGE II                              1                              7
  STAGE IIA                            13                             27
  STAGE IIB                             1                              1
  STAGE IIC                             0                              1
  STAGE III                             0                              4
  STAGE IIIA                            0                              7
  STAGE IIIB                            6                             19
  STAGE IIIC                            3                             11
  STAGE IV                              7                             11
  STAGE IVA                             2                              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
  AMP PEAK 17(17Q24.1) MUTATED    0  7 27  5
  AMP PEAK 17(17Q24.1) WILD-TYPE  9 21 85  9
D17V4, multiclass
    clus
vv   AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  T1                            0                              9
  T2                            7                             21
  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 17(17Q24.1) MUTATED   22  7 10
  AMP PEAK 17(17Q24.1) WILD-TYPE 62 38 23
D17V5, multiclass
    clus
vv   AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  N0                           22                             62
  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"
D17V6, binary
                                cls
clus                              0  1
  AMP PEAK 17(17Q24.1) MUTATED   27  9
  AMP PEAK 17(17Q24.1) WILD-TYPE 98 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q24.1) MUTATED     27    9
  AMP PEAK 17(17Q24.1) WILD-TYPE   98   15
   clus
vv  AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  0                           27                             98
  1                            9                             15
[1] 2 2
[1] FALSE
D17V7, binary
                                cls
clus                              0  1
  AMP PEAK 17(17Q24.1) MUTATED   18 21
  AMP PEAK 17(17Q24.1) WILD-TYPE 58 68
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q24.1) MUTATED     18   21
  AMP PEAK 17(17Q24.1) WILD-TYPE   58   68
        clus
vv       AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  FEMALE                           18                             58
  MALE                             21                             68
[1] 2 2
[1] FALSE
D17V8, binary
                                cls
clus                              0  1
  AMP PEAK 17(17Q24.1) MUTATED   29  3
  AMP PEAK 17(17Q24.1) WILD-TYPE 83 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q24.1) MUTATED     29    3
  AMP PEAK 17(17Q24.1) WILD-TYPE   83   17
     clus
vv    AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(17Q24.1) WILD-TYPE
  NO                            29                             83
  YES                            3                             17
[1] 2 2
[1] FALSE
D17V9, binary
                                cls
clus                               0   1
  AMP PEAK 17(17Q24.1) MUTATED    38   0
  AMP PEAK 17(17Q24.1) WILD-TYPE 108  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(17Q24.1) MUTATED     38    0
  AMP PEAK 17(17Q24.1) WILD-TYPE  108   13
                                clus
vv                               AMP PEAK 17(17Q24.1) MUTATED
  RECTAL ADENOCARCINOMA                                    38
  RECTAL MUCINOUS ADENOCARCINOMA                            0
                                clus
vv                               AMP PEAK 17(17Q24.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     108
  RECTAL MUCINOUS ADENOCARCINOMA                             13
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 17(17Q24.1) MUTATED   28  1  5  0
  AMP PEAK 17(17Q24.1) WILD-TYPE 95  1  7  4
D17V10, multiclass
    clus
vv   AMP PEAK 17(17Q24.1) MUTATED AMP PEAK 17(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"
D17V11, continuous

Clustering(18) Variable = AMP PEAK 18(20Q11.21) MUTATION ANALYSIS
D18V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 18(20Q11.21) MUTATED   114  25
  AMP PEAK 18(20Q11.21) WILD-TYPE  17   2
  AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE 
                            139                              19 
  AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE 
                             25                               2 
$`AMP PEAK 18(20Q11.21) MUTATED`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       43.04        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 
        6.05        13.78        44.78        47.44        48.20        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
        7.17        21.01        25.05        26.04        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       13.97        31.00        51.98        10.98        44.02        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.05        25.05       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         3.48         4.18        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        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

$`AMP PEAK 18(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        12.62        19.96         8.61        17.46 
TCGA-EI-7004 
        8.45 

  AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE 
                           0.39                            2.01 
  AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE 
                         129.27                           61.97 
  AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE 
                          24.00                           17.46 
[1] "0.4 - 129.3 (24.0)" "2.0 - 62.0 (17.5)" 
[1] "hr=" "1.3"
D18V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 18(20Q11.21) MUTATED        26        5        33         2
  AMP PEAK 18(20Q11.21) WILD-TYPE       4        3         7         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 18(20Q11.21) MUTATED           1         4          6         25
  AMP PEAK 18(20Q11.21) WILD-TYPE         0         0          1          0
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 18(20Q11.21) MUTATED           13       17         6
  AMP PEAK 18(20Q11.21) WILD-TYPE          1        1         1
D18V3, multiclass
            clus
vv           AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE
  STAGE I                               26                               4
  STAGE II                               5                               3
  STAGE IIA                             33                               7
  STAGE IIB                              2                               0
  STAGE IIC                              1                               0
  STAGE III                              4                               0
  STAGE IIIA                             6                               1
  STAGE IIIB                            25                               0
  STAGE IIIC                            13                               1
  STAGE IV                              17                               1
  STAGE IVA                              6                               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 18(20Q11.21) MUTATED    7 26 98 13
  AMP PEAK 18(20Q11.21) WILD-TYPE  2  2 14  1
D18V4, multiclass
    clus
vv   AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE
  T1                             7                               2
  T2                            26                               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 18(20Q11.21) MUTATED   70 43 30
  AMP PEAK 18(20Q11.21) WILD-TYPE 14  2  3
D18V5, multiclass
    clus
vv   AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE
  N0                            70                              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"
D18V6, binary
                                 cls
clus                                0   1
  AMP PEAK 18(20Q11.21) MUTATED   108  22
  AMP PEAK 18(20Q11.21) WILD-TYPE  17   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20Q11.21) MUTATED    108   22
  AMP PEAK 18(20Q11.21) WILD-TYPE   17    2
   clus
vv  AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE
  0                           108                              17
  1                            22                               2
[1] 2 2
[1] FALSE
D18V7, binary
                                 cls
clus                               0  1
  AMP PEAK 18(20Q11.21) MUTATED   67 79
  AMP PEAK 18(20Q11.21) WILD-TYPE  9 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20Q11.21) MUTATED     67   79
  AMP PEAK 18(20Q11.21) WILD-TYPE    9   10
        clus
vv       AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE
  FEMALE                            67                               9
  MALE                              79                              10
[1] 2 2
[1] FALSE
D18V8, binary
                                 cls
clus                               0  1
  AMP PEAK 18(20Q11.21) MUTATED   98 17
  AMP PEAK 18(20Q11.21) WILD-TYPE 14  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20Q11.21) MUTATED     98   17
  AMP PEAK 18(20Q11.21) WILD-TYPE   14    3
     clus
vv    AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(20Q11.21) WILD-TYPE
  NO                             98                              14
  YES                            17                               3
[1] 2 2
[1] FALSE
D18V9, binary
                                 cls
clus                                0   1
  AMP PEAK 18(20Q11.21) MUTATED   135   7
  AMP PEAK 18(20Q11.21) WILD-TYPE  11   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 18(20Q11.21) MUTATED    135    7
  AMP PEAK 18(20Q11.21) WILD-TYPE   11    6
                                clus
vv                               AMP PEAK 18(20Q11.21) MUTATED
  RECTAL ADENOCARCINOMA                                    135
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 18(20Q11.21) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       11
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 18(20Q11.21) MUTATED   108   2  11   3
  AMP PEAK 18(20Q11.21) WILD-TYPE  15   0   1   1
D18V10, multiclass
    clus
vv   AMP PEAK 18(20Q11.21) MUTATED AMP PEAK 18(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"
D18V11, continuous

Clustering(19) Variable = AMP PEAK 19(20Q11.23) MUTATION ANALYSIS
D19V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 19(20Q11.23) MUTATED   115  25
  AMP PEAK 19(20Q11.23) WILD-TYPE  16   2
  AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE 
                            140                              18 
  AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE 
                             25                               2 
$`AMP PEAK 19(20Q11.23) MUTATED`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       43.04        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       20.02        24.59        86.63        65.98        11.84        36.03 
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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         0.99        29.98 
TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       37.02         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
       36.95        35.01        14.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       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         3.48         4.18 
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        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`AMP PEAK 19(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        12.62        19.96         8.61        17.46         8.45 

  AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE 
                           0.39                            2.01 
  AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE 
                         129.27                           61.97 
  AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE 
                         24.065                          15.505 
[1] "0.4 - 129.3 (24.1)" "2.0 - 62.0 (15.5)" 
[1] "hr=" "1.2"
D19V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 19(20Q11.23) MUTATED        26        5        33         2
  AMP PEAK 19(20Q11.23) WILD-TYPE       4        3         7         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 19(20Q11.23) MUTATED           1         4          6         25
  AMP PEAK 19(20Q11.23) WILD-TYPE         0         0          1          0
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 19(20Q11.23) MUTATED           13       17         7
  AMP PEAK 19(20Q11.23) WILD-TYPE          1        1         0
D19V3, multiclass
            clus
vv           AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE
  STAGE I                               26                               4
  STAGE II                               5                               3
  STAGE IIA                             33                               7
  STAGE IIB                              2                               0
  STAGE IIC                              1                               0
  STAGE III                              4                               0
  STAGE IIIA                             6                               1
  STAGE IIIB                            25                               0
  STAGE IIIC                            13                               1
  STAGE IV                              17                               1
  STAGE IVA                              7                               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
  AMP PEAK 19(20Q11.23) MUTATED    7 26 99 13
  AMP PEAK 19(20Q11.23) WILD-TYPE  2  2 13  1
D19V4, multiclass
    clus
vv   AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE
  T1                             7                               2
  T2                            26                               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 19(20Q11.23) MUTATED   70 44 30
  AMP PEAK 19(20Q11.23) WILD-TYPE 14  1  3
D19V5, multiclass
    clus
vv   AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE
  N0                            70                              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"
D19V6, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q11.23) MUTATED   108  23
  AMP PEAK 19(20Q11.23) WILD-TYPE  17   1
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q11.23) MUTATED    108   23
  AMP PEAK 19(20Q11.23) WILD-TYPE   17    1
   clus
vv  AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE
  0                           108                              17
  1                            23                               1
[1] 2 2
[1] FALSE
D19V7, binary
                                 cls
clus                               0  1
  AMP PEAK 19(20Q11.23) MUTATED   68 79
  AMP PEAK 19(20Q11.23) WILD-TYPE  8 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q11.23) MUTATED     68   79
  AMP PEAK 19(20Q11.23) WILD-TYPE    8   10
        clus
vv       AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE
  FEMALE                            68                               8
  MALE                              79                              10
[1] 2 2
[1] FALSE
D19V8, binary
                                 cls
clus                               0  1
  AMP PEAK 19(20Q11.23) MUTATED   99 17
  AMP PEAK 19(20Q11.23) WILD-TYPE 13  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q11.23) MUTATED     99   17
  AMP PEAK 19(20Q11.23) WILD-TYPE   13    3
     clus
vv    AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(20Q11.23) WILD-TYPE
  NO                             99                              13
  YES                            17                               3
[1] 2 2
[1] FALSE
D19V9, binary
                                 cls
clus                                0   1
  AMP PEAK 19(20Q11.23) MUTATED   136   7
  AMP PEAK 19(20Q11.23) WILD-TYPE  10   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 19(20Q11.23) MUTATED    136    7
  AMP PEAK 19(20Q11.23) WILD-TYPE   10    6
                                clus
vv                               AMP PEAK 19(20Q11.23) MUTATED
  RECTAL ADENOCARCINOMA                                    136
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 19(20Q11.23) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       10
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 19(20Q11.23) MUTATED   108   2  11   3
  AMP PEAK 19(20Q11.23) WILD-TYPE  15   0   1   1
D19V10, multiclass
    clus
vv   AMP PEAK 19(20Q11.23) MUTATED AMP PEAK 19(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"
D19V11, continuous

Clustering(20) Variable = AMP PEAK 20(20Q13.33) MUTATION ANALYSIS
D20V1, survival
                                 sevent
clus2                               0   1
  AMP PEAK 20(20Q13.33) MUTATED   115  24
  AMP PEAK 20(20Q13.33) WILD-TYPE  16   3
  AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE 
                            139                              19 
  AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE 
                             24                               3 
$`AMP PEAK 20(20Q13.33) MUTATED`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       43.04        13.55        37.97        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03         7.07        36.03        20.05        24.00         1.02 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 
       46.03        34.03        34.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 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-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-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        35.01        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        19.99        36.03        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       38.56         2.50        43.20        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.97        25.05        25.05       126.44        41.36        57.24 
TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
      129.27        24.13        32.61         3.48         4.18        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        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

$`AMP PEAK 20(20Q13.33) 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-3999 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A025 
       19.04        13.02        28.04         3.98        20.98        49.97 
TCGA-AG-A02N TCGA-DT-5265 TCGA-DY-A1DG TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 
       61.97        12.62        51.48        19.96         8.61        17.46 
TCGA-EI-7004 
        8.45 

  AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE 
                           0.39                            2.01 
  AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE 
                         129.27                           61.97 
  AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE 
                          23.01                           19.04 
[1] "0.4 - 129.3 (23.0)" "2.0 - 62.0 (19.0)" 
[1] "hr=" "1"  
D20V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  AMP PEAK 20(20Q13.33) MUTATED        26        5        34         2
  AMP PEAK 20(20Q13.33) WILD-TYPE       4        3         6         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  AMP PEAK 20(20Q13.33) MUTATED           1         4          6         25
  AMP PEAK 20(20Q13.33) WILD-TYPE         0         0          1          0
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  AMP PEAK 20(20Q13.33) MUTATED           12       17         6
  AMP PEAK 20(20Q13.33) WILD-TYPE          2        1         1
D20V3, multiclass
            clus
vv           AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE
  STAGE I                               26                               4
  STAGE II                               5                               3
  STAGE IIA                             34                               6
  STAGE IIB                              2                               0
  STAGE IIC                              1                               0
  STAGE III                              4                               0
  STAGE IIIA                             6                               1
  STAGE IIIB                            25                               0
  STAGE IIIC                            12                               2
  STAGE IV                              17                               1
  STAGE IVA                              6                               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 20(20Q13.33) MUTATED    7 26 98 13
  AMP PEAK 20(20Q13.33) WILD-TYPE  2  2 14  1
D20V4, multiclass
    clus
vv   AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE
  T1                             7                               2
  T2                            26                               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 20(20Q13.33) MUTATED   71 43 29
  AMP PEAK 20(20Q13.33) WILD-TYPE 13  2  4
D20V5, multiclass
    clus
vv   AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE
  N0                            71                              13
  N1                            43                               2
  N2                            29                               4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V6, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20Q13.33) MUTATED   108  22
  AMP PEAK 20(20Q13.33) WILD-TYPE  17   2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q13.33) MUTATED    108   22
  AMP PEAK 20(20Q13.33) WILD-TYPE   17    2
   clus
vv  AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE
  0                           108                              17
  1                            22                               2
[1] 2 2
[1] FALSE
D20V7, binary
                                 cls
clus                               0  1
  AMP PEAK 20(20Q13.33) MUTATED   68 78
  AMP PEAK 20(20Q13.33) WILD-TYPE  8 11
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q13.33) MUTATED     68   78
  AMP PEAK 20(20Q13.33) WILD-TYPE    8   11
        clus
vv       AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE
  FEMALE                            68                               8
  MALE                              78                              11
[1] 2 2
[1] FALSE
D20V8, binary
                                 cls
clus                               0  1
  AMP PEAK 20(20Q13.33) MUTATED   99 17
  AMP PEAK 20(20Q13.33) WILD-TYPE 13  3
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q13.33) MUTATED     99   17
  AMP PEAK 20(20Q13.33) WILD-TYPE   13    3
     clus
vv    AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) WILD-TYPE
  NO                             99                              13
  YES                            17                               3
[1] 2 2
[1] FALSE
D20V9, binary
                                 cls
clus                                0   1
  AMP PEAK 20(20Q13.33) MUTATED   134   7
  AMP PEAK 20(20Q13.33) WILD-TYPE  12   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 20(20Q13.33) MUTATED    134    7
  AMP PEAK 20(20Q13.33) WILD-TYPE   12    6
                                clus
vv                               AMP PEAK 20(20Q13.33) MUTATED
  RECTAL ADENOCARCINOMA                                    134
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               AMP PEAK 20(20Q13.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       12
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 2 2
[1] FALSE
                                 vv
clus                               R0  R1  R2  RX
  AMP PEAK 20(20Q13.33) MUTATED   108   2  11   3
  AMP PEAK 20(20Q13.33) WILD-TYPE  15   0   1   1
D20V10, multiclass
    clus
vv   AMP PEAK 20(20Q13.33) MUTATED AMP PEAK 20(20Q13.33) 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"
D20V11, continuous

Clustering(21) Variable = AMP PEAK 21(XP22.2) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 21(XP22.2) MUTATED    24   6
  AMP PEAK 21(XP22.2) WILD-TYPE 107  21
  AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE 
                           30                           128 
  AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE 
                            6                            21 
$`AMP PEAK 21(XP22.2) MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-G5-6235 
       10.39        19.99        15.95        36.03        31.00        55.76 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3591 TCGA-AG-3592 
       16.83        20.02        86.63        36.03        34.03        34.03 
TCGA-AG-3609 TCGA-AG-3999 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A02N 
       19.99        28.04         3.98        46.03         9.07        61.97 
TCGA-AG-A032 TCGA-AH-6644 TCGA-AH-6897 TCGA-DC-4745 TCGA-DC-6154 TCGA-DT-5265 
       38.04        27.55        26.43        21.01        12.00        12.62 
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        11.87 

$`AMP PEAK 21(XP22.2) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A023 
        8.02        13.94        17.03        17.03        25.97        51.98 
TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       21.24        18.28        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       24.36        24.59        65.98        11.84        12.00        32.02 
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-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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        32.02        19.99        36.03        14.04 
TCGA-AG-4007 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
        1.02        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
        1.02         1.02        49.97         1.94        38.96        41.00 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       38.56         2.50        43.20        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A0XA 
       10.98        44.02        25.97        25.05        25.05       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 
        4.18        20.55        19.96        20.91        17.00        15.85 
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        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE 
                         3.98                          0.39 
  AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE 
                        86.63                        129.27 
  AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE 
                       20.515                        21.110 
[1] "4.0 - 86.6 (20.5)"  "0.4 - 129.3 (21.1)"
[1] "hr=" "1.2"
D21V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 21(XP22.2) MUTATED         4        5         3         0         0
  AMP PEAK 21(XP22.2) WILD-TYPE      26        3        37         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 21(XP22.2) MUTATED           0          2          7          2
  AMP PEAK 21(XP22.2) WILD-TYPE         4          5         18         12
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK 21(XP22.2) MUTATED          6         1
  AMP PEAK 21(XP22.2) WILD-TYPE       12         6
D21V3, multiclass
            clus
vv           AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE
  STAGE I                              4                            26
  STAGE II                             5                             3
  STAGE IIA                            3                            37
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            0                             4
  STAGE IIIA                           2                             5
  STAGE IIIB                           7                            18
  STAGE IIIC                           2                            12
  STAGE IV                             6                            12
  STAGE IVA                            1                             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 21(XP22.2) MUTATED    1  7 21  3
  AMP PEAK 21(XP22.2) WILD-TYPE  8 21 91 11
D21V4, multiclass
    clus
vv   AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE
  T1                           1                             8
  T2                           7                            21
  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 21(XP22.2) MUTATED   14 11  6
  AMP PEAK 21(XP22.2) WILD-TYPE 70 34 27
D21V5, multiclass
    clus
vv   AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE
  N0                          14                            70
  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"
D21V6, binary
                               cls
clus                              0   1
  AMP PEAK 21(XP22.2) MUTATED    22   7
  AMP PEAK 21(XP22.2) WILD-TYPE 103  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(XP22.2) MUTATED     22    7
  AMP PEAK 21(XP22.2) WILD-TYPE  103   17
   clus
vv  AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE
  0                          22                           103
  1                           7                            17
[1] 2 2
[1] FALSE
D21V7, binary
                               cls
clus                             0  1
  AMP PEAK 21(XP22.2) MUTATED   18 14
  AMP PEAK 21(XP22.2) WILD-TYPE 58 75
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(XP22.2) MUTATED     18   14
  AMP PEAK 21(XP22.2) WILD-TYPE   58   75
        clus
vv       AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE
  FEMALE                          18                            58
  MALE                            14                            75
[1] 2 2
[1] FALSE
D21V8, binary
                               cls
clus                             0  1
  AMP PEAK 21(XP22.2) MUTATED   23  4
  AMP PEAK 21(XP22.2) WILD-TYPE 89 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(XP22.2) MUTATED     23    4
  AMP PEAK 21(XP22.2) WILD-TYPE   89   16
     clus
vv    AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(XP22.2) WILD-TYPE
  NO                           23                            89
  YES                           4                            16
[1] 2 2
[1] FALSE
D21V9, binary
                               cls
clus                              0   1
  AMP PEAK 21(XP22.2) MUTATED    31   1
  AMP PEAK 21(XP22.2) WILD-TYPE 115  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 21(XP22.2) MUTATED     31    1
  AMP PEAK 21(XP22.2) WILD-TYPE  115   12
                                clus
vv                               AMP PEAK 21(XP22.2) MUTATED
  RECTAL ADENOCARCINOMA                                   31
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK 21(XP22.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    115
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 21(XP22.2) MUTATED   24  1  4  1
  AMP PEAK 21(XP22.2) WILD-TYPE 99  1  8  3
D21V10, multiclass
    clus
vv   AMP PEAK 21(XP22.2) MUTATED AMP PEAK 21(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"
D21V11, continuous

Clustering(22) Variable = AMP PEAK 22(XQ27.3) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 22(XQ27.3) MUTATED    29   7
  AMP PEAK 22(XQ27.3) WILD-TYPE 102  20
  AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE 
                           36                           122 
  AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE 
                            7                            20 
$`AMP PEAK 22(XQ27.3) MUTATED`
TCGA-AF-3913 TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 TCGA-AF-2692 TCGA-AF-2693 
       10.39        19.99        15.95        36.03        13.55        37.97 
TCGA-AF-5654 TCGA-AF-A56K TCGA-AG-3575 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3594 
       16.83        86.63        12.00        24.00        46.03         2.01 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3881 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3999 
       19.99         7.99        19.04        17.95        35.01        28.04 
TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A016 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6644 
        1.02        46.03         9.07        41.00        38.04        27.55 
TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6154 TCGA-DC-6156 TCGA-DY-A1DD 
       47.44        78.12        21.01        12.00        31.00        57.24 
TCGA-DY-A1DE TCGA-EI-6885 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6863 
      129.27        13.64         9.96        49.51         0.39        11.87 

$`AMP PEAK 22(XQ27.3) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A01N 
        8.02        13.94        17.03        17.03        25.97        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       51.98        21.24        18.28        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       39.48        17.23        43.04        34.49        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       24.36        20.02        24.59        65.98        11.84        36.03 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3591 
       32.02         7.07        36.03        20.05         1.02        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
       34.03        34.03        50.04        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 
       15.95        20.98         0.99        29.98        37.02        32.98 
TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 
        0.99         0.99        19.99         1.02        36.95        13.02 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       14.01         1.02        48.03        25.02        32.02        19.99 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       36.03        14.04         3.98        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 
       38.96        61.97        38.56         2.50        43.20        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       19.46         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        7.17        25.05        26.04        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
      126.44        41.36        24.13        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        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-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 
       11.51        10.78        17.46        11.97         8.45        42.35 
TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
       28.57        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE 
                         0.39                          0.99 
  AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE 
                       129.27                        126.44 
  AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE 
                        20.50                         21.11 
[1] "0.4 - 129.3 (20.5)" "1.0 - 126.4 (21.1)"
[1] "hr=" "1.1"
D22V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  AMP PEAK 22(XQ27.3) MUTATED         8        2         6         0         0
  AMP PEAK 22(XQ27.3) WILD-TYPE      22        6        34         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  AMP PEAK 22(XQ27.3) MUTATED           0          0          8          4
  AMP PEAK 22(XQ27.3) WILD-TYPE         4          7         17         10
                               vv
clus                            STAGE IV STAGE IVA
  AMP PEAK 22(XQ27.3) MUTATED          5         2
  AMP PEAK 22(XQ27.3) WILD-TYPE       13         5
D22V3, multiclass
            clus
vv           AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE
  STAGE I                              8                            22
  STAGE II                             2                             6
  STAGE IIA                            6                            34
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            0                             4
  STAGE IIIA                           0                             7
  STAGE IIIB                           8                            17
  STAGE IIIC                           4                            10
  STAGE IV                             5                            13
  STAGE IVA                            2                             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
  AMP PEAK 22(XQ27.3) MUTATED    2  6 22  6
  AMP PEAK 22(XQ27.3) WILD-TYPE  7 22 90  8
D22V4, multiclass
    clus
vv   AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE
  T1                           2                             7
  T2                           6                            22
  T3                          22                            90
  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 22(XQ27.3) MUTATED   16 10  9
  AMP PEAK 22(XQ27.3) WILD-TYPE 68 35 24
D22V5, multiclass
    clus
vv   AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE
  N0                          16                            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"
D22V6, binary
                               cls
clus                             0  1
  AMP PEAK 22(XQ27.3) MUTATED   26  7
  AMP PEAK 22(XQ27.3) WILD-TYPE 99 17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(XQ27.3) MUTATED     26    7
  AMP PEAK 22(XQ27.3) WILD-TYPE   99   17
   clus
vv  AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE
  0                          26                            99
  1                           7                            17
[1] 2 2
[1] FALSE
D22V7, binary
                               cls
clus                             0  1
  AMP PEAK 22(XQ27.3) MUTATED   19 18
  AMP PEAK 22(XQ27.3) WILD-TYPE 57 71
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(XQ27.3) MUTATED     19   18
  AMP PEAK 22(XQ27.3) WILD-TYPE   57   71
        clus
vv       AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE
  FEMALE                          19                            57
  MALE                            18                            71
[1] 2 2
[1] FALSE
D22V8, binary
                               cls
clus                             0  1
  AMP PEAK 22(XQ27.3) MUTATED   25  4
  AMP PEAK 22(XQ27.3) WILD-TYPE 87 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(XQ27.3) MUTATED     25    4
  AMP PEAK 22(XQ27.3) WILD-TYPE   87   16
     clus
vv    AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE
  NO                           25                            87
  YES                           4                            16
[1] 2 2
[1] FALSE
D22V9, binary
                               cls
clus                              0   1
  AMP PEAK 22(XQ27.3) MUTATED    33   1
  AMP PEAK 22(XQ27.3) WILD-TYPE 113  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 22(XQ27.3) MUTATED     33    1
  AMP PEAK 22(XQ27.3) WILD-TYPE  113   12
                                clus
vv                               AMP PEAK 22(XQ27.3) MUTATED
  RECTAL ADENOCARCINOMA                                   33
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               AMP PEAK 22(XQ27.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    113
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 22(XQ27.3) MUTATED   26  0  4  1
  AMP PEAK 22(XQ27.3) WILD-TYPE 97  2  8  3
D22V10, multiclass
    clus
vv   AMP PEAK 22(XQ27.3) MUTATED AMP PEAK 22(XQ27.3) WILD-TYPE
  R0                          26                            97
  R1                           0                             2
  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"
D22V11, continuous

Clustering(23) Variable = DEL PEAK  1(1P36.11) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.11) MUTATED   57 13
  DEL PEAK  1(1P36.11) WILD-TYPE 74 14
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            70                             88 
  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                            13                             14 
$`DEL PEAK  1(1P36.11) MUTATED`
TCGA-AF-3913 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6641 
       10.39        17.03        25.97        51.98        21.24        26.43 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       46.92        17.23        43.04        13.55        37.97        29.98 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       24.36        86.63        65.98        11.84        32.02        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3609 
       20.05        24.00        46.03        34.03         6.05        19.99 
TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 
        0.99        29.98        37.02        19.04        19.99         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 
       36.95         1.02        48.03        25.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 
       36.03        13.94        23.01         1.94        38.96        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-4749 
       38.56        43.20        13.78        44.78        48.20        25.05 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 
       31.00        12.00        13.97        31.00        51.98        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EF-5830 
       25.97        25.05       126.44       129.27        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6511 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6702 
        4.18        20.55        15.85        11.97         8.45        28.57 
TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6864 TCGA-G5-6572 
       32.19        19.66        12.46        47.08 

$`DEL PEAK  1(1P36.11) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 
        8.02        13.94        19.99        17.03        15.95        36.03 
TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-3400 TCGA-AF-3911 
       31.00        18.28        55.76        39.48        34.49        37.74 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       16.83        20.02        24.59        36.03        12.00         7.07 
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-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3742 
        0.99        15.95        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-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
       37.02         9.07         1.02         1.02        49.97        61.97 
TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
       41.00         2.50        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 
       33.17        47.44        78.12         7.17        21.01        26.04 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       10.98        25.05        12.62        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
       51.48        19.96        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6810 
       13.64        17.46         9.96        49.51        42.35         0.39 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       36.49        37.18        38.14        11.87 

  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE 
                          0.99                           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 
                         25.97                          18.28 
[1] "1.0 - 129.3 (26.0)" "0.4 - 78.1 (18.3)" 
[1] "hr=" "1.1"
D23V2, 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         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  1(1P36.11) MUTATED           1          3         13          8
  DEL PEAK  1(1P36.11) WILD-TYPE         3          4         12          6
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK  1(1P36.11) MUTATED          8         5
  DEL PEAK  1(1P36.11) WILD-TYPE       10         2
D23V3, 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                              1
  STAGE III                             1                              3
  STAGE IIIA                            3                              4
  STAGE IIIB                           13                             12
  STAGE IIIC                            8                              6
  STAGE IV                              8                             10
  STAGE IVA                             5                              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  1(1P36.11) MUTATED    2 14 48 10
  DEL PEAK  1(1P36.11) WILD-TYPE  7 14 64  4
D23V4, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  T1                            2                              7
  T2                           14                             14
  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 50 23 15
D23V5, multiclass
    clus
vv   DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  N0                           34                             50
  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"
D23V6, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   55 13
  DEL PEAK  1(1P36.11) WILD-TYPE 70 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     55   13
  DEL PEAK  1(1P36.11) WILD-TYPE   70   11
   clus
vv  DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  0                           55                             70
  1                           13                             11
[1] 2 2
[1] FALSE
D23V7, 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
D23V8, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.11) MUTATED   50 11
  DEL PEAK  1(1P36.11) WILD-TYPE 62  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.11) MUTATED     50   11
  DEL PEAK  1(1P36.11) WILD-TYPE   62    9
     clus
vv    DEL PEAK  1(1P36.11) MUTATED DEL PEAK  1(1P36.11) WILD-TYPE
  NO                            50                             62
  YES                           11                              9
[1] 2 2
[1] FALSE
D23V9, 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
D23V10, 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"
D23V11, continuous

Clustering(24) Variable = DEL PEAK  2(1P33) MUTATION ANALYSIS
D24V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  2(1P33) MUTATED   40  9
  DEL PEAK  2(1P33) WILD-TYPE 91 18
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                         49                         109 
  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                          9                          18 
$`DEL PEAK  2(1P33) MUTATED`
TCGA-AG-A00H TCGA-BM-6198 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-4110 
       25.97        21.24        46.92        17.23        13.55        29.98 
TCGA-AF-6136 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       24.36        86.63        65.98        11.84        32.02        36.03 
TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 TCGA-AG-3882 
       24.00        34.03        29.98        37.02        19.04        19.99 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-A00Y 
        1.02        48.03        19.99        28.04        36.03        23.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6621 
        1.94        38.96        38.04        38.56        43.20        13.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 
       47.44        48.20        21.01        25.05        31.00        13.97 
TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 
       51.98        44.02       126.44       129.27         3.48        20.55 
TCGA-EI-6511 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6813 
       15.85        13.64        11.97        28.57        32.19        19.66 
TCGA-G5-6572 
       47.08 

$`DEL PEAK  2(1P33) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       26.43        39.48        43.04        37.97        34.49        37.74 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       16.83        20.02        24.59        36.03        12.00         7.07 
TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3594 
       20.05         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 
       20.98         7.99         0.99        32.98         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-3901 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       25.02        32.02        14.04         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       20.98        13.94         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
        1.02        49.97        61.97        41.00         2.50        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 
       26.43        19.46         6.05        33.17        44.78        78.12 
TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 
        7.17        26.04        12.00        31.00        10.98        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF 
       25.05        25.05        12.62        41.36        57.24        24.13 
TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 
       51.48        32.61         4.18        19.96        20.91        17.00 
TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 
       18.28        17.69        16.34        16.31        16.41         8.61 
TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       11.51        10.78        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       42.35         0.39        36.49        37.18        38.14        11.87 
TCGA-F5-6864 
       12.46 

  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE 
                       1.02                        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 
                      28.57                       19.46 
[1] "1.0 - 129.3 (28.6)" "0.4 - 78.1 (19.5)" 
[1] "hr=" "1.4"
D24V2, 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         1
                             vv
clus                          STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  2(1P33) MUTATED           0          1         10          6
  DEL PEAK  2(1P33) WILD-TYPE         4          6         15          8
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  2(1P33) MUTATED          6         2
  DEL PEAK  2(1P33) WILD-TYPE       12         5
D24V3, 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                           1
  STAGE III                          0                           4
  STAGE IIIA                         1                           6
  STAGE IIIB                        10                          15
  STAGE IIIC                         6                           8
  STAGE IV                           6                          12
  STAGE IVA                          2                           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  2(1P33) MUTATED    1  8 39  4
  DEL PEAK  2(1P33) WILD-TYPE  8 20 73 10
D24V4, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  T1                         1                           8
  T2                         8                          20
  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 59 27 24
D24V5, multiclass
    clus
vv   DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  N0                        25                          59
  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"
D24V6, binary
                             cls
clus                           0  1
  DEL PEAK  2(1P33) MUTATED   40  8
  DEL PEAK  2(1P33) WILD-TYPE 85 16
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     40    8
  DEL PEAK  2(1P33) WILD-TYPE   85   16
   clus
vv  DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  0                        40                          85
  1                         8                          16
[1] 2 2
[1] FALSE
D24V7, 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
D24V8, binary
                             cls
clus                           0  1
  DEL PEAK  2(1P33) MUTATED   36  7
  DEL PEAK  2(1P33) WILD-TYPE 76 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(1P33) MUTATED     36    7
  DEL PEAK  2(1P33) WILD-TYPE   76   13
     clus
vv    DEL PEAK  2(1P33) MUTATED DEL PEAK  2(1P33) WILD-TYPE
  NO                         36                          76
  YES                         7                          13
[1] 2 2
[1] FALSE
D24V9, 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
D24V10, 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"
D24V11, continuous

Clustering(25) Variable = DEL PEAK  3(1P13.2) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(1P13.2) MUTATED   38 13
  DEL PEAK  3(1P13.2) WILD-TYPE 93 14
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           51                           107 
  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                           13                            14 
$`DEL PEAK  3(1P13.2) MUTATED`
TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2692 
       25.97        21.24        18.28        46.92        17.23        13.55 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       29.98        24.36        65.98        11.84        32.02        36.03 
TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3881 
       24.00        34.03         2.01        29.98        37.02        19.04 
TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 
       19.99         1.02        19.99        28.04        36.03         3.98 
TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6623 
       23.01         1.94        38.04        38.56        43.20        47.44 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6160 TCGA-DY-A0XA 
       25.05        31.00        13.97        51.98        44.02       126.44 
TCGA-DY-A1DC TCGA-DY-A1DE TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6511 
       41.36       129.27         3.48        20.55        17.00        15.85 
TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       11.51        13.64        11.97        28.57        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6863 TCGA-G5-6572 
       19.66        11.87        47.08 

$`DEL PEAK  3(1P13.2) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 
       15.95        36.03        31.00        51.98        55.76        26.43 
TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       39.48        43.04        37.97        34.49        37.74        16.83 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       20.02        24.59        86.63        36.03        12.00         7.07 
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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       12.03         6.05         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3883 
        7.99         0.99        32.98         0.99         0.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       17.95        36.95        13.02        35.01        14.01        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 
       25.02        32.02        14.04         1.02        46.03        20.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       13.94         6.02        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
       49.97        38.96        61.97        41.00         2.50        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       48.20        78.12         7.17        21.01        26.04        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       31.00        10.98        25.97        25.05        25.05        12.62 
TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6507 
       57.24        24.13        51.48        32.61         4.18        19.96 
TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 
       20.91        18.28        17.69        16.34        16.31        16.41 
TCGA-EI-6882 TCGA-EI-6884 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
        8.61        10.78        17.46         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 
       42.35         0.39        37.18        38.14        12.46 

  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE 
                         1.02                          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 
                        25.05                         20.02 
[1] "1.0 - 129.3 (25.1)" "0.4 - 86.6 (20.0)" 
[1] "hr=" "1.7"
D25V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  3(1P13.2) MUTATED         6        2        16         1         1
  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         4          6         16          7
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  3(1P13.2) MUTATED          6         2
  DEL PEAK  3(1P13.2) WILD-TYPE       12         5
D25V3, 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                            1                             0
  STAGE III                            0                             4
  STAGE IIIA                           1                             6
  STAGE IIIB                           9                            16
  STAGE IIIC                           7                             7
  STAGE IV                             6                            12
  STAGE IVA                            2                             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  3(1P13.2) MUTATED    1  6 41  5
  DEL PEAK  3(1P13.2) WILD-TYPE  8 22 71  9
D25V4, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  T1                           1                             8
  T2                           6                            22
  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 58 30 21
D25V5, multiclass
    clus
vv   DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  N0                          26                            58
  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"
D25V6, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P13.2) MUTATED   42  8
  DEL PEAK  3(1P13.2) WILD-TYPE 83 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     42    8
  DEL PEAK  3(1P13.2) WILD-TYPE   83   16
   clus
vv  DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  0                          42                            83
  1                           8                            16
[1] 2 2
[1] FALSE
D25V7, 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
D25V8, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P13.2) MUTATED   38  7
  DEL PEAK  3(1P13.2) WILD-TYPE 74 13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P13.2) MUTATED     38    7
  DEL PEAK  3(1P13.2) WILD-TYPE   74   13
     clus
vv    DEL PEAK  3(1P13.2) MUTATED DEL PEAK  3(1P13.2) WILD-TYPE
  NO                           38                            74
  YES                           7                            13
[1] 2 2
[1] FALSE
D25V9, 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
D25V10, 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"
D25V11, continuous

Clustering(26) Variable = DEL PEAK  4(2P12) MUTATION ANALYSIS
D26V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  4(2P12) MUTATED    12   1
  DEL PEAK  4(2P12) WILD-TYPE 119  26
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                         13                         145 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                          1                          26 
$`DEL PEAK  4(2P12) MUTATED`
TCGA-AG-3611 TCGA-AG-A00H TCGA-AF-6136 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3600 
       13.94        25.97        24.36        32.02        36.03         6.05 
TCGA-AG-3609 TCGA-AG-3881 TCGA-AG-3896 TCGA-AG-3999 TCGA-AG-A02X TCGA-DC-6156 
       19.99        19.04         1.02        28.04        41.00        31.00 
TCGA-F5-6571 
       42.35 

$`DEL PEAK  4(2P12) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        19.99        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        16.83        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        86.63        65.98        11.84        36.03        12.00 
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-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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 
       15.95        20.98         7.99         0.99        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 
       36.95        13.02        35.01        14.01        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        49.97         1.94        38.96 
TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 
       61.97        38.04        38.56         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 
       26.43        19.46         6.05        33.17        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
       26.04        31.00        12.00        13.97        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       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 
        3.48         4.18        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-F5-6702 TCGA-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  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 
                      42.35                      129.27 
  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE 
                      25.97                       20.98 
[1] "1.0 - 42.4 (26.0)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.9"
D26V2, 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         1
                             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         4          7         24         11
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  4(2P12) MUTATED          1         1
  DEL PEAK  4(2P12) WILD-TYPE       17         6
D26V3, 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                           1
  STAGE III                          0                           4
  STAGE IIIA                         0                           7
  STAGE IIIB                         1                          24
  STAGE IIIC                         3                          11
  STAGE IV                           1                          17
  STAGE IVA                          1                           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  4(2P12) MUTATED     0   2  10   1
  DEL PEAK  4(2P12) WILD-TYPE   9  26 102  13
D26V4, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  T1                         0                           9
  T2                         2                          26
  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 77 43 29
D26V5, multiclass
    clus
vv   DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  N0                         7                          77
  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"
D26V6, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED    10   2
  DEL PEAK  4(2P12) WILD-TYPE 115  22
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED     10    2
  DEL PEAK  4(2P12) WILD-TYPE  115   22
   clus
vv  DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  0                        10                         115
  1                         2                          22
[1] 2 2
[1] FALSE
D26V7, 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
D26V8, binary
                             cls
clus                            0   1
  DEL PEAK  4(2P12) MUTATED     8   3
  DEL PEAK  4(2P12) WILD-TYPE 104  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  4(2P12) MUTATED      8    3
  DEL PEAK  4(2P12) WILD-TYPE  104   17
     clus
vv    DEL PEAK  4(2P12) MUTATED DEL PEAK  4(2P12) WILD-TYPE
  NO                          8                         104
  YES                         3                          17
[1] 2 2
[1] FALSE
D26V9, 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
D26V10, 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"
D26V11, continuous

Clustering(27) Variable = DEL PEAK  5(3P14.2) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P14.2) MUTATED    26   5
  DEL PEAK  5(3P14.2) WILD-TYPE 105  22
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                           31                           127 
  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                            5                            22 
$`DEL PEAK  5(3P14.2) MUTATED`
TCGA-AG-3580 TCGA-AG-4008 TCGA-BM-6198 TCGA-G5-6233 TCGA-AF-2691 TCGA-AF-2693 
        8.02        17.03        21.24        18.28        43.04        37.97 
TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3581 TCGA-AG-3583 
       34.49        29.98        86.63        11.84         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3592 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 
       24.00        34.03        37.02        32.98        19.04        19.99 
TCGA-AG-3885 TCGA-AG-4007 TCGA-AG-A00C TCGA-AG-A02G TCGA-AH-6544 TCGA-CI-6619 
       17.95         1.02         6.02        38.96        38.56         6.05 
TCGA-CI-6623 TCGA-DC-5337 TCGA-DC-6158 TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6508 
       47.44        26.04        10.98        25.05        12.62        20.91 
TCGA-F5-6810 
        0.39 

$`DEL PEAK  5(3P14.2) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A014 
       10.39        13.94        19.99        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 
       36.03        31.00        51.98        55.76        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 
       39.48        17.23        13.55        37.74        16.83        24.36 
TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 
       20.02        24.59        65.98        36.03        12.00        32.02 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 
       36.03         1.02        46.03        34.03        34.03         2.01 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       50.04        12.03         6.05         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3878 
       20.98         7.99         0.99        29.98         0.99         0.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
        1.02        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00Y 
       14.04         3.98        46.03        20.98        13.94        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        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         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       26.43        19.46        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        21.01        25.05        31.00        12.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       13.97        31.00        51.98        44.02        25.97        25.05 
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         3.48         4.18        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        42.35        28.57        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        37.18        38.14        11.87        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE 
                         0.39                          0.99 
  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 
                        20.91                         21.01 
[1] "0.4 - 86.6 (20.9)"  "1.0 - 129.3 (21.0)"
[1] "hr=" "1.1"
D27V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  5(3P14.2) MUTATED         9        1         7         0         0
  DEL PEAK  5(3P14.2) WILD-TYPE      21        7        33         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         4          7         21         14
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  5(3P14.2) MUTATED          6         1
  DEL PEAK  5(3P14.2) WILD-TYPE       12         6
D27V3, 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                            7                            33
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            0                             4
  STAGE IIIA                           0                             7
  STAGE IIIB                           4                            21
  STAGE IIIC                           0                            14
  STAGE IV                             6                            12
  STAGE IVA                            1                             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  5(3P14.2) MUTATED    4  6 18  2
  DEL PEAK  5(3P14.2) WILD-TYPE  5 22 94 12
D27V4, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  T1                           4                             5
  T2                           6                            22
  T3                          18                            94
  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   17  8  5
  DEL PEAK  5(3P14.2) WILD-TYPE 67 37 28
D27V5, multiclass
    clus
vv   DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  N0                          17                            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"
D27V6, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P14.2) MUTATED    20   7
  DEL PEAK  5(3P14.2) WILD-TYPE 105  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     20    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                          20                           105
  1                           7                            17
[1] 2 2
[1] FALSE
D27V7, 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
D27V8, binary
                               cls
clus                             0  1
  DEL PEAK  5(3P14.2) MUTATED   22  5
  DEL PEAK  5(3P14.2) WILD-TYPE 90 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P14.2) MUTATED     22    5
  DEL PEAK  5(3P14.2) WILD-TYPE   90   15
     clus
vv    DEL PEAK  5(3P14.2) MUTATED DEL PEAK  5(3P14.2) WILD-TYPE
  NO                           22                            90
  YES                           5                            15
[1] 2 2
[1] FALSE
D27V9, 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
D27V10, 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"
D27V11, continuous

Clustering(28) Variable = DEL PEAK  6(3Q26.31) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  6(3Q26.31) MUTATED    15   3
  DEL PEAK  6(3Q26.31) WILD-TYPE 116  24
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                            18                            140 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                             3                             24 
$`DEL PEAK  6(3Q26.31) MUTATED`
TCGA-AG-A014 TCGA-G5-6233 TCGA-AF-3400 TCGA-AF-4110 TCGA-AG-3578 TCGA-AG-3583 
       15.95        18.28        34.49        29.98        32.02        20.05 
TCGA-AG-3731 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A02G TCGA-CI-6619 
       37.02        36.03        14.04         1.02        38.96         6.05 
TCGA-DC-6682 TCGA-DT-5265 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-7002 
       25.05        12.62        19.96        20.91         8.61        11.97 

$`DEL PEAK  6(3Q26.31) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       25.97        36.03        31.00        51.98        21.24        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.97        37.74        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       86.63        65.98        11.84        36.03        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        20.98         7.99         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-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4021 
       48.03        25.02        32.02        19.99        28.04         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N 
        9.07         1.02         1.02        49.97         1.94        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         2.50        43.20        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46        33.17        13.78        44.78        47.44 
TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       48.20        78.12         7.17        21.01        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.97        25.05       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         3.48         4.18 
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        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
       32.19        36.49        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                          1.02                           0.39 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                         38.96                         129.27 
  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE 
                        20.005                         22.125 
[1] "1.0 - 39.0 (20.0)"  "0.4 - 129.3 (22.1)"
[1] "hr=" "1.6"
D28V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  6(3Q26.31) MUTATED         1        1         6         0         0
  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          0
  DEL PEAK  6(3Q26.31) WILD-TYPE         4          7         24         14
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK  6(3Q26.31) MUTATED          7         1
  DEL PEAK  6(3Q26.31) WILD-TYPE       11         6
D28V3, 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                             0                              1
  STAGE III                             0                              4
  STAGE IIIA                            0                              7
  STAGE IIIB                            1                             24
  STAGE IIIC                            0                             14
  STAGE IV                              7                             11
  STAGE IVA                             1                              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  6(3Q26.31) MUTATED    0  2 14  2
  DEL PEAK  6(3Q26.31) WILD-TYPE  9 26 98 12
D28V4, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  T1                            0                              9
  T2                            2                             26
  T3                           14                             98
  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  6(3Q26.31) MUTATED    8  4  6
  DEL PEAK  6(3Q26.31) WILD-TYPE 76 41 27
D28V5, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  N0                            8                             76
  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"
D28V6, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q26.31) MUTATED    10   7
  DEL PEAK  6(3Q26.31) WILD-TYPE 115  17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED     10    7
  DEL PEAK  6(3Q26.31) WILD-TYPE  115   17
   clus
vv  DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  0                           10                            115
  1                            7                             17
[1] 2 2
[1] FALSE
D28V7, binary
                                cls
clus                              0  1
  DEL PEAK  6(3Q26.31) MUTATED    3 15
  DEL PEAK  6(3Q26.31) WILD-TYPE 73 74
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED      3   15
  DEL PEAK  6(3Q26.31) WILD-TYPE   73   74
        clus
vv       DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  FEMALE                            3                             73
  MALE                             15                             74
[1] 2 2
[1] FALSE
D28V8, binary
                                cls
clus                              0  1
  DEL PEAK  6(3Q26.31) MUTATED   13  2
  DEL PEAK  6(3Q26.31) WILD-TYPE 99 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED     13    2
  DEL PEAK  6(3Q26.31) WILD-TYPE   99   18
     clus
vv    DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  NO                            13                             99
  YES                            2                             18
[1] 2 2
[1] FALSE
D28V9, binary
                                cls
clus                               0   1
  DEL PEAK  6(3Q26.31) MUTATED    12   5
  DEL PEAK  6(3Q26.31) WILD-TYPE 134   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  6(3Q26.31) MUTATED     12    5
  DEL PEAK  6(3Q26.31) WILD-TYPE  134    8
                                clus
vv                               DEL PEAK  6(3Q26.31) MUTATED
  RECTAL ADENOCARCINOMA                                    12
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK  6(3Q26.31) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     134
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK  6(3Q26.31) MUTATED    12   0   4   1
  DEL PEAK  6(3Q26.31) WILD-TYPE 111   2   8   3
D28V10, multiclass
    clus
vv   DEL PEAK  6(3Q26.31) MUTATED DEL PEAK  6(3Q26.31) WILD-TYPE
  R0                           12                            111
  R1                            0                              2
  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"
D28V11, continuous

Clustering(29) Variable = DEL PEAK  7(4P13) MUTATION ANALYSIS
D29V1, survival
                             sevent
clus2                          0  1
  DEL PEAK  7(4P13) MUTATED   49  8
  DEL PEAK  7(4P13) WILD-TYPE 82 19
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                         57                         101 
  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                          8                          19 
$`DEL PEAK  7(4P13) MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6641 
       13.94        19.99        17.03        25.97        21.24        26.43 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       46.92        17.23        43.04        34.49        37.74        29.98 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3582 TCGA-AG-3592 TCGA-AG-3593 
       24.36        24.59        65.98        36.03        34.03        34.03 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 
       20.98        29.98        37.02        32.98        19.04         1.02 
TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3909 
       17.95        35.01         1.02        48.03        32.02        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A02G 
       28.04        36.03        14.04        13.94        23.01        38.96 
TCGA-AG-A02X TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 TCGA-DC-5869 TCGA-DC-6156 
       41.00        43.20         6.05        33.17        31.00        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 
       51.98        10.98        44.02       126.44       129.27        32.61 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6571 
        4.18        15.85        16.34        16.41        11.97        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6813 
       28.57         0.39        19.66 

$`DEL PEAK  7(4P13) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       10.39         8.02        17.03        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 
       51.98        18.28        55.76        39.48        13.55        37.97 
TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       16.83        20.02        86.63        11.84        36.03        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       32.02         7.07        20.05        24.00         1.02        46.03 
TCGA-AG-3591 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-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-4007 
       19.99        36.95        13.02        14.01        25.02         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 
        3.98        46.03        20.98         6.02        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 
        1.02         1.02        49.97         1.94        61.97        38.04 
TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6621 
       38.56         2.50        27.55        26.43        19.46        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6682 
       25.05        26.04        12.00        13.97        25.97        25.05 
TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       25.05        12.62        41.36        57.24        24.13        51.48 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        3.48        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 
       17.46         8.45         9.96        49.51        32.19        36.49 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        11.87        12.46        47.08 

  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE 
                       0.39                        0.99 
  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 
                      28.57                       19.96 
[1] "0.4 - 129.3 (28.6)" "1.0 - 86.6 (20.0)" 
[1] "hr=" "1.6"
D29V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  7(4P13) MUTATED        10        1        15         0         0
  DEL PEAK  7(4P13) WILD-TYPE      20        7        25         2         1
                             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         3          4         14          7
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK  7(4P13) MUTATED          7         4
  DEL PEAK  7(4P13) WILD-TYPE       11         3
D29V3, multiclass
            clus
vv           DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  STAGE I                           10                          20
  STAGE II                           1                           7
  STAGE IIA                         15                          25
  STAGE IIB                          0                           2
  STAGE IIC                          0                           1
  STAGE III                          1                           3
  STAGE IIIA                         3                           4
  STAGE IIIB                        11                          14
  STAGE IIIC                         7                           7
  STAGE IV                           7                          11
  STAGE IVA                          4                           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  7(4P13) MUTATED    2 11 42  4
  DEL PEAK  7(4P13) WILD-TYPE  7 17 70 10
D29V4, multiclass
    clus
vv   DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  T1                         2                           7
  T2                        11                          17
  T3                        42                          70
  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   26 20 13
  DEL PEAK  7(4P13) WILD-TYPE 58 25 20
D29V5, multiclass
    clus
vv   DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  N0                        26                          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"
D29V6, binary
                             cls
clus                           0  1
  DEL PEAK  7(4P13) MUTATED   44  9
  DEL PEAK  7(4P13) WILD-TYPE 81 15
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED     44    9
  DEL PEAK  7(4P13) WILD-TYPE   81   15
   clus
vv  DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  0                        44                          81
  1                         9                          15
[1] 2 2
[1] FALSE
D29V7, 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
D29V8, binary
                             cls
clus                           0  1
  DEL PEAK  7(4P13) MUTATED   40  9
  DEL PEAK  7(4P13) WILD-TYPE 72 11
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  7(4P13) MUTATED     40    9
  DEL PEAK  7(4P13) WILD-TYPE   72   11
     clus
vv    DEL PEAK  7(4P13) MUTATED DEL PEAK  7(4P13) WILD-TYPE
  NO                         40                          72
  YES                         9                          11
[1] 2 2
[1] FALSE
D29V9, 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
D29V10, 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"
D29V11, continuous

Clustering(30) Variable = DEL PEAK  8(4Q22.1) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(4Q22.1) MUTATED   60  8
  DEL PEAK  8(4Q22.1) WILD-TYPE 71 19
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                           68                            90 
  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                            8                            19 
$`DEL PEAK  8(4Q22.1) MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 
       13.94        19.99        17.03        25.97        21.24        18.28 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       26.43        46.92        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 
       34.49        37.74        29.98        24.36        65.98        36.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3732 
       34.03        34.03         6.05        20.98        29.98        32.98 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3909 
       19.04         1.02        17.95         1.02        48.03        19.99 
TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C 
       28.04        36.03        14.04         1.02        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 
       23.01         1.94        41.00        38.56        43.20         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 
       33.17        13.78        48.20        25.05        31.00        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DE 
       51.98        10.98        44.02        25.05       126.44       129.27 
TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6881 
        4.18        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        42.35        28.57         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 
       36.49        19.66 

$`DEL PEAK  8(4Q22.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
       10.39         8.02        17.03        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       51.98        55.76        39.48        16.83        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        36.03        12.00        32.02         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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4021 
       13.02        35.01        14.01        25.02        32.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       46.03        20.98        37.02         9.07         1.02         1.02 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
       49.97        38.96        61.97        38.04         2.50        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 
       26.43        19.46        44.78        47.44        78.12         7.17 
TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 TCGA-DC-6683 
       21.01        26.04        12.00        13.97        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 
       12.62        41.36        57.24        24.13        51.48        32.61 
TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6514 
        3.48        20.55        19.96        18.28        17.69        16.31 
TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-F5-6464 
        8.61        11.51        10.78        13.64        17.46         9.96 
TCGA-F5-6465 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       49.51        37.18        38.14        11.87        12.46        47.08 

  DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE 
                         0.39                          0.99 
  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 
                       24.705                        20.035 
[1] "0.4 - 129.3 (24.7)" "1.0 - 86.6 (20.0)" 
[1] "hr=" "1.8"
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  8(4Q22.1) MUTATED        12        3        19         0         0
  DEL PEAK  8(4Q22.1) WILD-TYPE      18        5        21         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  8(4Q22.1) MUTATED           1          2         14          9
  DEL PEAK  8(4Q22.1) WILD-TYPE         3          5         11          5
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  8(4Q22.1) MUTATED          5         4
  DEL PEAK  8(4Q22.1) WILD-TYPE       13         3
D30V3, 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                           19                            21
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            1                             3
  STAGE IIIA                           2                             5
  STAGE IIIB                          14                            11
  STAGE IIIC                           9                             5
  STAGE IV                             5                            13
  STAGE IVA                            4                             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  8(4Q22.1) MUTATED    2 11 52  7
  DEL PEAK  8(4Q22.1) WILD-TYPE  7 17 60  7
D30V4, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  T1                           2                             7
  T2                          11                            17
  T3                          52                            60
  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   34 21 17
  DEL PEAK  8(4Q22.1) WILD-TYPE 50 24 16
D30V5, multiclass
    clus
vv   DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  N0                          34                            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"
D30V6, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   56  9
  DEL PEAK  8(4Q22.1) WILD-TYPE 69 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     56    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                          56                            69
  1                           9                            15
[1] 2 2
[1] FALSE
D30V7, 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
D30V8, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q22.1) MUTATED   47 10
  DEL PEAK  8(4Q22.1) WILD-TYPE 65 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q22.1) MUTATED     47   10
  DEL PEAK  8(4Q22.1) WILD-TYPE   65   10
     clus
vv    DEL PEAK  8(4Q22.1) MUTATED DEL PEAK  8(4Q22.1) WILD-TYPE
  NO                           47                            65
  YES                          10                            10
[1] 2 2
[1] FALSE
D30V9, 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
D30V10, 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"
D30V11, continuous

Clustering(31) Variable = DEL PEAK  9(4Q35.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(4Q35.1) MUTATED   57 10
  DEL PEAK  9(4Q35.1) WILD-TYPE 74 17
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           67                            91 
  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                           10                            17 
$`DEL PEAK  9(4Q35.1) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 
       10.39        13.94        19.99        25.97        21.24        18.28 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 
       26.43        46.92        17.23        43.04        13.55        37.97 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-A56L TCGA-AG-3582 
       34.49        37.74        29.98        24.36        65.98        36.03 
TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3728 
       46.03        34.03        34.03         6.05        20.98        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3898 
       32.98         0.99        19.04         1.02        17.95        48.03 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4021 TCGA-AG-A008 
       19.99        28.04        36.03        14.04         3.98        13.94 
TCGA-AG-A00Y TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6620 
       23.01        41.00        38.56        43.20         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6156 TCGA-DC-6157 
       13.78        48.20        25.05        31.00        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 
       10.98        44.02       126.44       129.27        24.13         4.18 
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 
       42.35        28.57         0.39        32.19        36.49        37.18 
TCGA-F5-6864 
       12.46 

$`DEL PEAK  9(4Q35.1) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
        8.02        17.03        17.03        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 
       51.98        55.76        39.48        16.83        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       86.63        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 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-3726 TCGA-AG-3727 
       12.03         0.99        15.95        19.99         7.99         0.99 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       37.02         0.99        19.99        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4022 
       14.01         1.02        25.02        32.02         1.02        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
       20.98         6.02        37.02         9.07         1.02         1.02 
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         2.50 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
       27.55        26.43        19.46        44.78        47.44        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6681 
        7.17        21.01        26.04        12.00        13.97        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       25.05        25.05        12.62        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         3.48        20.55        19.96        20.91        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       17.69        16.31         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 
       17.46         8.45        49.51        19.66        38.14        11.87 
TCGA-G5-6572 
       47.08 

  DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE 
                         0.39                          0.99 
  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 
                        25.97                         19.99 
[1] "0.4 - 129.3 (26.0)" "1.0 - 86.6 (20.0)" 
[1] "hr=" "1.4"
D31V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK  9(4Q35.1) MUTATED        13        2        18         0         0
  DEL PEAK  9(4Q35.1) WILD-TYPE      17        6        22         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK  9(4Q35.1) MUTATED           1          2         13         10
  DEL PEAK  9(4Q35.1) WILD-TYPE         3          5         12          4
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK  9(4Q35.1) MUTATED          6         4
  DEL PEAK  9(4Q35.1) WILD-TYPE       12         3
D31V3, 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                           18                            22
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            1                             3
  STAGE IIIA                           2                             5
  STAGE IIIB                          13                            12
  STAGE IIIC                          10                             4
  STAGE IV                             6                            12
  STAGE IVA                            4                             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  9(4Q35.1) MUTATED    3 11 53  4
  DEL PEAK  9(4Q35.1) WILD-TYPE  6 17 59 10
D31V4, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  T1                           3                             6
  T2                          11                            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   33 20 18
  DEL PEAK  9(4Q35.1) WILD-TYPE 51 25 15
D31V5, multiclass
    clus
vv   DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  N0                          33                            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"
D31V6, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   54 10
  DEL PEAK  9(4Q35.1) WILD-TYPE 71 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     54   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                          54                            71
  1                          10                            14
[1] 2 2
[1] FALSE
D31V7, 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
D31V8, binary
                               cls
clus                             0  1
  DEL PEAK  9(4Q35.1) MUTATED   47 10
  DEL PEAK  9(4Q35.1) WILD-TYPE 65 10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q35.1) MUTATED     47   10
  DEL PEAK  9(4Q35.1) WILD-TYPE   65   10
     clus
vv    DEL PEAK  9(4Q35.1) MUTATED DEL PEAK  9(4Q35.1) WILD-TYPE
  NO                           47                            65
  YES                          10                            10
[1] 2 2
[1] FALSE
D31V9, 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
D31V10, 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"
D31V11, continuous

Clustering(32) Variable = DEL PEAK 10(5Q12.1) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(5Q12.1) MUTATED   40 10
  DEL PEAK 10(5Q12.1) WILD-TYPE 91 17
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                           50                           108 
  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE 
                           10                            17 
$`DEL PEAK 10(5Q12.1) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-BM-6198 TCGA-G5-6233 
       10.39        13.94        17.03        17.03        21.24        18.28 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 
       26.43        46.92        17.23        43.04        37.74        24.36 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AG-3591 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 
       24.59        86.63        34.03        20.98        29.98        37.02 
TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3999 
       32.98        19.04        19.99         1.02        48.03        28.04 
TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
       36.03         3.98        23.01         1.94        38.96        41.00 
TCGA-CI-6620 TCGA-CL-5918 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       33.17         7.17        31.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG 
       10.98        25.05       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 
       28.57        32.19 

$`DEL PEAK 10(5Q12.1) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N 
        8.02        19.99        25.97        15.95        36.03        31.00 
TCGA-AG-A023 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       51.98        55.76        39.48        13.55        37.97        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       29.98        16.83        20.02        65.98        11.84        36.03 
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-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-3600 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 
       12.03         6.05         0.99        15.95        19.99         7.99 
TCGA-AG-3727 TCGA-AG-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-3901 TCGA-AG-3902 TCGA-AG-3909 
       13.02        35.01        14.01        25.02        32.02        19.99 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
       14.04         1.02        46.03        20.98        13.94         6.02 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
       37.02         9.07         1.02         1.02        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         2.50        43.20        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
       19.46         6.05        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 
       78.12        21.01        25.05        26.04        12.00        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DF TCGA-DY-A1H8 
       25.97        25.05        12.62        41.36        24.13        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        3.48         4.18        19.96        20.91        17.00        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-6917 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6812 
       10.78        17.46         9.96        42.35         0.39        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        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 
                        25.74                         19.99 
[1] "1.0 - 129.3 (25.7)" "0.4 - 78.1 (20.0)" 
[1] "hr=" "1"  
D32V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 10(5Q12.1) MUTATED         8        3        16         0         0
  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         3          4         20         10
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 10(5Q12.1) MUTATED          7         4
  DEL PEAK 10(5Q12.1) WILD-TYPE       11         3
D32V3, 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                            0                             1
  STAGE III                            1                             3
  STAGE IIIA                           3                             4
  STAGE IIIB                           5                            20
  STAGE IIIC                           4                            10
  STAGE IV                             7                            11
  STAGE IVA                            4                             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 10(5Q12.1) MUTATED    2  9 38  4
  DEL PEAK 10(5Q12.1) WILD-TYPE  7 19 74 10
D32V4, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  T1                           2                             7
  T2                           9                            19
  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 57 30 22
D32V5, multiclass
    clus
vv   DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  N0                          27                            57
  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"
D32V6, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q12.1) MUTATED   37 10
  DEL PEAK 10(5Q12.1) WILD-TYPE 88 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED     37   10
  DEL PEAK 10(5Q12.1) WILD-TYPE   88   14
   clus
vv  DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  0                          37                            88
  1                          10                            14
[1] 2 2
[1] FALSE
D32V7, 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
D32V8, binary
                               cls
clus                             0  1
  DEL PEAK 10(5Q12.1) MUTATED   38  5
  DEL PEAK 10(5Q12.1) WILD-TYPE 74 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(5Q12.1) MUTATED     38    5
  DEL PEAK 10(5Q12.1) WILD-TYPE   74   15
     clus
vv    DEL PEAK 10(5Q12.1) MUTATED DEL PEAK 10(5Q12.1) WILD-TYPE
  NO                           38                            74
  YES                           5                            15
[1] 2 2
[1] FALSE
D32V9, 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
D32V10, 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"
D32V11, continuous

Clustering(33) Variable = DEL PEAK 11(5Q22.2) MUTATION ANALYSIS
D33V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(5Q22.2) MUTATED   42 12
  DEL PEAK 11(5Q22.2) WILD-TYPE 89 15
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           54                           104 
  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE 
                           12                            15 
$`DEL PEAK 11(5Q22.2) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-BM-6198 
       10.39        13.94        19.99        17.03        17.03        21.24 
TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-6136 
       18.28        46.92        17.23        43.04        37.74        24.36 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3725 
       24.59        86.63        65.98        32.02        34.03        20.98 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 
       29.98        37.02        32.98        19.04        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A00C TCGA-AG-A00Y 
       48.03        28.04        36.03         3.98         6.02        23.01 
TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6903 TCGA-CI-6620 TCGA-CL-5918 
        1.94        38.96        41.00        19.46        33.17         7.17 
TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       31.00        13.97        31.00        51.98        10.98        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG TCGA-EI-6506 TCGA-EI-6507 
      126.44        41.36        57.24        51.48        20.55        19.96 
TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6881 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6864 
       18.28        16.34        16.41         9.96        28.57        12.46 

$`DEL PEAK 11(5Q22.2) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
        8.02        25.97        15.95        36.03        31.00        51.98 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       55.76        26.43        39.48        13.55        37.97        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       29.98        16.83        20.02        11.84        36.03        12.00 
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-3592 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 
       34.03        34.03         2.01        50.04        12.03         6.05 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3742 
        0.99        15.95        19.99         7.99         0.99         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-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-4005 TCGA-AG-4007 
       14.01        25.02        32.02        19.99        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98        13.94        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 
        1.02        49.97        61.97        38.04        38.56         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6622 
       43.20        27.55        26.43         6.05        13.78        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 
       47.44        48.20        78.12        21.01        25.05        26.04 
TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A1DE 
       12.00        44.02        25.97        25.05        12.62       129.27 
TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6508 TCGA-EI-6509 
       24.13        32.61         3.48         4.18        20.91        17.00 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.31         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         8.45        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-G5-6572 
       11.87        47.08 

  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 
                       23.685                        20.480 
[1] "1.0 - 126.4 (23.7)" "0.4 - 129.3 (20.5)"
[1] "hr=" "1.3"
D33V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 11(5Q22.2) MUTATED         8        3        16         0         0
  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         3          5         13          8
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 11(5Q22.2) MUTATED          5         4
  DEL PEAK 11(5Q22.2) WILD-TYPE       13         3
D33V3, 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                            0                             1
  STAGE III                            1                             3
  STAGE IIIA                           2                             5
  STAGE IIIB                          12                            13
  STAGE IIIC                           6                             8
  STAGE IV                             5                            13
  STAGE IVA                            4                             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 11(5Q22.2) MUTATED    1 10 43  5
  DEL PEAK 11(5Q22.2) WILD-TYPE  8 18 69  9
D33V4, multiclass
    clus
vv   DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  T1                           1                             8
  T2                          10                            18
  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 56 26 21
D33V5, multiclass
    clus
vv   DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  N0                          28                            56
  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"
D33V6, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q22.2) MUTATED   45  8
  DEL PEAK 11(5Q22.2) WILD-TYPE 80 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED     45    8
  DEL PEAK 11(5Q22.2) WILD-TYPE   80   16
   clus
vv  DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  0                          45                            80
  1                           8                            16
[1] 2 2
[1] FALSE
D33V7, 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
D33V8, binary
                               cls
clus                             0  1
  DEL PEAK 11(5Q22.2) MUTATED   41  6
  DEL PEAK 11(5Q22.2) WILD-TYPE 71 14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(5Q22.2) MUTATED     41    6
  DEL PEAK 11(5Q22.2) WILD-TYPE   71   14
     clus
vv    DEL PEAK 11(5Q22.2) MUTATED DEL PEAK 11(5Q22.2) WILD-TYPE
  NO                           41                            71
  YES                           6                            14
[1] 2 2
[1] FALSE
D33V9, 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
D33V10, 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"
D33V11, continuous

Clustering(34) Variable = DEL PEAK 12(6P25.3) MUTATION ANALYSIS
D34V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(6P25.3) MUTATED    19   4
  DEL PEAK 12(6P25.3) WILD-TYPE 112  23
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                           23                           135 
  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE 
                            4                            23 
$`DEL PEAK 12(6P25.3) MUTATED`
TCGA-AG-3611 TCGA-BM-6198 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       13.94        21.24        17.23        13.55        37.97        34.49 
TCGA-AF-4110 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 
       29.98        24.00        34.03        34.03        34.03        50.04 
TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A011 TCGA-CI-6621 TCGA-DC-4745 
       36.03         3.98        13.94        37.02        13.78        21.01 
TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A1DF TCGA-EI-6511 TCGA-EI-6883 
       25.05        12.62        24.13        15.85        11.51 

$`DEL PEAK 12(6P25.3) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2691 TCGA-AF-3911 TCGA-AF-5654 
       26.43        46.92        39.48        43.04        37.74        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       36.03        12.00        32.02         7.07        36.03        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3594 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3605 
        1.02        46.03         2.01        12.03         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
       15.95        19.99        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-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
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-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
       14.04         1.02        46.03        20.98         6.02        23.01 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        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         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       27.55        26.43        19.46         6.05        33.17        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 
       47.44        48.20        78.12         7.17        25.05        26.04 
TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 
       31.00        12.00        13.97        31.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.97        25.05       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         3.48         4.18        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        42.35        28.57 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        0.39        32.19        36.49        19.66        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  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 
                        24.00                         20.91 
[1] "4.0 - 50.0 (24.0)"  "0.4 - 129.3 (20.9)"
[1] "hr=" "1.4"
D34V2, 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         0
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 12(6P25.3) MUTATED           0          0          4          2
  DEL PEAK 12(6P25.3) WILD-TYPE         4          7         21         12
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 12(6P25.3) MUTATED          2         1
  DEL PEAK 12(6P25.3) WILD-TYPE       16         6
D34V3, 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                             0
  STAGE III                            0                             4
  STAGE IIIA                           0                             7
  STAGE IIIB                           4                            21
  STAGE IIIC                           2                            12
  STAGE IV                             2                            16
  STAGE IVA                            1                             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 12(6P25.3) MUTATED    0  2 21  1
  DEL PEAK 12(6P25.3) WILD-TYPE  9 26 91 13
D34V4, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  T1                           0                             9
  T2                           2                            26
  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 69 41 28
D34V5, multiclass
    clus
vv   DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  N0                          15                            69
  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"
D34V6, binary
                               cls
clus                              0   1
  DEL PEAK 12(6P25.3) MUTATED    18   2
  DEL PEAK 12(6P25.3) WILD-TYPE 107  22
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     18    2
  DEL PEAK 12(6P25.3) WILD-TYPE  107   22
   clus
vv  DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  0                          18                           107
  1                           2                            22
[1] 2 2
[1] FALSE
D34V7, 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
D34V8, binary
                               cls
clus                             0  1
  DEL PEAK 12(6P25.3) MUTATED   16  5
  DEL PEAK 12(6P25.3) WILD-TYPE 96 15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(6P25.3) MUTATED     16    5
  DEL PEAK 12(6P25.3) WILD-TYPE   96   15
     clus
vv    DEL PEAK 12(6P25.3) MUTATED DEL PEAK 12(6P25.3) WILD-TYPE
  NO                           16                            96
  YES                           5                            15
[1] 2 2
[1] FALSE
D34V9, 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
D34V10, 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"
D34V11, continuous

Clustering(35) Variable = DEL PEAK 13(6Q26) MUTATION ANALYSIS
D35V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(6Q26) MUTATED    23   5
  DEL PEAK 13(6Q26) WILD-TYPE 108  22
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                         28                         130 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                          5                          22 
$`DEL PEAK 13(6Q26) MUTATED`
TCGA-AG-3611 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       13.94        18.28        26.43        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3584 
       37.97        34.49        37.74        12.00        32.02        24.00 
TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3609 
       46.03        34.03        34.03         2.01         6.05        19.99 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A011 TCGA-AH-6544 TCGA-AH-6644 
       14.04         1.02        13.94        37.02        38.56        27.55 
TCGA-CI-6623 TCGA-DC-6682 TCGA-DT-5265 TCGA-F5-6863 
       47.44        25.05        12.62        11.87 

$`DEL PEAK 13(6Q26) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        21.24        55.76 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 
       46.92        39.48        29.98        16.83        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 
       24.59        86.63        65.98        11.84        36.03         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3599 
       36.03        20.05         1.02        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        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-3882 
       37.02        32.98         0.99         0.99        19.04        19.99 
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-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
       36.03         3.98        46.03        20.98         6.02        23.01 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G 
        9.07         1.02         1.02        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         2.50        43.20        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 
       19.46         6.05        33.17        13.78        44.78        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE 
       25.97        25.05       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         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       19.96        20.91        17.00        18.28        15.85        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       16.34        16.31        16.41         8.61        11.51        10.78 
TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 
       13.64        17.46        11.97         8.45         9.96        49.51 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57         0.39        32.19        36.49        19.66 
TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       37.18        38.14        12.46        47.08 

  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                       1.02                        0.39 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                      47.44                      129.27 
  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE 
                     24.525                      20.980 
[1] "1.0 - 47.4 (24.5)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.3"
D35V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 13(6Q26) MUTATED         5        2         9         0         0
  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         4          6         23          9
                             vv
clus                          STAGE IV STAGE IVA
  DEL PEAK 13(6Q26) MUTATED          3         0
  DEL PEAK 13(6Q26) WILD-TYPE       15         7
D35V3, 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                          0                           1
  STAGE III                          0                           4
  STAGE IIIA                         1                           6
  STAGE IIIB                         2                          23
  STAGE IIIC                         5                           9
  STAGE IV                           3                          15
  STAGE IVA                          0                           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 13(6Q26) MUTATED    3  3 21  3
  DEL PEAK 13(6Q26) WILD-TYPE  6 25 91 11
D35V4, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  T1                         3                           6
  T2                         3                          25
  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 68 41 24
D35V5, multiclass
    clus
vv   DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  N0                        16                          68
  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"
D35V6, binary
                             cls
clus                            0   1
  DEL PEAK 13(6Q26) MUTATED    22   4
  DEL PEAK 13(6Q26) WILD-TYPE 103  20
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     22    4
  DEL PEAK 13(6Q26) WILD-TYPE  103   20
   clus
vv  DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  0                        22                         103
  1                         4                          20
[1] 2 2
[1] FALSE
D35V7, 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
D35V8, binary
                             cls
clus                           0  1
  DEL PEAK 13(6Q26) MUTATED   19  7
  DEL PEAK 13(6Q26) WILD-TYPE 93 13
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(6Q26) MUTATED     19    7
  DEL PEAK 13(6Q26) WILD-TYPE   93   13
     clus
vv    DEL PEAK 13(6Q26) MUTATED DEL PEAK 13(6Q26) WILD-TYPE
  NO                         19                          93
  YES                         7                          13
[1] 2 2
[1] FALSE
D35V9, 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
D35V10, 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"
D35V11, continuous

Clustering(36) Variable = DEL PEAK 14(7Q31.1) MUTATION ANALYSIS
D36V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(7Q31.1) MUTATED     4   0
  DEL PEAK 14(7Q31.1) WILD-TYPE 127  27
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            4                           154 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                            0                            27 
$`DEL PEAK 14(7Q31.1) MUTATED`
TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-A008 TCGA-DC-6682 
       34.03         6.05        13.94        25.05 

$`DEL PEAK 14(7Q31.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6233 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 
       18.28        55.76        26.43        46.92        39.48        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 
       43.04        13.55        37.97        34.49        37.74        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L 
       16.83        24.36        20.02        24.59        86.63        65.98 
TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 
       11.84        36.03        12.00        32.02         7.07        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-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-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-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02         3.98        46.03        20.98         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        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         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
       43.20        27.55        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF 
       12.62       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         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                         6.05                          0.39 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                        34.03                        129.27 
  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE 
                       19.495                        20.995 
[1] "6.0 - 34.0 (19.5)"  "0.4 - 129.3 (21.0)"
[1] "hr="     "9200000"
D36V2, 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         1
                               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         4          7         25         13
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 14(7Q31.1) MUTATED          0         0
  DEL PEAK 14(7Q31.1) WILD-TYPE       18         7
D36V3, 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                             1
  STAGE III                            0                             4
  STAGE IIIA                           0                             7
  STAGE IIIB                           0                            25
  STAGE IIIC                           1                            13
  STAGE IV                             0                            18
  STAGE IVA                            0                             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 14(7Q31.1) MUTATED     0   1   3   0
  DEL PEAK 14(7Q31.1) WILD-TYPE   9  27 109  14
D36V4, multiclass
    clus
vv   DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  T1                           0                             9
  T2                           1                            27
  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 81 45 32
D36V5, multiclass
    clus
vv   DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  N0                           3                            81
  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"
D36V6, binary
                               cls
clus                              0   1
  DEL PEAK 14(7Q31.1) MUTATED     4   0
  DEL PEAK 14(7Q31.1) WILD-TYPE 121  24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      4    0
  DEL PEAK 14(7Q31.1) WILD-TYPE  121   24
   clus
vv  DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  0                           4                           121
  1                           0                            24
[1] 2 2
[1] FALSE
D36V7, 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
D36V8, binary
                               cls
clus                              0   1
  DEL PEAK 14(7Q31.1) MUTATED     2   2
  DEL PEAK 14(7Q31.1) WILD-TYPE 110  18
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(7Q31.1) MUTATED      2    2
  DEL PEAK 14(7Q31.1) WILD-TYPE  110   18
     clus
vv    DEL PEAK 14(7Q31.1) MUTATED DEL PEAK 14(7Q31.1) WILD-TYPE
  NO                            2                           110
  YES                           2                            18
[1] 2 2
[1] FALSE
D36V9, 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
D36V10, 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"
D36V11, continuous

Clustering(37) Variable = DEL PEAK 15(8P23.2) MUTATION ANALYSIS
D37V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 15(8P23.2) MUTATED   75 19
  DEL PEAK 15(8P23.2) WILD-TYPE 56  8
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           94                            64 
  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                           19                             8 
$`DEL PEAK 15(8P23.2) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 
       15.95        31.00        51.98        21.24        18.28        26.43 
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        37.97        34.49 
TCGA-AF-3911 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 
       37.74        24.36        20.02        24.59        65.98        32.02 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 
       36.03        24.00         1.02        46.03        34.03        34.03 
TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3726 TCGA-AG-3727 
       34.03         2.01         6.05         0.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3893 
       29.98        32.98         0.99        19.04         1.02        35.01 
TCGA-AG-3896 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
        1.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
        1.02         3.98        20.98        23.01         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AH-6547 TCGA-AH-6644 
        1.02         1.94        38.96        41.00         2.50        27.55 
TCGA-CI-6621 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 
       13.78        48.20        78.12        21.01        25.05        31.00 
TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 
       13.97        31.00        51.98        10.98        25.05        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-EF-5830 
       12.62       126.44        41.36        57.24       129.27         3.48 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6513 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
        4.18        15.85        16.34        11.51        10.78        13.64 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45         9.96        42.35        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
       36.49        19.66        11.87        12.46 

$`DEL PEAK 15(8P23.2) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A015 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-4110 TCGA-AF-5654 
        8.02        36.03        55.76        46.92        29.98        16.83 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 
       86.63        11.84        36.03        12.00         7.07        20.05 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3731 
       50.04        12.03        15.95        19.99        20.98        37.02 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        0.99        19.99        17.95        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 
       48.03        25.02        46.03        13.94         6.02        37.02 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6897 
       49.97        61.97        38.04        38.56        43.20        26.43 
TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5918 
       19.46         6.05        33.17        44.78        47.44         7.17 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6160 TCGA-DC-6681 TCGA-DY-A1DF TCGA-DY-A1DG 
       26.04        12.00        44.02        25.97        24.13        51.48 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6465 
       17.69        16.31        16.41         8.61        17.46        49.51 
TCGA-F5-6811 TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 
       32.19        37.18        38.14        47.08 

  DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE 
                         0.39                          0.99 
  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 
                       20.500                        24.575 
[1] "0.4 - 129.3 (20.5)" "1.0 - 86.6 (24.6)" 
[1] "hr=" "2"  
D37V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 15(8P23.2) MUTATED        16        4        23         1         1
  DEL PEAK 15(8P23.2) WILD-TYPE      14        4        17         1         0
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 15(8P23.2) MUTATED           3          4         17          8
  DEL PEAK 15(8P23.2) WILD-TYPE         1          3          8          6
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 15(8P23.2) MUTATED         15         2
  DEL PEAK 15(8P23.2) WILD-TYPE        3         5
D37V3, 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                           23                            17
  STAGE IIB                            1                             1
  STAGE IIC                            1                             0
  STAGE III                            3                             1
  STAGE IIIA                           4                             3
  STAGE IIIB                          17                             8
  STAGE IIIC                           8                             6
  STAGE IV                            15                             3
  STAGE IVA                            2                             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 15(8P23.2) MUTATED    3 18 67 11
  DEL PEAK 15(8P23.2) WILD-TYPE  6 10 45  3
D37V4, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  T1                           3                             6
  T2                          18                            10
  T3                          67                            45
  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   47 29 22
  DEL PEAK 15(8P23.2) WILD-TYPE 37 16 11
D37V5, multiclass
    clus
vv   DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  N0                          47                            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"
D37V6, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED   73 16
  DEL PEAK 15(8P23.2) WILD-TYPE 52  8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     73   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                          73                            52
  1                          16                             8
[1] 2 2
[1] FALSE
D37V7, 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
D37V8, binary
                               cls
clus                             0  1
  DEL PEAK 15(8P23.2) MUTATED   65 11
  DEL PEAK 15(8P23.2) WILD-TYPE 47  9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 15(8P23.2) MUTATED     65   11
  DEL PEAK 15(8P23.2) WILD-TYPE   47    9
     clus
vv    DEL PEAK 15(8P23.2) MUTATED DEL PEAK 15(8P23.2) WILD-TYPE
  NO                           65                            47
  YES                          11                             9
[1] 2 2
[1] FALSE
D37V9, 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
D37V10, 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"
D37V11, continuous

Clustering(38) Variable = DEL PEAK 16(8Q11.1) MUTATION ANALYSIS
D38V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 16(8Q11.1) MUTATED    11   5
  DEL PEAK 16(8Q11.1) WILD-TYPE 120  22
  DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE 
                           16                           142 
  DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE 
                            5                            22 
$`DEL PEAK 16(8Q11.1) MUTATED`
TCGA-AG-3611 TCGA-AG-3890 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-3400 TCGA-AG-3582 
       13.94        17.03        39.48        13.55        34.49        36.03 
TCGA-AG-3728 TCGA-AG-3909 TCGA-AG-A02G TCGA-AG-A02X TCGA-DC-6155 TCGA-DC-6156 
       29.98        19.99        38.96        41.00        13.97        31.00 
TCGA-DY-A1DG TCGA-EI-6513 TCGA-F5-6810 TCGA-F5-6813 
       51.48        16.34         0.39        19.66 

$`DEL PEAK 16(8Q11.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        19.99        17.03        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       36.03        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       26.43        46.92        17.23        43.04        37.97        37.74 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
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-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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 
       15.95        19.99        20.98         7.99         0.99        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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 
       17.95        36.95        13.02        35.01        14.01         1.02 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       48.03        25.02        32.02        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 
       23.01        37.02         9.07         1.02         1.02        49.97 
TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6547 TCGA-AH-6643 
        1.94        61.97        38.04        38.56         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 
       25.05        26.04        31.00        12.00        51.98        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        24.13        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
        4.18        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 
       15.85        17.69        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-F5-6811 TCGA-F5-6812 TCGA-F5-6814 
       49.51        42.35        28.57        32.19        36.49        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE 
                         0.39                          0.99 
  DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE 
                        51.48                        129.27 
  DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE 
                       24.985                        20.995 
[1] "0.4 - 51.5 (25.0)"  "1.0 - 129.3 (21.0)"
[1] "hr=" "2.2"
D38V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 16(8Q11.1) MUTATED         2        0         3         0         0
  DEL PEAK 16(8Q11.1) WILD-TYPE      28        8        37         2         1
                               vv
clus                            STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 16(8Q11.1) MUTATED           0          1          4          1
  DEL PEAK 16(8Q11.1) WILD-TYPE         4          6         21         13
                               vv
clus                            STAGE IV STAGE IVA
  DEL PEAK 16(8Q11.1) MUTATED          3         2
  DEL PEAK 16(8Q11.1) WILD-TYPE       15         5
D38V3, multiclass
            clus
vv           DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE
  STAGE I                              2                            28
  STAGE II                             0                             8
  STAGE IIA                            3                            37
  STAGE IIB                            0                             2
  STAGE IIC                            0                             1
  STAGE III                            0                             4
  STAGE IIIA                           1                             6
  STAGE IIIB                           4                            21
  STAGE IIIC                           1                            13
  STAGE IV                             3                            15
  STAGE IVA                            2                             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 16(8Q11.1) MUTATED     0   4  10   2
  DEL PEAK 16(8Q11.1) WILD-TYPE   9  24 102  12
D38V4, multiclass
    clus
vv   DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE
  T1                           0                             9
  T2                           4                            24
  T3                          10                           102
  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 16(8Q11.1) MUTATED    5  8  3
  DEL PEAK 16(8Q11.1) WILD-TYPE 79 37 30
D38V5, multiclass
    clus
vv   DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE
  N0                           5                            79
  N1                           8                            37
  N2                           3                            30
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V6, binary
                               cls
clus                              0   1
  DEL PEAK 16(8Q11.1) MUTATED    11   5
  DEL PEAK 16(8Q11.1) WILD-TYPE 114  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8Q11.1) MUTATED     11    5
  DEL PEAK 16(8Q11.1) WILD-TYPE  114   19
   clus
vv  DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE
  0                          11                           114
  1                           5                            19
[1] 2 2
[1] FALSE
D38V7, binary
                               cls
clus                             0  1
  DEL PEAK 16(8Q11.1) MUTATED    4 13
  DEL PEAK 16(8Q11.1) WILD-TYPE 72 76
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8Q11.1) MUTATED      4   13
  DEL PEAK 16(8Q11.1) WILD-TYPE   72   76
        clus
vv       DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE
  FEMALE                           4                            72
  MALE                            13                            76
[1] 2 2
[1] FALSE
D38V8, binary
                               cls
clus                              0   1
  DEL PEAK 16(8Q11.1) MUTATED    12   1
  DEL PEAK 16(8Q11.1) WILD-TYPE 100  19
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8Q11.1) MUTATED     12    1
  DEL PEAK 16(8Q11.1) WILD-TYPE  100   19
     clus
vv    DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE
  NO                           12                           100
  YES                           1                            19
[1] 2 2
[1] FALSE
D38V9, binary
                               cls
clus                              0   1
  DEL PEAK 16(8Q11.1) MUTATED    15   1
  DEL PEAK 16(8Q11.1) WILD-TYPE 131  12
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 16(8Q11.1) MUTATED     15    1
  DEL PEAK 16(8Q11.1) WILD-TYPE  131   12
                                clus
vv                               DEL PEAK 16(8Q11.1) MUTATED
  RECTAL ADENOCARCINOMA                                   15
  RECTAL MUCINOUS ADENOCARCINOMA                           1
                                clus
vv                               DEL PEAK 16(8Q11.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    131
  RECTAL MUCINOUS ADENOCARCINOMA                            12
[1] 2 2
[1] FALSE
                               vv
clus                             R0  R1  R2  RX
  DEL PEAK 16(8Q11.1) MUTATED    14   0   2   0
  DEL PEAK 16(8Q11.1) WILD-TYPE 109   2  10   4
D38V10, multiclass
    clus
vv   DEL PEAK 16(8Q11.1) MUTATED DEL PEAK 16(8Q11.1) WILD-TYPE
  R0                          14                           109
  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"
D38V11, continuous

Clustering(39) Variable = DEL PEAK 17(10Q21.1) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(10Q21.1) MUTATED   33  5
  DEL PEAK 17(10Q21.1) WILD-TYPE 98 22
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                            38                            120 
  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE 
                             5                             22 
$`DEL PEAK 17(10Q21.1) MUTATED`
TCGA-AG-A00H TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-5654 
       25.97        26.43        46.92        13.55        34.49        16.83 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3587 
       24.59        65.98        32.02        36.03        20.05        46.03 
TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3883 
       34.03        34.03        34.03         6.05        29.98         1.02 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
       36.95         1.02        19.99        13.94         6.02        23.01 
TCGA-AG-A026 TCGA-AG-A02X TCGA-CI-6622 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 
        1.94        41.00        44.78        48.20        13.97        51.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 
       25.05        25.05       129.27        17.00        16.31        16.41 
TCGA-F5-6702 TCGA-F5-6864 
       28.57        12.46 

$`DEL PEAK 17(10Q21.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       15.95        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 
       55.76        39.48        17.23        43.04        37.97        37.74 
TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 
       29.98        24.36        20.02        86.63        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 
       12.00         7.07        24.00         1.02         2.01        50.04 
TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        20.98         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-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       19.99        17.95        13.02        35.01        14.01        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       25.02        32.02        28.04        36.03        14.04         1.02 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
        3.98        46.03        20.98        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
        1.02        49.97        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       33.17        13.78        47.44        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       25.05        26.04        31.00        12.00        31.00        10.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.97        12.62       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 
       24.13        51.48        32.61         3.48         4.18        20.55 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       19.96        20.91        18.28        15.85        17.69        16.34 
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-F5-6810 TCGA-F5-6811 
        8.45         9.96        49.51        42.35         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       36.49        19.66        37.18        38.14        11.87        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 
                        25.510                         20.285 
[1] "1.0 - 129.3 (25.5)" "0.4 - 126.4 (20.3)"
[1] "hr=" "1.6"
D39V2, 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         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 17(10Q21.1) MUTATED           0          3          6          4
  DEL PEAK 17(10Q21.1) WILD-TYPE         4          4         19         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 17(10Q21.1) MUTATED          3         1
  DEL PEAK 17(10Q21.1) WILD-TYPE       15         6
D39V3, 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                              1
  STAGE III                             0                              4
  STAGE IIIA                            3                              4
  STAGE IIIB                            6                             19
  STAGE IIIC                            4                             10
  STAGE IV                              3                             15
  STAGE IVA                             1                              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 17(10Q21.1) MUTATED    1  9 28  3
  DEL PEAK 17(10Q21.1) WILD-TYPE  8 19 84 11
D39V4, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  T1                            1                              8
  T2                            9                             19
  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 61 34 26
D39V5, multiclass
    clus
vv   DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  N0                           23                             61
  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"
D39V6, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q21.1) MUTATED   36  3
  DEL PEAK 17(10Q21.1) WILD-TYPE 89 21
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     36    3
  DEL PEAK 17(10Q21.1) WILD-TYPE   89   21
   clus
vv  DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  0                           36                             89
  1                            3                             21
[1] 2 2
[1] FALSE
D39V7, 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
D39V8, binary
                                cls
clus                              0  1
  DEL PEAK 17(10Q21.1) MUTATED   22 11
  DEL PEAK 17(10Q21.1) WILD-TYPE 90  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(10Q21.1) MUTATED     22   11
  DEL PEAK 17(10Q21.1) WILD-TYPE   90    9
     clus
vv    DEL PEAK 17(10Q21.1) MUTATED DEL PEAK 17(10Q21.1) WILD-TYPE
  NO                            22                             90
  YES                           11                              9
[1] 2 2
[1] FALSE
D39V9, 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
D39V10, 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"
D39V11, continuous

Clustering(40) Variable = DEL PEAK 18(10Q25.2) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(10Q25.2) MUTATED   39  5
  DEL PEAK 18(10Q25.2) WILD-TYPE 92 22
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                            44                            114 
  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                             5                             22 
$`DEL PEAK 18(10Q25.2) MUTATED`
TCGA-AG-3890 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 
       17.03        25.97        21.24        26.43        46.92        39.48 
TCGA-AF-2692 TCGA-AF-3400 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3591 
       13.55        34.49        24.59        65.98        32.02        34.03 
TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3896 
       34.03         6.05        29.98        19.04        36.95         1.02 
TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4021 TCGA-AG-A008 TCGA-AG-A011 
       25.02        19.99        36.03         3.98        13.94        37.02 
TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6897 TCGA-CI-6624 TCGA-DC-6155 TCGA-DC-6157 
        1.02        41.00        26.43        48.20        13.97        51.98 
TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-EF-5831 
       44.02        25.05        25.05       129.27        24.13         4.18 
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        36.49 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`DEL PEAK 18(10Q25.2) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        13.94        19.99        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 TCGA-AF-2690 
       36.03        31.00        51.98        18.28        55.76        17.23 
TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 
       43.04        37.97        37.74        29.98        16.83        24.36 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       20.02        86.63        11.84        36.03        12.00         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-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
        2.01        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       20.98         7.99         0.99        37.02        32.98         0.99 
TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3893 
        0.99        19.99         1.02        17.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-4007 
       14.01        48.03        32.02        28.04        14.04         1.02 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A016 TCGA-AG-A01J 
       46.03        20.98         6.02        23.01         9.07         1.02 
TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6544 
       49.97         1.94        38.96        61.97        38.04        38.56 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        43.20        27.55        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       13.78        44.78        47.44        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 
       25.05        26.04        31.00        12.00        31.00        10.98 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DG 
       25.97        12.62       126.44        41.36        57.24        51.48 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 
       32.61         3.48        20.55        19.96        20.91        18.28 
TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 
       15.85        17.69        16.34         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        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19        19.66        37.18        38.14        11.87 

  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE 
                          1.02                           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 
                        25.510                         20.005 
[1] "1.0 - 129.3 (25.5)" "0.4 - 126.4 (20.0)"
[1] "hr=" "1.9"
D40V2, 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         1
                                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         3          4         18          8
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 18(10Q25.2) MUTATED          4         1
  DEL PEAK 18(10Q25.2) WILD-TYPE       14         6
D40V3, 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                              1
  STAGE III                             1                              3
  STAGE IIIA                            3                              4
  STAGE IIIB                            7                             18
  STAGE IIIC                            6                              8
  STAGE IV                              4                             14
  STAGE IVA                             1                              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 18(10Q25.2) MUTATED    1  9 36  1
  DEL PEAK 18(10Q25.2) WILD-TYPE  8 19 76 13
D40V4, multiclass
    clus
vv   DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  T1                            1                              8
  T2                            9                             19
  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 59 34 22
D40V5, multiclass
    clus
vv   DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  N0                           25                             59
  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"
D40V6, binary
                                cls
clus                              0  1
  DEL PEAK 18(10Q25.2) MUTATED   40  4
  DEL PEAK 18(10Q25.2) WILD-TYPE 85 20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED     40    4
  DEL PEAK 18(10Q25.2) WILD-TYPE   85   20
   clus
vv  DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  0                           40                             85
  1                            4                             20
[1] 2 2
[1] FALSE
D40V7, 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
D40V8, binary
                                cls
clus                              0  1
  DEL PEAK 18(10Q25.2) MUTATED   30  8
  DEL PEAK 18(10Q25.2) WILD-TYPE 82 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(10Q25.2) MUTATED     30    8
  DEL PEAK 18(10Q25.2) WILD-TYPE   82   12
     clus
vv    DEL PEAK 18(10Q25.2) MUTATED DEL PEAK 18(10Q25.2) WILD-TYPE
  NO                            30                             82
  YES                            8                             12
[1] 2 2
[1] FALSE
D40V9, 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
D40V10, 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"
D40V11, continuous

Clustering(41) Variable = DEL PEAK 19(11Q22.3) MUTATION ANALYSIS
D41V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(11Q22.3) MUTATED    30   4
  DEL PEAK 19(11Q22.3) WILD-TYPE 101  23
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                            34                            124 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                             4                             23 
$`DEL PEAK 19(11Q22.3) MUTATED`
TCGA-AG-3611 TCGA-BM-6198 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-4110 
       13.94        21.24        43.04        13.55        37.97        29.98 
TCGA-AF-6136 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3587 TCGA-AG-3591 
       24.36        24.59        32.02         7.07        46.03        34.03 
TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3885 
        2.01         6.05         0.99        32.98        19.04        17.95 
TCGA-AG-3896 TCGA-AG-A008 TCGA-AG-A020 TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 
        1.02        13.94         1.02        41.00        38.56        43.20 
TCGA-AH-6644 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DT-5265 TCGA-DY-A1DF 
       27.55        13.97        10.98        44.02        12.62        24.13 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6881 TCGA-EI-7004 
       20.91        17.00        16.41         8.45 

$`DEL PEAK 19(11Q22.3) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39         8.02        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-3400 TCGA-AF-3911 
       26.43        46.92        39.48        17.23        34.49        37.74 
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-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3592 
       12.00        36.03        20.05        24.00         1.02        34.03 
TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 
       34.03        50.04        12.03         0.99        15.95        19.99 
TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       20.98         7.99        29.98        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99         1.02        36.95        13.02        35.01        14.01 
TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 
       48.03        25.02        32.02        19.99        28.04        36.03 
TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C 
       14.04         1.02         3.98        46.03        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6897 TCGA-AH-6903 
       38.96        61.97        38.04         2.50        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       12.00        31.00        51.98        25.97        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 
      126.44        41.36        57.24       129.27        51.48        32.61 
TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 
        3.48         4.18        20.55        19.96        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-6885 TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       13.64        17.46        11.97         9.96        49.51        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 
       28.57         0.39        32.19        36.49        19.66        37.18 
TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       38.14        11.87        12.46        47.08 

  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                          0.99                           0.39 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                         46.03                         129.27 
  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE 
                        19.975                         22.010 
[1] "1.0 - 46.0 (20.0)"  "0.4 - 129.3 (22.0)"
[1] "hr=" "1.1"
D41V2, 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         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 19(11Q22.3) MUTATED           2          2          5          4
  DEL PEAK 19(11Q22.3) WILD-TYPE         2          5         20         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 19(11Q22.3) MUTATED          1         1
  DEL PEAK 19(11Q22.3) WILD-TYPE       17         6
D41V3, 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                              1
  STAGE III                             2                              2
  STAGE IIIA                            2                              5
  STAGE IIIB                            5                             20
  STAGE IIIC                            4                             10
  STAGE IV                              1                             17
  STAGE IVA                             1                              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 19(11Q22.3) MUTATED    1 10 24  3
  DEL PEAK 19(11Q22.3) WILD-TYPE  8 18 88 11
D41V4, multiclass
    clus
vv   DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  T1                            1                              8
  T2                           10                             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
  DEL PEAK 19(11Q22.3) MUTATED   19 11  7
  DEL PEAK 19(11Q22.3) WILD-TYPE 65 34 26
D41V5, multiclass
    clus
vv   DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  N0                           19                             65
  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 19(11Q22.3) MUTATED   31  1
  DEL PEAK 19(11Q22.3) WILD-TYPE 94 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED     31    1
  DEL PEAK 19(11Q22.3) WILD-TYPE   94   23
   clus
vv  DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  0                           31                             94
  1                            1                             23
[1] 2 2
[1] FALSE
D41V7, 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
D41V8, binary
                                cls
clus                              0  1
  DEL PEAK 19(11Q22.3) MUTATED   23  7
  DEL PEAK 19(11Q22.3) WILD-TYPE 89 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(11Q22.3) MUTATED     23    7
  DEL PEAK 19(11Q22.3) WILD-TYPE   89   13
     clus
vv    DEL PEAK 19(11Q22.3) MUTATED DEL PEAK 19(11Q22.3) WILD-TYPE
  NO                            23                             89
  YES                            7                             13
[1] 2 2
[1] FALSE
D41V9, 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
D41V10, 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"
D41V11, continuous

Clustering(42) Variable = DEL PEAK 20(12Q13.2) MUTATION ANALYSIS
D42V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(12Q13.2) MUTATED    15   3
  DEL PEAK 20(12Q13.2) WILD-TYPE 116  24
  DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE 
                            18                            140 
  DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE 
                             3                             24 
$`DEL PEAK 20(12Q13.2) MUTATED`
TCGA-AG-A014 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-4110 TCGA-AF-6136 TCGA-AG-3587 
       15.95        43.04        34.49        29.98        24.36        46.03 
TCGA-AG-3593 TCGA-AG-3728 TCGA-AG-3898 TCGA-AH-6544 TCGA-DC-6155 TCGA-DC-6158 
       34.03        29.98        48.03        38.56        13.97        10.98 
TCGA-DY-A1DF TCGA-EI-6509 TCGA-EI-6514 TCGA-EI-6881 TCGA-F5-6702 TCGA-F5-6812 
       24.13        17.00        16.31        16.41        28.57        36.49 

$`DEL PEAK 20(12Q13.2) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 
       25.97        36.03        31.00        51.98        21.24        18.28 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 
       55.76        26.43        46.92        39.48        17.23        13.55 
TCGA-AF-2693 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       37.97        37.74        16.83        20.02        24.59        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 
       65.98        11.84        36.03        12.00        32.02         7.07 
TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3592 
       36.03        20.05        24.00         1.02        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-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-3883 TCGA-AG-3885 
        0.99         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3901 
       36.95        13.02        35.01        14.01         1.02        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 
       32.02        19.99        28.04        36.03        14.04         1.02 
TCGA-AG-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-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        49.97         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 
       38.96        61.97        41.00        38.04         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6157 
       25.05        26.04        31.00        12.00        31.00        51.98 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA 
       44.02        25.97        25.05        25.05        12.62       126.44 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       41.36        57.24       129.27        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 
        4.18        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-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6571 
       17.46        11.97         8.45         9.96        49.51        42.35 
TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 
        0.39        32.19        19.66        37.18        38.14        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE 
                         10.98                           0.39 
  DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE 
                         48.03                         129.27 
  DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE 
                        29.275                         20.730 
[1] "11.0 - 48.0 (29.3)" "0.4 - 129.3 (20.7)"
[1] "hr=" "1"  
D42V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 20(12Q13.2) MUTATED         4        0         6         0         0
  DEL PEAK 20(12Q13.2) WILD-TYPE      26        8        34         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 20(12Q13.2) MUTATED           0          2          2          3
  DEL PEAK 20(12Q13.2) WILD-TYPE         4          5         23         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 20(12Q13.2) MUTATED          0         2
  DEL PEAK 20(12Q13.2) WILD-TYPE       18         5
D42V3, multiclass
            clus
vv           DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE
  STAGE I                               4                             26
  STAGE II                              0                              8
  STAGE IIA                             6                             34
  STAGE IIB                             0                              2
  STAGE IIC                             0                              1
  STAGE III                             0                              4
  STAGE IIIA                            2                              5
  STAGE IIIB                            2                             23
  STAGE IIIC                            3                             11
  STAGE IV                              0                             18
  STAGE IVA                             2                              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(12Q13.2) MUTATED    1  4 14  1
  DEL PEAK 20(12Q13.2) WILD-TYPE  8 24 98 13
D42V4, multiclass
    clus
vv   DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE
  T1                            1                              8
  T2                            4                             24
  T3                           14                             98
  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 20(12Q13.2) MUTATED   10  6  4
  DEL PEAK 20(12Q13.2) WILD-TYPE 74 39 29
D42V5, multiclass
    clus
vv   DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE
  N0                           10                             74
  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"
D42V6, binary
                                cls
clus                               0   1
  DEL PEAK 20(12Q13.2) MUTATED    16   2
  DEL PEAK 20(12Q13.2) WILD-TYPE 109  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12Q13.2) MUTATED     16    2
  DEL PEAK 20(12Q13.2) WILD-TYPE  109   22
   clus
vv  DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE
  0                           16                            109
  1                            2                             22
[1] 2 2
[1] FALSE
D42V7, binary
                                cls
clus                              0  1
  DEL PEAK 20(12Q13.2) MUTATED    8 12
  DEL PEAK 20(12Q13.2) WILD-TYPE 68 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12Q13.2) MUTATED      8   12
  DEL PEAK 20(12Q13.2) WILD-TYPE   68   77
        clus
vv       DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE
  FEMALE                            8                             68
  MALE                             12                             77
[1] 2 2
[1] FALSE
D42V8, binary
                                cls
clus                               0   1
  DEL PEAK 20(12Q13.2) MUTATED    12   4
  DEL PEAK 20(12Q13.2) WILD-TYPE 100  16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12Q13.2) MUTATED     12    4
  DEL PEAK 20(12Q13.2) WILD-TYPE  100   16
     clus
vv    DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE
  NO                            12                            100
  YES                            4                             16
[1] 2 2
[1] FALSE
D42V9, binary
                                cls
clus                               0   1
  DEL PEAK 20(12Q13.2) MUTATED    18   1
  DEL PEAK 20(12Q13.2) WILD-TYPE 128  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(12Q13.2) MUTATED     18    1
  DEL PEAK 20(12Q13.2) WILD-TYPE  128   12
                                clus
vv                               DEL PEAK 20(12Q13.2) MUTATED
  RECTAL ADENOCARCINOMA                                    18
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 20(12Q13.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     128
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 20(12Q13.2) MUTATED    17   0   0   0
  DEL PEAK 20(12Q13.2) WILD-TYPE 106   2  12   4
D42V10, multiclass
    clus
vv   DEL PEAK 20(12Q13.2) MUTATED DEL PEAK 20(12Q13.2) WILD-TYPE
  R0                           17                            106
  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"
D42V11, continuous

Clustering(43) Variable = DEL PEAK 21(14Q11.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(14Q11.2) MUTATED   57  9
  DEL PEAK 21(14Q11.2) WILD-TYPE 74 18
  DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE 
                            66                             92 
  DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE 
                             9                             18 
$`DEL PEAK 21(14Q11.2) MUTATED`
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       17.03        17.03        25.97        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 
       26.43        39.48        13.55        37.97        34.49        37.74 
TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3591 
       24.59        65.98        11.84        36.03         7.07        34.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3742 
       34.03        34.03        50.04         6.05         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3999 
       19.99         1.02        17.95        35.01         1.02        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G 
       36.03        14.04         6.02        23.01         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 
       38.04        38.56         6.05        33.17        47.44        48.20 
TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 
        7.17        25.05        31.00        13.97        51.98        10.98 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6506 
       25.05        25.05       129.27        24.13        51.48        20.55 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6884 
       20.91        17.00        16.34        16.31        16.41        10.78 
TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6863 
       11.97        42.35         0.39        32.19        36.49        11.87 

$`DEL PEAK 21(14Q11.2) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 
       10.39         8.02        13.94        19.99        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-4110 
       31.00        51.98        46.92        17.23        43.04        29.98 
TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3575 TCGA-AG-3578 
       16.83        24.36        20.02        86.63        12.00        32.02 
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-3725 TCGA-AG-3726 
       12.03         0.99        15.95        19.99        20.98         7.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3881 TCGA-AG-3887 
       29.98        37.02        32.98         0.99        19.04        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       13.02        14.01        48.03        25.02        32.02        19.99 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
        1.02         3.98        46.03        20.98        13.94        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        9.07         1.02         1.02        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6621 
        2.50        43.20        27.55        26.43        19.46        13.78 
TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 
       44.78        78.12        21.01        26.04        12.00        31.00 
TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       44.02        25.97        12.62       126.44        41.36        57.24 
TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6507 TCGA-EI-6510 TCGA-EI-6511 
       32.61         3.48         4.18        19.96        18.28        15.85 
TCGA-EI-6512 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7004 
       17.69         8.61        11.51        13.64        17.46         8.45 
TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6702 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 
        9.96        49.51        28.57        19.66        37.18        38.14 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

  DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE 
                          0.39                           0.99 
  DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE 
                        24.360                         20.035 
[1] "0.4 - 129.3 (24.4)" "1.0 - 126.4 (20.0)"
[1] "hr=" "1.4"
D43V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 21(14Q11.2) MUTATED        12        2        20         0         0
  DEL PEAK 21(14Q11.2) WILD-TYPE      18        6        20         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 21(14Q11.2) MUTATED           1          4         12          7
  DEL PEAK 21(14Q11.2) WILD-TYPE         3          3         13          7
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 21(14Q11.2) MUTATED          6         2
  DEL PEAK 21(14Q11.2) WILD-TYPE       12         5
D43V3, multiclass
            clus
vv           DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE
  STAGE I                              12                             18
  STAGE II                              2                              6
  STAGE IIA                            20                             20
  STAGE IIB                             0                              2
  STAGE IIC                             0                              1
  STAGE III                             1                              3
  STAGE IIIA                            4                              3
  STAGE IIIB                           12                             13
  STAGE IIIC                            7                              7
  STAGE IV                              6                             12
  STAGE IVA                             2                              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 21(14Q11.2) MUTATED    3 12 50  4
  DEL PEAK 21(14Q11.2) WILD-TYPE  6 16 62 10
D43V4, multiclass
    clus
vv   DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE
  T1                            3                              6
  T2                           12                             16
  T3                           50                             62
  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 21(14Q11.2) MUTATED   34 23 12
  DEL PEAK 21(14Q11.2) WILD-TYPE 50 22 21
D43V5, multiclass
    clus
vv   DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE
  N0                           34                             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"
D43V6, binary
                                cls
clus                              0  1
  DEL PEAK 21(14Q11.2) MUTATED   54  8
  DEL PEAK 21(14Q11.2) WILD-TYPE 71 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(14Q11.2) MUTATED     54    8
  DEL PEAK 21(14Q11.2) WILD-TYPE   71   16
   clus
vv  DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE
  0                           54                             71
  1                            8                             16
[1] 2 2
[1] FALSE
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(14Q11.2) MUTATED   31 39
  DEL PEAK 21(14Q11.2) WILD-TYPE 45 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(14Q11.2) MUTATED     31   39
  DEL PEAK 21(14Q11.2) WILD-TYPE   45   50
        clus
vv       DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE
  FEMALE                           31                             45
  MALE                             39                             50
[1] 2 2
[1] FALSE
D43V8, binary
                                cls
clus                              0  1
  DEL PEAK 21(14Q11.2) MUTATED   44 11
  DEL PEAK 21(14Q11.2) WILD-TYPE 68  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(14Q11.2) MUTATED     44   11
  DEL PEAK 21(14Q11.2) WILD-TYPE   68    9
     clus
vv    DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(14Q11.2) WILD-TYPE
  NO                            44                             68
  YES                           11                              9
[1] 2 2
[1] FALSE
D43V9, binary
                                cls
clus                              0  1
  DEL PEAK 21(14Q11.2) MUTATED   66  2
  DEL PEAK 21(14Q11.2) WILD-TYPE 80 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(14Q11.2) MUTATED     66    2
  DEL PEAK 21(14Q11.2) WILD-TYPE   80   11
                                clus
vv                               DEL PEAK 21(14Q11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 21(14Q11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      80
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 21(14Q11.2) MUTATED   51  2  2  2
  DEL PEAK 21(14Q11.2) WILD-TYPE 72  0 10  2
D43V10, multiclass
    clus
vv   DEL PEAK 21(14Q11.2) MUTATED DEL PEAK 21(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"
D43V11, continuous

Clustering(44) Variable = DEL PEAK 22(14Q31.1) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(14Q31.1) MUTATED   57 10
  DEL PEAK 22(14Q31.1) WILD-TYPE 74 17
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                            67                             91 
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                            10                             17 
$`DEL PEAK 22(14Q31.1) MUTATED`
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       17.03        17.03        25.97        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2692 TCGA-AF-3911 TCGA-AF-A56L 
       26.43        39.48        17.23        13.55        37.74        65.98 
TCGA-AF-A56N TCGA-AG-3582 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       11.84        36.03        46.03        34.03        34.03        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3742 
       50.04        12.03         6.05         0.99        37.02         0.99 
TCGA-AG-3881 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
       19.04         1.02        17.95        35.01         1.02        48.03 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A026 TCGA-AG-A02G 
       36.03        14.04         6.02        23.01         1.94        38.96 
TCGA-AG-A032 TCGA-AH-6544 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6623 TCGA-CI-6624 
       38.04        38.56         6.05        33.17        47.44        48.20 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 
        7.17        21.01        25.05        31.00        13.97        51.98 
TCGA-DC-6158 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG 
       10.98        25.05        25.05        41.36       129.27        51.48 
TCGA-EI-6506 TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 
       20.55        17.00        16.34        16.31        16.41        11.51 
TCGA-EI-6884 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 
       10.78        11.97        42.35         0.39        32.19        36.49 
TCGA-F5-6863 
       11.87 

$`DEL PEAK 22(14Q31.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A014 TCGA-AG-A015 
       10.39         8.02        13.94        19.99        15.95        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2693 TCGA-AF-3400 
       31.00        51.98        46.92        43.04        37.97        34.49 
TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K 
       29.98        16.83        24.36        20.02        24.59        86.63 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00        32.02         7.07        20.05        24.00 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
        1.02         2.01         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3887 
        7.99        29.98        32.98         0.99        19.99        36.95 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
       13.02        14.01        25.02        32.02        19.99        28.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A011 
        1.02         3.98        46.03        20.98        13.94        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AG-A02X 
        9.07         1.02         1.02        49.97        61.97        41.00 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6621 
        2.50        43.20        27.55        26.43        19.46        13.78 
TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6160 
       44.78        78.12        26.04        12.00        31.00        44.02 
TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 
       25.97        12.62       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 
        3.48         4.18        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        19.66        37.18        38.14        12.46 
TCGA-G5-6572 
       47.08 

  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                          0.39                           0.99 
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE 
                         23.01                          20.91 
[1] "0.4 - 129.3 (23.0)" "1.0 - 126.4 (20.9)"
[1] "hr=" "1.3"
D44V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 22(14Q31.1) MUTATED        11        2        22         0         1
  DEL PEAK 22(14Q31.1) WILD-TYPE      19        6        18         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 22(14Q31.1) MUTATED           1          4         12          6
  DEL PEAK 22(14Q31.1) WILD-TYPE         3          3         13          8
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 22(14Q31.1) MUTATED          7         2
  DEL PEAK 22(14Q31.1) WILD-TYPE       11         5
D44V3, multiclass
            clus
vv           DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  STAGE I                              11                             19
  STAGE II                              2                              6
  STAGE IIA                            22                             18
  STAGE IIB                             0                              2
  STAGE IIC                             1                              0
  STAGE III                             1                              3
  STAGE IIIA                            4                              3
  STAGE IIIB                           12                             13
  STAGE IIIC                            6                              8
  STAGE IV                              7                             11
  STAGE IVA                             2                              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 22(14Q31.1) MUTATED    3 11 54  3
  DEL PEAK 22(14Q31.1) WILD-TYPE  6 17 58 11
D44V4, multiclass
    clus
vv   DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  T1                            3                              6
  T2                           11                             17
  T3                           54                             58
  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 22(14Q31.1) MUTATED   36 25 10
  DEL PEAK 22(14Q31.1) WILD-TYPE 48 20 23
D44V5, multiclass
    clus
vv   DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  N0                           36                             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"
D44V6, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q31.1) MUTATED   56 10
  DEL PEAK 22(14Q31.1) WILD-TYPE 69 14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q31.1) MUTATED     56   10
  DEL PEAK 22(14Q31.1) WILD-TYPE   69   14
   clus
vv  DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  0                           56                             69
  1                           10                             14
[1] 2 2
[1] FALSE
D44V7, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q31.1) MUTATED   31 41
  DEL PEAK 22(14Q31.1) WILD-TYPE 45 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q31.1) MUTATED     31   41
  DEL PEAK 22(14Q31.1) WILD-TYPE   45   48
        clus
vv       DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  FEMALE                           31                             45
  MALE                             41                             48
[1] 2 2
[1] FALSE
D44V8, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q31.1) MUTATED   46 10
  DEL PEAK 22(14Q31.1) WILD-TYPE 66 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q31.1) MUTATED     46   10
  DEL PEAK 22(14Q31.1) WILD-TYPE   66   10
     clus
vv    DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(14Q31.1) WILD-TYPE
  NO                            46                             66
  YES                           10                             10
[1] 2 2
[1] FALSE
D44V9, binary
                                cls
clus                              0  1
  DEL PEAK 22(14Q31.1) MUTATED   68  1
  DEL PEAK 22(14Q31.1) WILD-TYPE 78 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(14Q31.1) MUTATED     68    1
  DEL PEAK 22(14Q31.1) WILD-TYPE   78   12
                                clus
vv                               DEL PEAK 22(14Q31.1) MUTATED
  RECTAL ADENOCARCINOMA                                    68
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 22(14Q31.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      78
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 22(14Q31.1) MUTATED   52  2  4  2
  DEL PEAK 22(14Q31.1) WILD-TYPE 71  0  8  2
D44V10, multiclass
    clus
vv   DEL PEAK 22(14Q31.1) MUTATED DEL PEAK 22(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"
D44V11, continuous

Clustering(45) Variable = DEL PEAK 23(15Q21.1) MUTATION ANALYSIS
D45V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 23(15Q21.1) MUTATED   64 13
  DEL PEAK 23(15Q21.1) WILD-TYPE 67 14
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            77                             81 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                            13                             14 
$`DEL PEAK 23(15Q21.1) MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 
       13.94        19.99        17.03        17.03        25.97        21.24 
TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3911 
       18.28        26.43        46.92        43.04        13.55        37.74 
TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3578 TCGA-AG-3582 
       29.98        24.59        65.98        11.84        32.02        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       20.05        24.00        46.03        34.03        34.03        34.03 
TCGA-AG-3600 TCGA-AG-3725 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3732 TCGA-AG-3742 
        6.05        20.98         0.99        29.98        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 
       19.04        19.99        35.01         1.02        25.02        19.99 
TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A008 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J 
       28.04        14.04        13.94        23.01        37.02         1.02 
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        43.20 
TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-5869 
        6.05        13.78        47.44        48.20         7.17        31.00 
TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DD 
       13.97        51.98        25.05        25.05        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 
       24.13        51.48         3.48         4.18        15.85        16.31 
TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-7002 
       16.41         8.61        11.51        10.78        13.64        11.97 
TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 
       42.35        28.57        32.19        36.49        19.66 

$`DEL PEAK 23(15Q21.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       10.39         8.02        15.95        36.03        31.00        51.98 
TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-5654 
       55.76        39.48        17.23        37.97        34.49        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       24.36        20.02        86.63        36.03        12.00         7.07 
TCGA-AG-3586 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3608 
        1.02         2.01        50.04        12.03         0.99        15.95 
TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3883 TCGA-AG-3885 
       19.99         7.99        37.02         0.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 
       36.95        13.02        14.01        48.03        32.02        36.03 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A016 
        1.02         3.98        46.03        20.98         6.02         9.07 
TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 
        1.02        49.97        61.97         2.50        27.55        26.43 
TCGA-AH-6903 TCGA-CI-6620 TCGA-CI-6622 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-4749 
       19.46        33.17        44.78        78.12        21.01        25.05 
TCGA-DC-5337 TCGA-DC-6154 TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 
       26.04        12.00        31.00        10.98        44.02        25.97 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 
       12.62       126.44       129.27        32.61        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6917 
       20.91        17.00        18.28        17.69        16.34        17.46 
TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 
        8.45         9.96        49.51         0.39        37.18        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                          0.99                           0.39 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                         65.98                         129.27 
  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE 
                         24.13                          20.02 
[1] "1.0 - 66.0 (24.1)"  "0.4 - 129.3 (20.0)"
[1] "hr=" "1.1"
D45V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 23(15Q21.1) MUTATED        12        1        23         1         1
  DEL PEAK 23(15Q21.1) WILD-TYPE      18        7        17         1         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 23(15Q21.1) MUTATED           2          4         13          8
  DEL PEAK 23(15Q21.1) WILD-TYPE         2          3         12          6
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 23(15Q21.1) MUTATED          9         3
  DEL PEAK 23(15Q21.1) WILD-TYPE        9         4
D45V3, multiclass
            clus
vv           DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  STAGE I                              12                             18
  STAGE II                              1                              7
  STAGE IIA                            23                             17
  STAGE IIB                             1                              1
  STAGE IIC                             1                              0
  STAGE III                             2                              2
  STAGE IIIA                            4                              3
  STAGE IIIB                           13                             12
  STAGE IIIC                            8                              6
  STAGE IV                              9                              9
  STAGE IVA                             3                              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 23(15Q21.1) MUTATED    4 11 59  5
  DEL PEAK 23(15Q21.1) WILD-TYPE  5 17 53  9
D45V4, multiclass
    clus
vv   DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  T1                            4                              5
  T2                           11                             17
  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 23(15Q21.1) MUTATED   38 25 16
  DEL PEAK 23(15Q21.1) WILD-TYPE 46 20 17
D45V5, multiclass
    clus
vv   DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  N0                           38                             46
  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"
D45V6, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   61 11
  DEL PEAK 23(15Q21.1) WILD-TYPE 64 13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     61   11
  DEL PEAK 23(15Q21.1) WILD-TYPE   64   13
   clus
vv  DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  0                           61                             64
  1                           11                             13
[1] 2 2
[1] FALSE
D45V7, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   32 47
  DEL PEAK 23(15Q21.1) WILD-TYPE 44 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     32   47
  DEL PEAK 23(15Q21.1) WILD-TYPE   44   42
        clus
vv       DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  FEMALE                           32                             44
  MALE                             47                             42
[1] 2 2
[1] FALSE
D45V8, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   52 11
  DEL PEAK 23(15Q21.1) WILD-TYPE 60  9
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     52   11
  DEL PEAK 23(15Q21.1) WILD-TYPE   60    9
     clus
vv    DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(15Q21.1) WILD-TYPE
  NO                            52                             60
  YES                           11                              9
[1] 2 2
[1] FALSE
D45V9, binary
                                cls
clus                              0  1
  DEL PEAK 23(15Q21.1) MUTATED   70  6
  DEL PEAK 23(15Q21.1) WILD-TYPE 76  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 23(15Q21.1) MUTATED     70    6
  DEL PEAK 23(15Q21.1) WILD-TYPE   76    7
                                clus
vv                               DEL PEAK 23(15Q21.1) MUTATED
  RECTAL ADENOCARCINOMA                                    70
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 23(15Q21.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      76
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 23(15Q21.1) MUTATED   59  1  4  2
  DEL PEAK 23(15Q21.1) WILD-TYPE 64  1  8  2
D45V10, multiclass
    clus
vv   DEL PEAK 23(15Q21.1) MUTATED DEL PEAK 23(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"
D45V11, continuous

Clustering(46) Variable = DEL PEAK 24(15Q22.33) MUTATION ANALYSIS
D46V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 24(15Q22.33) MUTATED   62 12
  DEL PEAK 24(15Q22.33) WILD-TYPE 69 15
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             74                              84 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                             12                              15 
$`DEL PEAK 24(15Q22.33) MUTATED`
TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-BM-6198 
       13.94        19.99        17.03        17.03        25.97        21.24 
TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       18.28        26.43        46.92        43.04        13.55        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3582 
       37.74        29.98        24.59        65.98        32.02        36.03 
TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3600 TCGA-AG-3608 
       20.05        24.00        34.03        34.03         6.05        15.95 
TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3893 
       20.98        29.98         0.99        19.04        19.99        35.01 
TCGA-AG-3896 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4005 TCGA-AG-A008 
        1.02        25.02        19.99        28.04        14.04        13.94 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
       23.01        37.02         1.02        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6623 TCGA-CL-5918 
       38.56        43.20         6.05        13.78        47.44         7.17 
TCGA-DC-4745 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6682 TCGA-DC-6683 
       21.01        31.00        13.97        51.98        25.05        25.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DE TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 
       41.36        57.24       129.27        24.13        51.48         3.48 
TCGA-EF-5831 TCGA-EI-6511 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 
        4.18        15.85        16.31        16.41        11.51        10.78 
TCGA-EI-6885 TCGA-EI-7002 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       13.64        11.97        42.35        28.57        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6864 
       19.66        12.46 

$`DEL PEAK 24(15Q22.33) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 
       10.39         8.02        15.95        36.03        31.00        51.98 
TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6136 
       55.76        39.48        17.23        37.97        16.83        24.36 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       20.02        86.63        11.84        36.03        12.00         7.07 
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-3609 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-3878 TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 
        0.99         1.02        17.95        36.95        13.02        14.01 
TCGA-AG-3898 TCGA-AG-3902 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 
       48.03        32.02        36.03         1.02         3.98        46.03 
TCGA-AG-A002 TCGA-AG-A00C TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       20.98         6.02         9.07         1.02        49.97         1.94 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       61.97         2.50        27.55        26.43        19.46        33.17 
TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-6154 
       44.78        48.20        78.12        25.05        26.04        12.00 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA 
       31.00        10.98        44.02        25.97        12.62       126.44 
TCGA-DY-A1H8 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 
       32.61        20.55        19.96        20.91        17.00        18.28 
TCGA-EI-6512 TCGA-EI-6513 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       17.69        16.34         8.61        17.46         8.45         9.96 
TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       49.51         0.39        37.18        38.14        11.87        47.08 

  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                           0.99                            0.39 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                         129.27                          126.44 
  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE 
                         24.065                          20.005 
[1] "1.0 - 129.3 (24.1)" "0.4 - 126.4 (20.0)"
[1] "hr=" "1.1"
D46V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  DEL PEAK 24(15Q22.33) MUTATED         9        1        23         1
  DEL PEAK 24(15Q22.33) WILD-TYPE      21        7        17         1
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 24(15Q22.33) MUTATED           1         1          4         15
  DEL PEAK 24(15Q22.33) WILD-TYPE         0         3          3         10
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 24(15Q22.33) MUTATED            8        9         3
  DEL PEAK 24(15Q22.33) WILD-TYPE          6        9         4
D46V3, multiclass
            clus
vv           DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  STAGE I                                9                              21
  STAGE II                               1                               7
  STAGE IIA                             23                              17
  STAGE IIB                              1                               1
  STAGE IIC                              1                               0
  STAGE III                              1                               3
  STAGE IIIA                             4                               3
  STAGE IIIB                            15                              10
  STAGE IIIC                             8                               6
  STAGE IV                               9                               9
  STAGE IVA                              3                               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 24(15Q22.33) MUTATED    4  8 61  4
  DEL PEAK 24(15Q22.33) WILD-TYPE  5 20 51 10
D46V4, multiclass
    clus
vv   DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  T1                             4                               5
  T2                             8                              20
  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 24(15Q22.33) MUTATED   35 25 17
  DEL PEAK 24(15Q22.33) WILD-TYPE 49 20 16
D46V5, multiclass
    clus
vv   DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  N0                            35                              49
  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"
D46V6, binary
                                 cls
clus                               0  1
  DEL PEAK 24(15Q22.33) MUTATED   59 11
  DEL PEAK 24(15Q22.33) WILD-TYPE 66 13
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(15Q22.33) MUTATED     59   11
  DEL PEAK 24(15Q22.33) WILD-TYPE   66   13
   clus
vv  DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  0                            59                              66
  1                            11                              13
[1] 2 2
[1] FALSE
D46V7, binary
                                 cls
clus                               0  1
  DEL PEAK 24(15Q22.33) MUTATED   33 44
  DEL PEAK 24(15Q22.33) WILD-TYPE 43 45
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(15Q22.33) MUTATED     33   44
  DEL PEAK 24(15Q22.33) WILD-TYPE   43   45
        clus
vv       DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  FEMALE                            33                              43
  MALE                              44                              45
[1] 2 2
[1] FALSE
D46V8, binary
                                 cls
clus                               0  1
  DEL PEAK 24(15Q22.33) MUTATED   52 10
  DEL PEAK 24(15Q22.33) WILD-TYPE 60 10
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(15Q22.33) MUTATED     52   10
  DEL PEAK 24(15Q22.33) WILD-TYPE   60   10
     clus
vv    DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(15Q22.33) WILD-TYPE
  NO                             52                              60
  YES                            10                              10
[1] 2 2
[1] FALSE
D46V9, binary
                                 cls
clus                               0  1
  DEL PEAK 24(15Q22.33) MUTATED   68  6
  DEL PEAK 24(15Q22.33) WILD-TYPE 78  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(15Q22.33) MUTATED     68    6
  DEL PEAK 24(15Q22.33) WILD-TYPE   78    7
                                clus
vv                               DEL PEAK 24(15Q22.33) MUTATED
  RECTAL ADENOCARCINOMA                                     68
  RECTAL MUCINOUS ADENOCARCINOMA                             6
                                clus
vv                               DEL PEAK 24(15Q22.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       78
  RECTAL MUCINOUS ADENOCARCINOMA                               7
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 24(15Q22.33) MUTATED   58  0  4  2
  DEL PEAK 24(15Q22.33) WILD-TYPE 65  2  8  2
D46V10, multiclass
    clus
vv   DEL PEAK 24(15Q22.33) MUTATED DEL PEAK 24(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"
D46V11, continuous

Clustering(47) Variable = DEL PEAK 25(16P13.3) MUTATION ANALYSIS
D47V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 25(16P13.3) MUTATED    12   2
  DEL PEAK 25(16P13.3) WILD-TYPE 119  25
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                            14                            144 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                             2                             25 
$`DEL PEAK 25(16P13.3) MUTATED`
TCGA-G5-6233 TCGA-AG-3578 TCGA-AG-3591 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3726 
       18.28        32.02        34.03         6.05        19.99         7.99 
TCGA-AG-3728 TCGA-AG-3881 TCGA-AG-4005 TCGA-AG-A02G TCGA-DC-6682 TCGA-EI-6882 
       29.98        19.04        14.04        38.96        25.05         8.61 
TCGA-F5-6811 TCGA-F5-6814 
       32.19        37.18 

$`DEL PEAK 25(16P13.3) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 
       36.03        12.00         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-3725 TCGA-AG-3727 TCGA-AG-3731 
       12.03         0.99        15.95        20.98         0.99        37.02 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99         0.99        19.99         1.02        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-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 
       25.02        32.02        19.99        28.04        36.03         1.02 
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-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       37.02         9.07         1.02         1.02        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         2.50        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 TCGA-DT-5265 
       51.98        10.98        44.02        25.97        25.05        12.62 
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         3.48         4.18        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-6883 TCGA-EI-6884 TCGA-EI-6885 TCGA-EI-6917 TCGA-EI-7002 
       16.41        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        42.35        28.57         0.39 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       36.49        19.66        38.14        11.87        12.46        47.08 

  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                          6.05                           0.39 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                         38.96                         129.27 
  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE 
                        22.520                         20.995 
[1] "6.0 - 39.0 (22.5)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "1.2"
D47V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 25(16P13.3) MUTATED         1        0         7         0         0
  DEL PEAK 25(16P13.3) WILD-TYPE      29        8        33         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 25(16P13.3) MUTATED           0          0          1          2
  DEL PEAK 25(16P13.3) WILD-TYPE         4          7         24         12
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 25(16P13.3) MUTATED          2         0
  DEL PEAK 25(16P13.3) WILD-TYPE       16         7
D47V3, multiclass
            clus
vv           DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  STAGE I                               1                             29
  STAGE II                              0                              8
  STAGE IIA                             7                             33
  STAGE IIB                             0                              2
  STAGE IIC                             0                              1
  STAGE III                             0                              4
  STAGE IIIA                            0                              7
  STAGE IIIB                            1                             24
  STAGE IIIC                            2                             12
  STAGE IV                              2                             16
  STAGE IVA                             0                              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 25(16P13.3) MUTATED     0   2  12   0
  DEL PEAK 25(16P13.3) WILD-TYPE   9  26 100  14
D47V4, multiclass
    clus
vv   DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  T1                            0                              9
  T2                            2                             26
  T3                           12                            100
  T4                            0                             14
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 25(16P13.3) MUTATED    8  2  4
  DEL PEAK 25(16P13.3) WILD-TYPE 76 43 29
D47V5, multiclass
    clus
vv   DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  N0                            8                             76
  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"
D47V6, binary
                                cls
clus                               0   1
  DEL PEAK 25(16P13.3) MUTATED    12   2
  DEL PEAK 25(16P13.3) WILD-TYPE 113  22
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16P13.3) MUTATED     12    2
  DEL PEAK 25(16P13.3) WILD-TYPE  113   22
   clus
vv  DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  0                           12                            113
  1                            2                             22
[1] 2 2
[1] FALSE
D47V7, binary
                                cls
clus                              0  1
  DEL PEAK 25(16P13.3) MUTATED    6  8
  DEL PEAK 25(16P13.3) WILD-TYPE 70 81
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16P13.3) MUTATED      6    8
  DEL PEAK 25(16P13.3) WILD-TYPE   70   81
        clus
vv       DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  FEMALE                            6                             70
  MALE                              8                             81
[1] 2 2
[1] FALSE
D47V8, binary
                                cls
clus                               0   1
  DEL PEAK 25(16P13.3) MUTATED    12   2
  DEL PEAK 25(16P13.3) WILD-TYPE 100  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16P13.3) MUTATED     12    2
  DEL PEAK 25(16P13.3) WILD-TYPE  100   18
     clus
vv    DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  NO                            12                            100
  YES                            2                             18
[1] 2 2
[1] FALSE
D47V9, binary
                                cls
clus                               0   1
  DEL PEAK 25(16P13.3) MUTATED    11   2
  DEL PEAK 25(16P13.3) WILD-TYPE 135  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(16P13.3) MUTATED     11    2
  DEL PEAK 25(16P13.3) WILD-TYPE  135   11
                                clus
vv                               DEL PEAK 25(16P13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    11
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 25(16P13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     135
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 25(16P13.3) MUTATED    11   0   1   0
  DEL PEAK 25(16P13.3) WILD-TYPE 112   2  11   4
D47V10, multiclass
    clus
vv   DEL PEAK 25(16P13.3) MUTATED DEL PEAK 25(16P13.3) WILD-TYPE
  R0                           11                            112
  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"
D47V11, continuous

Clustering(48) Variable = DEL PEAK 26(16Q23.1) MUTATION ANALYSIS
D48V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 26(16Q23.1) MUTATED    20   3
  DEL PEAK 26(16Q23.1) WILD-TYPE 111  24
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                            23                            135 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                             3                             24 
$`DEL PEAK 26(16Q23.1) MUTATED`
TCGA-G5-6233 TCGA-AF-6672 TCGA-AG-3578 TCGA-AG-3582 TCGA-AG-3591 TCGA-AG-3600 
       18.28        24.59        32.02        36.03        34.03         6.05 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3726 TCGA-AG-3732 TCGA-AG-3881 TCGA-AG-3883 
       19.99        20.98         7.99        32.98        19.04         1.02 
TCGA-AG-4005 TCGA-AH-6544 TCGA-AH-6644 TCGA-DC-6682 TCGA-DY-A1DE TCGA-EI-6883 
       14.04        38.56        27.55        25.05       129.27        11.51 
TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6811 TCGA-F5-6814 
       11.97         8.45         9.96        32.19        37.18 

$`DEL PEAK 26(16Q23.1) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 
       25.97        15.95        36.03        31.00        51.98        21.24 
TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       55.76        26.43        46.92        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 
       13.55        37.97        34.49        37.74        29.98        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 
       24.36        20.02        86.63        65.98        11.84        36.03 
TCGA-AG-3575 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 TCGA-AG-3587 
       12.00         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-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 
       15.95         0.99        29.98        37.02         0.99         0.99 
TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 
       19.99        17.95        36.95        13.02        35.01        14.01 
TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 
        1.02        48.03        25.02        32.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       36.03         1.02         3.98        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 
        6.02        23.01        37.02         9.07         1.02         1.02 
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-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 
        2.50        43.20        26.43        19.46         6.05        33.17 
TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 
       13.78        44.78        47.44        48.20        78.12         7.17 
TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 
       21.01        25.05        26.04        31.00        12.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6683 
       31.00        51.98        10.98        44.02        25.97        25.05 
TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1DG 
       12.62       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         3.48         4.18        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 
       42.35        28.57         0.39        36.49        19.66        38.14 
TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       11.87        12.46        47.08 

  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                          1.02                           0.39 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE 
                         20.98                          21.01 
[1] "1.0 - 129.3 (21.0)" "0.4 - 126.4 (21.0)"
[1] "hr=" "1.1"
D48V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 26(16Q23.1) MUTATED         3        0         7         0         1
  DEL PEAK 26(16Q23.1) WILD-TYPE      27        8        33         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 26(16Q23.1) MUTATED           1          0          0          3
  DEL PEAK 26(16Q23.1) WILD-TYPE         3          7         25         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 26(16Q23.1) MUTATED          4         0
  DEL PEAK 26(16Q23.1) WILD-TYPE       14         7
D48V3, multiclass
            clus
vv           DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  STAGE I                               3                             27
  STAGE II                              0                              8
  STAGE IIA                             7                             33
  STAGE IIB                             0                              2
  STAGE IIC                             1                              0
  STAGE III                             1                              3
  STAGE IIIA                            0                              7
  STAGE IIIB                            0                             25
  STAGE IIIC                            3                             11
  STAGE IV                              4                             14
  STAGE IVA                             0                              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 26(16Q23.1) MUTATED    0  3 17  3
  DEL PEAK 26(16Q23.1) WILD-TYPE  9 25 95 11
D48V4, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  T1                            0                              9
  T2                            3                             25
  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
  DEL PEAK 26(16Q23.1) MUTATED   11  2  9
  DEL PEAK 26(16Q23.1) WILD-TYPE 73 43 24
D48V5, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  N0                           11                             73
  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"
D48V6, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED    17   4
  DEL PEAK 26(16Q23.1) WILD-TYPE 108  20
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     17    4
  DEL PEAK 26(16Q23.1) WILD-TYPE  108   20
   clus
vv  DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  0                           17                            108
  1                            4                             20
[1] 2 2
[1] FALSE
D48V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q23.1) MUTATED   11 12
  DEL PEAK 26(16Q23.1) WILD-TYPE 65 77
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     11   12
  DEL PEAK 26(16Q23.1) WILD-TYPE   65   77
        clus
vv       DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  FEMALE                           11                             65
  MALE                             12                             77
[1] 2 2
[1] FALSE
D48V8, binary
                                cls
clus                              0  1
  DEL PEAK 26(16Q23.1) MUTATED   18  3
  DEL PEAK 26(16Q23.1) WILD-TYPE 94 17
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     18    3
  DEL PEAK 26(16Q23.1) WILD-TYPE   94   17
     clus
vv    DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(16Q23.1) WILD-TYPE
  NO                            18                             94
  YES                            3                             17
[1] 2 2
[1] FALSE
D48V9, binary
                                cls
clus                               0   1
  DEL PEAK 26(16Q23.1) MUTATED    20   2
  DEL PEAK 26(16Q23.1) WILD-TYPE 126  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(16Q23.1) MUTATED     20    2
  DEL PEAK 26(16Q23.1) WILD-TYPE  126   11
                                clus
vv                               DEL PEAK 26(16Q23.1) MUTATED
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
                                clus
vv                               DEL PEAK 26(16Q23.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     126
  RECTAL MUCINOUS ADENOCARCINOMA                             11
[1] 2 2
[1] FALSE
                                vv
clus                              R0  R1  R2  RX
  DEL PEAK 26(16Q23.1) MUTATED    16   0   1   0
  DEL PEAK 26(16Q23.1) WILD-TYPE 107   2  11   4
D48V10, multiclass
    clus
vv   DEL PEAK 26(16Q23.1) MUTATED DEL PEAK 26(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"
D48V11, continuous

Clustering(49) Variable = DEL PEAK 27(17P11.2) MUTATION ANALYSIS
D49V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 27(17P11.2) MUTATED   88 18
  DEL PEAK 27(17P11.2) WILD-TYPE 43  9
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                           106                             52 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                            18                              9 
$`DEL PEAK 27(17P11.2) MUTATED`
TCGA-AG-3611 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H TCGA-AG-A014 TCGA-AG-A01N 
       13.94        17.03        17.03        25.97        15.95        31.00 
TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 
       51.98        21.24        55.76        39.48        17.23        43.04 
TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 
       13.55        37.97        34.49        37.74        29.98        24.36 
TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3575 TCGA-AG-3578 
       20.02        86.63        65.98        11.84        12.00        32.02 
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-3593 TCGA-AG-3594 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 TCGA-AG-3725 
       34.03         2.01         0.99        15.95        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 
        7.99         0.99        37.02        32.98         0.99        19.04 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3902 
        1.02        17.95        35.01         1.02        48.03        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A026 
       13.94         6.02        23.01        37.02         1.02         1.94 
TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 
       41.00        38.56        43.20        27.55        26.43         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-6155 
       33.17        13.78        44.78         7.17        25.05        13.97 
TCGA-DC-6156 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       31.00        10.98        44.02        25.05        25.05        12.62 
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-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6512 
        3.48         4.18        20.91        17.00        18.28        17.69 
TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7002 
       16.34        16.31        16.41        11.51        10.78        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        42.35        28.57         0.39 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6863 TCGA-F5-6864 
       19.66        37.18        11.87        12.46 

$`DEL PEAK 27(17P11.2) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-A015 TCGA-G5-6233 TCGA-G5-6641 
       10.39         8.02        19.99        36.03        18.28        26.43 
TCGA-AF-2687 TCGA-AF-5654 TCGA-AF-6672 TCGA-AG-3574 TCGA-AG-3583 TCGA-AG-3592 
       46.92        16.83        24.59        36.03        20.05        34.03 
TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3728 TCGA-AG-3878 TCGA-AG-3882 
       50.04        12.03         6.05        29.98         0.99        19.99 
TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3901 TCGA-AG-4022 TCGA-AG-A002 
       36.95        13.02        14.01        25.02        46.03        20.98 
TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A032 
        9.07         1.02        49.97        38.96        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-DC-4745 
        2.50        19.46        47.44        48.20        78.12        21.01 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6681 TCGA-DY-A1H8 
       26.04        31.00        12.00        51.98        25.97        32.61 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6511 TCGA-EI-6882 TCGA-EI-6885 TCGA-EI-6917 
       20.55        19.96        15.85         8.61        13.64        17.46 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6861 TCGA-G5-6572 
       32.19        36.49        38.14        47.08 

  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                          0.39                           0.99 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                        129.27                          78.12 
  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE 
                        20.465                         24.805 
[1] "0.4 - 129.3 (20.5)" "1.0 - 78.1 (24.8)" 
[1] "hr=" "1.1"
D49V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 27(17P11.2) MUTATED        17        5        30         2         1
  DEL PEAK 27(17P11.2) WILD-TYPE      13        3        10         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 27(17P11.2) MUTATED           3          4         17         11
  DEL PEAK 27(17P11.2) WILD-TYPE         1          3          8          3
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 27(17P11.2) MUTATED         12         5
  DEL PEAK 27(17P11.2) WILD-TYPE        6         2
D49V3, multiclass
            clus
vv           DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  STAGE I                              17                             13
  STAGE II                              5                              3
  STAGE IIA                            30                             10
  STAGE IIB                             2                              0
  STAGE IIC                             1                              0
  STAGE III                             3                              1
  STAGE IIIA                            4                              3
  STAGE IIIB                           17                              8
  STAGE IIIC                           11                              3
  STAGE IV                             12                              6
  STAGE IVA                             5                              2
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             T1 T2 T3 T4
  DEL PEAK 27(17P11.2) MUTATED    2 19 79 12
  DEL PEAK 27(17P11.2) WILD-TYPE  7  9 33  2
D49V4, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  T1                            2                              7
  T2                           19                              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 27(17P11.2) MUTATED   57 30 24
  DEL PEAK 27(17P11.2) WILD-TYPE 27 15  9
D49V5, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  N0                           57                             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"
D49V6, binary
                                cls
clus                              0  1
  DEL PEAK 27(17P11.2) MUTATED   85 17
  DEL PEAK 27(17P11.2) WILD-TYPE 40  7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED     85   17
  DEL PEAK 27(17P11.2) WILD-TYPE   40    7
   clus
vv  DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  0                           85                             40
  1                           17                              7
[1] 2 2
[1] FALSE
D49V7, binary
                                cls
clus                              0  1
  DEL PEAK 27(17P11.2) MUTATED   54 59
  DEL PEAK 27(17P11.2) WILD-TYPE 22 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED     54   59
  DEL PEAK 27(17P11.2) WILD-TYPE   22   30
        clus
vv       DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  FEMALE                           54                             22
  MALE                             59                             30
[1] 2 2
[1] FALSE
D49V8, binary
                                cls
clus                              0  1
  DEL PEAK 27(17P11.2) MUTATED   75 12
  DEL PEAK 27(17P11.2) WILD-TYPE 37  8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED     75   12
  DEL PEAK 27(17P11.2) WILD-TYPE   37    8
     clus
vv    DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(17P11.2) WILD-TYPE
  NO                            75                             37
  YES                           12                              8
[1] 2 2
[1] FALSE
D49V9, binary
                                cls
clus                               0   1
  DEL PEAK 27(17P11.2) MUTATED   102   6
  DEL PEAK 27(17P11.2) WILD-TYPE  44   7
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 27(17P11.2) MUTATED    102    6
  DEL PEAK 27(17P11.2) WILD-TYPE   44    7
                                clus
vv                               DEL PEAK 27(17P11.2) MUTATED
  RECTAL ADENOCARCINOMA                                   102
  RECTAL MUCINOUS ADENOCARCINOMA                            6
                                clus
vv                               DEL PEAK 27(17P11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      44
  RECTAL MUCINOUS ADENOCARCINOMA                              7
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 27(17P11.2) MUTATED   82  2  9  3
  DEL PEAK 27(17P11.2) WILD-TYPE 41  0  3  1
D49V10, multiclass
    clus
vv   DEL PEAK 27(17P11.2) MUTATED DEL PEAK 27(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"
D49V11, continuous

Clustering(50) Variable = DEL PEAK 28(18P11.31) MUTATION ANALYSIS
D50V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 28(18P11.31) MUTATED   99 20
  DEL PEAK 28(18P11.31) WILD-TYPE 32  7
  DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE 
                            119                              39 
  DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE 
                             20                               7 
$`DEL PEAK 28(18P11.31) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        31.00        51.98        21.24        18.28        55.76 
TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-3400 
       46.92        39.48        17.23        43.04        13.55        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6655 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       37.74        29.98        20.02        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3587 
       36.03         7.07        36.03        20.05        24.00        46.03 
TCGA-AG-3592 TCGA-AG-3593 TCGA-AG-3598 TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3725 
       34.03        34.03        50.04         0.99        15.95        20.98 
TCGA-AG-3726 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3882 
        7.99        29.98        37.02        32.98         0.99        19.99 
TCGA-AG-3883 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 
        1.02        36.95        35.01         1.02        48.03        25.02 
TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4007 TCGA-AG-4021 
       32.02        19.99        28.04        36.03         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       46.03        13.94         6.02        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 
        1.02         1.94        41.00        38.04        38.56        43.20 
TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 
       27.55        26.43        19.46         6.05        33.17        13.78 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
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-6509 TCGA-EI-6510 TCGA-EI-6511 
        3.48         4.18        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-6885 TCGA-EI-7002 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       13.64        11.97        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 
       32.19        36.49        19.66        11.87        12.46 

$`DEL PEAK 28(18P11.31) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A015 TCGA-G5-6641 TCGA-AF-2693 TCGA-AF-5654 TCGA-AF-6136 
        8.02        36.03        26.43        37.97        16.83        24.36 
TCGA-AF-6672 TCGA-AG-3575 TCGA-AG-3578 TCGA-AG-3586 TCGA-AG-3591 TCGA-AG-3594 
       24.59        12.00        32.02         1.02        34.03         2.01 
TCGA-AG-3599 TCGA-AG-3600 TCGA-AG-3609 TCGA-AG-3727 TCGA-AG-3878 TCGA-AG-3881 
       12.03         6.05        19.99         0.99         0.99        19.04 
TCGA-AG-3885 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-4005 TCGA-AG-A002 TCGA-AG-A00Y 
       17.95        13.02        14.01        14.04        20.98        23.01 
TCGA-AG-A025 TCGA-AG-A02G TCGA-AG-A02N TCGA-AH-6547 TCGA-DT-5265 TCGA-DY-A1H8 
       49.97        38.96        61.97         2.50        12.62        32.61 
TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6882 TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 
       19.96        20.91         8.61        17.46         8.45         9.96 
TCGA-F5-6814 TCGA-F5-6861 TCGA-G5-6572 
       37.18        38.14        47.08 

  DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE 
                           0.39                            0.99 
  DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE 
                         129.27                           61.97 
  DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE 
                          25.02                           19.04 
[1] "0.4 - 129.3 (25.0)" "1.0 - 62.0 (19.0)" 
[1] "hr=" "1.5"
D50V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  DEL PEAK 28(18P11.31) MUTATED        21        4        30         2
  DEL PEAK 28(18P11.31) WILD-TYPE       9        4        10         0
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 28(18P11.31) MUTATED           1         2          4         22
  DEL PEAK 28(18P11.31) WILD-TYPE         0         2          3          3
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 28(18P11.31) MUTATED           11       15         7
  DEL PEAK 28(18P11.31) WILD-TYPE          3        3         0
D50V3, multiclass
            clus
vv           DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE
  STAGE I                               21                               9
  STAGE II                               4                               4
  STAGE IIA                             30                              10
  STAGE IIB                              2                               0
  STAGE IIC                              1                               0
  STAGE III                              2                               2
  STAGE IIIA                             4                               3
  STAGE IIIB                            22                               3
  STAGE IIIC                            11                               3
  STAGE IV                              15                               3
  STAGE IVA                              7                               0
[1] 11  2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                              T1 T2 T3 T4
  DEL PEAK 28(18P11.31) MUTATED    4 21 88 11
  DEL PEAK 28(18P11.31) WILD-TYPE  5  7 24  3
D50V4, multiclass
    clus
vv   DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE
  T1                             4                               5
  T2                            21                               7
  T3                            88                              24
  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 28(18P11.31) MUTATED   60 37 26
  DEL PEAK 28(18P11.31) WILD-TYPE 24  8  7
D50V5, multiclass
    clus
vv   DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE
  N0                            60                              24
  N1                            37                               8
  N2                            26                               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"
D50V6, binary
                                 cls
clus                               0  1
  DEL PEAK 28(18P11.31) MUTATED   93 22
  DEL PEAK 28(18P11.31) WILD-TYPE 32  2
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(18P11.31) MUTATED     93   22
  DEL PEAK 28(18P11.31) WILD-TYPE   32    2
   clus
vv  DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE
  0                            93                              32
  1                            22                               2
[1] 2 2
[1] FALSE
D50V7, binary
                                 cls
clus                               0  1
  DEL PEAK 28(18P11.31) MUTATED   57 68
  DEL PEAK 28(18P11.31) WILD-TYPE 19 21
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(18P11.31) MUTATED     57   68
  DEL PEAK 28(18P11.31) WILD-TYPE   19   21
        clus
vv       DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE
  FEMALE                            57                              19
  MALE                              68                              21
[1] 2 2
[1] FALSE
D50V8, binary
                                 cls
clus                               0  1
  DEL PEAK 28(18P11.31) MUTATED   86 13
  DEL PEAK 28(18P11.31) WILD-TYPE 26  7
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(18P11.31) MUTATED     86   13
  DEL PEAK 28(18P11.31) WILD-TYPE   26    7
     clus
vv    DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE
  NO                             86                              26
  YES                            13                               7
[1] 2 2
[1] FALSE
D50V9, binary
                                 cls
clus                                0   1
  DEL PEAK 28(18P11.31) MUTATED   116   7
  DEL PEAK 28(18P11.31) WILD-TYPE  30   6
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 28(18P11.31) MUTATED    116    7
  DEL PEAK 28(18P11.31) WILD-TYPE   30    6
                                clus
vv                               DEL PEAK 28(18P11.31) MUTATED
  RECTAL ADENOCARCINOMA                                    116
  RECTAL MUCINOUS ADENOCARCINOMA                             7
                                clus
vv                               DEL PEAK 28(18P11.31) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       30
  RECTAL MUCINOUS ADENOCARCINOMA                               6
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 28(18P11.31) MUTATED   92  2 11  3
  DEL PEAK 28(18P11.31) WILD-TYPE 31  0  1  1
D50V10, multiclass
    clus
vv   DEL PEAK 28(18P11.31) MUTATED DEL PEAK 28(18P11.31) WILD-TYPE
  R0                            92                              31
  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"
D50V11, continuous

Clustering(51) Variable = DEL PEAK 29(18Q21.2) MUTATION ANALYSIS
D51V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 29(18Q21.2) MUTATED   115  23
  DEL PEAK 29(18Q21.2) WILD-TYPE  16   4
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                           138                             20 
  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                            23                              4 
$`DEL PEAK 29(18Q21.2) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        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-3725 TCGA-AG-3726 TCGA-AG-3727 
        6.05         0.99        15.95        20.98         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 
       29.98        37.02        32.98         0.99        19.04        19.99 
TCGA-AG-3883 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 
        1.02        17.95        36.95        35.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y 
        1.02         3.98        46.03        13.94         6.02        23.01 
TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G 
       37.02         9.07         1.02         1.02         1.94        38.96 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 
       41.00        38.04        38.56        43.20        27.55        26.43 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 
        6.05        33.17        13.78        44.78        47.44        48.20 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 
       78.12         7.17        21.01        25.05        26.04        31.00 
TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 
       12.00        13.97        31.00        51.98        10.98        44.02 
TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC 
       25.97        25.05        25.05        12.62       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         3.48         4.18 
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-EI-7004 TCGA-F5-6465 TCGA-F5-6571 TCGA-F5-6702 TCGA-F5-6810 
       11.97         8.45        49.51        42.35        28.57         0.39 
TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       32.19        36.49        19.66        11.87        12.46        47.08 

$`DEL PEAK 29(18Q21.2) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A015 TCGA-AF-5654 TCGA-AG-3599 TCGA-AG-3609 TCGA-AG-3878 
        8.02        36.03        16.83        12.03        19.99         0.99 
TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 
       13.02        14.01        20.98        49.97        61.97         2.50 
TCGA-AH-6903 TCGA-DY-A1H8 TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 
       19.46        32.61        19.96         8.61        17.46         9.96 
TCGA-F5-6814 TCGA-F5-6861 
       37.18        38.14 

  DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE 
                          0.39                           0.99 
  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 
                        24.065                         18.460 
[1] "0.4 - 129.3 (24.1)" "1.0 - 62.0 (18.5)" 
[1] "hr=" "1.5"
D51V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 29(18Q21.2) MUTATED        22        7        35         2         1
  DEL PEAK 29(18Q21.2) WILD-TYPE       8        1         5         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 29(18Q21.2) MUTATED           4          5         24         12
  DEL PEAK 29(18Q21.2) WILD-TYPE         0          2          1          2
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 29(18Q21.2) MUTATED         18         7
  DEL PEAK 29(18Q21.2) WILD-TYPE        0         0
D51V3, 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                            35                              5
  STAGE IIB                             2                              0
  STAGE IIC                             1                              0
  STAGE III                             4                              0
  STAGE IIIA                            5                              2
  STAGE IIIB                           24                              1
  STAGE IIIC                           12                              2
  STAGE IV                             18                              0
  STAGE IVA                             7                              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  23 102  13
  DEL PEAK 29(18Q21.2) WILD-TYPE   4   5  10   1
D51V4, multiclass
    clus
vv   DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  T1                            5                              4
  T2                           23                              5
  T3                          102                             10
  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   69 42 31
  DEL PEAK 29(18Q21.2) WILD-TYPE 15  3  2
D51V5, multiclass
    clus
vv   DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  N0                           69                             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"
D51V6, binary
                                cls
clus                               0   1
  DEL PEAK 29(18Q21.2) MUTATED   106  24
  DEL PEAK 29(18Q21.2) WILD-TYPE  19   0
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED    106   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                          106                             19
  1                           24                              0
[1] 2 2
[1] FALSE
D51V7, 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
D51V8, binary
                                cls
clus                              0  1
  DEL PEAK 29(18Q21.2) MUTATED   97 19
  DEL PEAK 29(18Q21.2) WILD-TYPE 15  1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 29(18Q21.2) MUTATED     97   19
  DEL PEAK 29(18Q21.2) WILD-TYPE   15    1
     clus
vv    DEL PEAK 29(18Q21.2) MUTATED DEL PEAK 29(18Q21.2) WILD-TYPE
  NO                            97                             15
  YES                           19                              1
[1] 2 2
[1] FALSE
D51V9, 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
D51V10, 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"
D51V11, continuous

Clustering(52) Variable = DEL PEAK 30(18Q22.1) MUTATION ANALYSIS
D52V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 30(18Q22.1) MUTATED   111  23
  DEL PEAK 30(18Q22.1) WILD-TYPE  20   4
  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                           134                             24 
  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                            23                              4 
$`DEL PEAK 30(18Q22.1) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3893 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 
       36.95        35.01         1.02        48.03        25.02        32.02 
TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 
       19.99        28.04        36.03        14.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
       46.03        13.94         6.02        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 
        1.02         1.02         1.94        38.96        41.00        38.04 
TCGA-AH-6544 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 
       38.56        43.20        27.55        26.43         6.05        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 
       44.78        47.44        48.20        78.12         7.17        21.01 
TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 
       25.05        26.04        31.00        12.00        13.97        31.00 
TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       51.98        10.98        44.02        25.97        25.05        25.05 
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 
        3.48         4.18        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        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       28.57         0.39        32.19        36.49        19.66        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`DEL PEAK 30(18Q22.1) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A015 TCGA-AF-5654 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 
        8.02        36.03        16.83         1.02        12.03        19.99 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-A002 TCGA-AG-A025 
       37.02         0.99        13.02        14.01        20.98        49.97 
TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6621 TCGA-DT-5265 TCGA-DY-A1H8 
       61.97         2.50        19.46        13.78        12.62        32.61 
TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
       19.96         8.61        17.46         9.96        37.18        38.14 

  DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE 
                          0.39                           0.99 
  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 
                        24.245                         17.145 
[1] "0.4 - 129.3 (24.2)" "1.0 - 62.0 (17.1)" 
[1] "hr=" "1.3"
D52V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 30(18Q22.1) MUTATED        22        6        35         2         1
  DEL PEAK 30(18Q22.1) WILD-TYPE       8        2         5         0         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 30(18Q22.1) MUTATED           3          5         23         12
  DEL PEAK 30(18Q22.1) WILD-TYPE         1          2          2          2
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 30(18Q22.1) MUTATED         17         7
  DEL PEAK 30(18Q22.1) WILD-TYPE        1         0
D52V3, 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                            35                              5
  STAGE IIB                             2                              0
  STAGE IIC                             1                              0
  STAGE III                             3                              1
  STAGE IIIA                            5                              2
  STAGE IIIB                           23                              2
  STAGE IIIC                           12                              2
  STAGE IV                             17                              1
  STAGE IVA                             7                              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 98 13
  DEL PEAK 30(18Q22.1) WILD-TYPE  4  5 14  1
D52V4, multiclass
    clus
vv   DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  T1                            5                              4
  T2                           23                              5
  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
  DEL PEAK 30(18Q22.1) MUTATED   68 40 30
  DEL PEAK 30(18Q22.1) WILD-TYPE 16  5  3
D52V5, multiclass
    clus
vv   DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  N0                           68                             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"
D52V6, binary
                                cls
clus                               0   1
  DEL PEAK 30(18Q22.1) MUTATED   104  23
  DEL PEAK 30(18Q22.1) WILD-TYPE  21   1
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q22.1) MUTATED    104   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                          104                             21
  1                           23                              1
[1] 2 2
[1] FALSE
D52V7, 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
D52V8, binary
                                cls
clus                              0  1
  DEL PEAK 30(18Q22.1) MUTATED   96 18
  DEL PEAK 30(18Q22.1) WILD-TYPE 16  2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 30(18Q22.1) MUTATED     96   18
  DEL PEAK 30(18Q22.1) WILD-TYPE   16    2
     clus
vv    DEL PEAK 30(18Q22.1) MUTATED DEL PEAK 30(18Q22.1) WILD-TYPE
  NO                            96                             16
  YES                           18                              2
[1] 2 2
[1] FALSE
D52V9, 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
D52V10, 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"
D52V11, continuous

Clustering(53) Variable = DEL PEAK 31(18Q23) MUTATION ANALYSIS
D53V1, survival
                              sevent
clus2                            0   1
  DEL PEAK 31(18Q23) MUTATED   111  23
  DEL PEAK 31(18Q23) WILD-TYPE  20   4
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                         134                           24 
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                          23                            4 
$`DEL PEAK 31(18Q23) MUTATED`
TCGA-AF-3913 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
       10.39        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        31.00        51.98        21.24        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 
       26.43        46.92        39.48        17.23        43.04        13.55 
TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       37.97        34.49        37.74        29.98        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 
       24.59        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-3725 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 
        0.99        15.95        20.98         7.99         0.99        29.98 
TCGA-AG-3732 TCGA-AG-3742 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3883 TCGA-AG-3885 
       32.98         0.99        19.04        19.99         1.02        17.95 
TCGA-AG-3887 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 
       36.95         1.02        48.03        25.02        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-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J 
       13.94         6.02        23.01        37.02         9.07         1.02 
TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 
        1.02         1.94        38.96        41.00        38.04        38.56 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 
       43.20        27.55        26.43         6.05        33.17        44.78 
TCGA-CI-6623 TCGA-CI-6624 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 
       47.44        48.20        78.12         7.17        21.01        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6155 TCGA-DC-6156 TCGA-DC-6157 
       26.04        31.00        12.00        13.97        31.00        51.98 
TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 
       10.98        44.02        25.97        25.05        25.05        12.62 
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 
        3.48         4.18        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        42.35 
TCGA-F5-6702 TCGA-F5-6810 TCGA-F5-6811 TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6863 
       28.57         0.39        32.19        36.49        19.66        11.87 
TCGA-F5-6864 TCGA-G5-6572 
       12.46        47.08 

$`DEL PEAK 31(18Q23) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-A015 TCGA-AF-5654 TCGA-AG-3586 TCGA-AG-3599 TCGA-AG-3609 
        8.02        36.03        16.83         1.02        12.03        19.99 
TCGA-AG-3731 TCGA-AG-3878 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-A002 
       37.02         0.99        13.02        35.01        14.01        20.98 
TCGA-AG-A025 TCGA-AG-A02N TCGA-AH-6547 TCGA-AH-6903 TCGA-CI-6621 TCGA-DY-A1H8 
       49.97        61.97         2.50        19.46        13.78        32.61 
TCGA-EI-6507 TCGA-EI-6882 TCGA-EI-6917 TCGA-F5-6464 TCGA-F5-6814 TCGA-F5-6861 
       19.96         8.61        17.46         9.96        37.18        38.14 

  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                        0.39                         0.99 
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                      129.27                        61.97 
  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE 
                      24.065                       18.460 
[1] "0.4 - 129.3 (24.1)" "1.0 - 62.0 (18.5)" 
[1] "hr=" "1.3"
D53V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 31(18Q23) MUTATED        22        7        35         2         1
  DEL PEAK 31(18Q23) WILD-TYPE       8        1         5         0         0
                              vv
clus                           STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 31(18Q23) MUTATED           3          5         22         12
  DEL PEAK 31(18Q23) WILD-TYPE         1          2          3          2
                              vv
clus                           STAGE IV STAGE IVA
  DEL PEAK 31(18Q23) MUTATED         17         7
  DEL PEAK 31(18Q23) WILD-TYPE        1         0
D53V3, multiclass
            clus
vv           DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  STAGE I                            22                            8
  STAGE II                            7                            1
  STAGE IIA                          35                            5
  STAGE IIB                           2                            0
  STAGE IIC                           1                            0
  STAGE III                           3                            1
  STAGE IIIA                          5                            2
  STAGE IIIB                         22                            3
  STAGE IIIC                         12                            2
  STAGE IV                           17                            1
  STAGE IVA                           7                            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 31(18Q23) MUTATED    5 23 98 13
  DEL PEAK 31(18Q23) WILD-TYPE  4  5 14  1
D53V4, multiclass
    clus
vv   DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  T1                          5                            4
  T2                         23                            5
  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
  DEL PEAK 31(18Q23) MUTATED   69 39 30
  DEL PEAK 31(18Q23) WILD-TYPE 15  6  3
D53V5, multiclass
    clus
vv   DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  N0                         69                           15
  N1                         39                            6
  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"
D53V6, binary
                              cls
clus                             0   1
  DEL PEAK 31(18Q23) MUTATED   104  23
  DEL PEAK 31(18Q23) WILD-TYPE  21   1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(18Q23) MUTATED    104   23
  DEL PEAK 31(18Q23) WILD-TYPE   21    1
   clus
vv  DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  0                        104                           21
  1                         23                            1
[1] 2 2
[1] FALSE
D53V7, binary
                              cls
clus                            0  1
  DEL PEAK 31(18Q23) MUTATED   66 75
  DEL PEAK 31(18Q23) WILD-TYPE 10 14
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(18Q23) MUTATED     66   75
  DEL PEAK 31(18Q23) WILD-TYPE   10   14
        clus
vv       DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  FEMALE                         66                           10
  MALE                           75                           14
[1] 2 2
[1] FALSE
D53V8, binary
                              cls
clus                            0  1
  DEL PEAK 31(18Q23) MUTATED   95 19
  DEL PEAK 31(18Q23) WILD-TYPE 17  1
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(18Q23) MUTATED     95   19
  DEL PEAK 31(18Q23) WILD-TYPE   17    1
     clus
vv    DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  NO                          95                           17
  YES                         19                            1
[1] 2 2
[1] FALSE
D53V9, binary
                              cls
clus                             0   1
  DEL PEAK 31(18Q23) MUTATED   126  11
  DEL PEAK 31(18Q23) WILD-TYPE  20   2
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 31(18Q23) MUTATED    126   11
  DEL PEAK 31(18Q23) WILD-TYPE   20    2
                                clus
vv                               DEL PEAK 31(18Q23) MUTATED
  RECTAL ADENOCARCINOMA                                 126
  RECTAL MUCINOUS ADENOCARCINOMA                         11
                                clus
vv                               DEL PEAK 31(18Q23) WILD-TYPE
  RECTAL ADENOCARCINOMA                                    20
  RECTAL MUCINOUS ADENOCARCINOMA                            2
[1] 2 2
[1] FALSE
                              vv
clus                            R0  R1  R2  RX
  DEL PEAK 31(18Q23) MUTATED   103   2  11   4
  DEL PEAK 31(18Q23) WILD-TYPE  20   0   1   0
D53V10, multiclass
    clus
vv   DEL PEAK 31(18Q23) MUTATED DEL PEAK 31(18Q23) WILD-TYPE
  R0                        103                           20
  R1                          2                            0
  R2                         11                            1
  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

Clustering(54) Variable = DEL PEAK 32(19P13.3) MUTATION ANALYSIS
D54V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 32(19P13.3) MUTATED    25   7
  DEL PEAK 32(19P13.3) WILD-TYPE 106  20
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                            32                            126 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                             7                             20 
$`DEL PEAK 32(19P13.3) MUTATED`
TCGA-AG-3611 TCGA-AG-4008 TCGA-AG-A014 TCGA-G5-6233 TCGA-AF-2687 TCGA-AF-2689 
       13.94        17.03        15.95        18.28        46.92        39.48 
TCGA-AF-4110 TCGA-AG-3575 TCGA-AG-3582 TCGA-AG-3608 TCGA-AG-3725 TCGA-AG-3732 
       29.98        12.00        36.03        15.95        20.98        32.98 
TCGA-AG-3881 TCGA-AG-3893 TCGA-AG-A016 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6624 
       19.04        35.01         9.07         6.05        33.17        48.20 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DT-5265 TCGA-DY-A1DE 
       25.05        31.00        13.97        10.98        12.62       129.27 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EI-6509 TCGA-EI-6513 TCGA-EI-6885 TCGA-F5-6571 
       24.13        51.48        17.00        16.34        13.64        42.35 
TCGA-F5-6702 TCGA-F5-6810 
       28.57         0.39 

$`DEL PEAK 32(19P13.3) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-A00H TCGA-AG-A015 
       10.39         8.02        19.99        17.03        25.97        36.03 
TCGA-AG-A01N TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-G5-6641 TCGA-AF-2690 
       31.00        51.98        21.24        55.76        26.43        17.23 
TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 
       43.04        13.55        37.97        34.49        37.74        16.83 
TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56L TCGA-AF-A56N 
       24.36        20.02        24.59        86.63        65.98        11.84 
TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3586 
       36.03        32.02         7.07        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-3599 TCGA-AG-3600 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3726 TCGA-AG-3727 
       12.03         6.05         0.99        19.99         7.99         0.99 
TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3742 TCGA-AG-3878 TCGA-AG-3882 TCGA-AG-3883 
       29.98        37.02         0.99         0.99        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        13.02        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C 
        1.02         3.98        46.03        20.98        13.94         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 
       23.01        37.02         1.02         1.02        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         2.50 
TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6621 TCGA-CI-6622 
       43.20        27.55        26.43        19.46        13.78        44.78 
TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-5337 TCGA-DC-6154 
       47.44        78.12         7.17        21.01        26.04        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6160 TCGA-DC-6681 TCGA-DC-6682 TCGA-DC-6683 
       31.00        51.98        44.02        25.97        25.05        25.05 
TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1H8 TCGA-EF-5830 TCGA-EF-5831 
      126.44        41.36        57.24        32.61         3.48         4.18 
TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 
       20.55        19.96        20.91        18.28        15.85        17.69 
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-7002 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6811 TCGA-F5-6812 
       11.97         8.45         9.96        49.51        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                          0.39                           0.99 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE 
                        20.010                         21.125 
[1] "0.4 - 129.3 (20.0)" "1.0 - 126.4 (21.1)"
[1] "hr=" "1.5"
D54V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 32(19P13.3) MUTATED         5        3         7         0         0
  DEL PEAK 32(19P13.3) WILD-TYPE      25        5        33         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 32(19P13.3) MUTATED           1          1          4          3
  DEL PEAK 32(19P13.3) WILD-TYPE         3          6         21         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 32(19P13.3) MUTATED          5         4
  DEL PEAK 32(19P13.3) WILD-TYPE       13         3
D54V3, multiclass
            clus
vv           DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  STAGE I                               5                             25
  STAGE II                              3                              5
  STAGE IIA                             7                             33
  STAGE IIB                             0                              2
  STAGE IIC                             0                              1
  STAGE III                             1                              3
  STAGE IIIA                            1                              6
  STAGE IIIB                            4                             21
  STAGE IIIC                            3                             11
  STAGE IV                              5                             13
  STAGE IVA                             4                              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 32(19P13.3) MUTATED    0  6 27  2
  DEL PEAK 32(19P13.3) WILD-TYPE  9 22 85 12
D54V4, multiclass
    clus
vv   DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  T1                            0                              9
  T2                            6                             22
  T3                           27                             85
  T4                            2                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 32(19P13.3) MUTATED   15 12  8
  DEL PEAK 32(19P13.3) WILD-TYPE 69 33 25
D54V5, multiclass
    clus
vv   DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  N0                           15                             69
  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"
D54V6, binary
                                cls
clus                              0  1
  DEL PEAK 32(19P13.3) MUTATED   26  8
  DEL PEAK 32(19P13.3) WILD-TYPE 99 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED     26    8
  DEL PEAK 32(19P13.3) WILD-TYPE   99   16
   clus
vv  DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  0                           26                             99
  1                            8                             16
[1] 2 2
[1] FALSE
D54V7, binary
                                cls
clus                              0  1
  DEL PEAK 32(19P13.3) MUTATED   16 20
  DEL PEAK 32(19P13.3) WILD-TYPE 60 69
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED     16   20
  DEL PEAK 32(19P13.3) WILD-TYPE   60   69
        clus
vv       DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  FEMALE                           16                             60
  MALE                             20                             69
[1] 2 2
[1] FALSE
D54V8, binary
                                cls
clus                              0  1
  DEL PEAK 32(19P13.3) MUTATED   24  2
  DEL PEAK 32(19P13.3) WILD-TYPE 88 18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED     24    2
  DEL PEAK 32(19P13.3) WILD-TYPE   88   18
     clus
vv    DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) WILD-TYPE
  NO                            24                             88
  YES                            2                             18
[1] 2 2
[1] FALSE
D54V9, binary
                                cls
clus                               0   1
  DEL PEAK 32(19P13.3) MUTATED    33   1
  DEL PEAK 32(19P13.3) WILD-TYPE 113  12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 32(19P13.3) MUTATED     33    1
  DEL PEAK 32(19P13.3) WILD-TYPE  113   12
                                clus
vv                               DEL PEAK 32(19P13.3) MUTATED
  RECTAL ADENOCARCINOMA                                    33
  RECTAL MUCINOUS ADENOCARCINOMA                            1
                                clus
vv                               DEL PEAK 32(19P13.3) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     113
  RECTAL MUCINOUS ADENOCARCINOMA                             12
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 32(19P13.3) MUTATED   24  0  3  1
  DEL PEAK 32(19P13.3) WILD-TYPE 99  2  9  3
D54V10, multiclass
    clus
vv   DEL PEAK 32(19P13.3) MUTATED DEL PEAK 32(19P13.3) 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"
D54V11, continuous

Clustering(55) Variable = DEL PEAK 33(20P12.1) MUTATION ANALYSIS
D55V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 33(20P12.1) MUTATED    29  15
  DEL PEAK 33(20P12.1) WILD-TYPE 102  12
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            44                            114 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                            15                             12 
$`DEL PEAK 33(20P12.1) MUTATED`
TCGA-AF-3913 TCGA-AG-A01N TCGA-G5-6641 TCGA-AF-2689 TCGA-AF-4110 TCGA-AF-A56K 
       10.39        31.00        26.43        39.48        29.98        86.63 
TCGA-AF-A56L TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3583 
       65.98        11.84        36.03        32.02         7.07        20.05 
TCGA-AG-3584 TCGA-AG-3600 TCGA-AG-3608 TCGA-AG-3742 TCGA-AG-3883 TCGA-AG-3902 
       24.00         6.05        15.95         0.99         1.02        32.02 
TCGA-AG-4022 TCGA-AG-A008 TCGA-AG-A01J TCGA-AG-A026 TCGA-AG-A02G TCGA-AH-6547 
       46.03        13.94         1.02         1.94        38.96         2.50 
TCGA-AH-6643 TCGA-CI-6624 TCGA-DC-6154 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6683 
       43.20        48.20        12.00        10.98        44.02        25.05 
TCGA-DY-A1DC TCGA-DY-A1DD TCGA-DY-A1DF TCGA-DY-A1H8 TCGA-EF-5831 TCGA-EI-6511 
       41.36        57.24        24.13        32.61         4.18        15.85 
TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-7004 TCGA-F5-6571 
       17.69        16.41        11.51        10.78         8.45        42.35 
TCGA-F5-6702 TCGA-F5-6864 
       28.57        12.46 

$`DEL PEAK 33(20P12.1) WILD-TYPE`
TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A00H 
        8.02        13.94        19.99        17.03        17.03        25.97 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        51.98        21.24        18.28        55.76 
TCGA-AF-2687 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-3400 
       46.92        17.23        43.04        13.55        37.97        34.49 
TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 TCGA-AG-3575 
       37.74        16.83        24.36        20.02        24.59        12.00 
TCGA-AG-3582 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3593 
       36.03         1.02        46.03        34.03        34.03        34.03 
TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3599 TCGA-AG-3605 TCGA-AG-3609 TCGA-AG-3725 
        2.01        50.04        12.03         0.99        19.99        20.98 
TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3878 
        7.99         0.99        29.98        37.02        32.98         0.99 
TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3885 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 
       19.04        19.99        17.95        36.95        13.02        35.01 
TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 TCGA-AG-3901 TCGA-AG-3909 TCGA-AG-3999 
       14.01         1.02        48.03        25.02        19.99        28.04 
TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-4007 TCGA-AG-4021 TCGA-AG-A002 TCGA-AG-A00C 
       36.03        14.04         1.02         3.98        20.98         6.02 
TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A02N 
       23.01        37.02         9.07         1.02        49.97        61.97 
TCGA-AG-A02X TCGA-AG-A032 TCGA-AH-6544 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 
       41.00        38.04        38.56        27.55        26.43        19.46 
TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 
        6.05        33.17        13.78        44.78        47.44        78.12 
TCGA-CL-5918 TCGA-DC-4745 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6155 
        7.17        21.01        25.05        26.04        31.00        13.97 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DC-6682 TCGA-DT-5265 TCGA-DY-A0XA 
       31.00        51.98        25.97        25.05        12.62       126.44 
TCGA-DY-A1DE TCGA-DY-A1DG TCGA-EF-5830 TCGA-EI-6506 TCGA-EI-6507 TCGA-EI-6508 
      129.27        51.48         3.48        20.55        19.96        20.91 
TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6513 TCGA-EI-6514 TCGA-EI-6882 TCGA-EI-6885 
       17.00        18.28        16.34        16.31         8.61        13.64 
TCGA-EI-6917 TCGA-EI-7002 TCGA-F5-6464 TCGA-F5-6465 TCGA-F5-6810 TCGA-F5-6811 
       17.46        11.97         9.96        49.51         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-G5-6572 
       36.49        19.66        37.18        38.14        11.87        47.08 

  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                          0.99                           0.39 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                         86.63                         129.27 
  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE 
                        22.025                         20.995 
[1] "1.0 - 86.6 (22.0)"  "0.4 - 129.3 (21.0)"
[1] "hr=" "3.2"
D55V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 33(20P12.1) MUTATED         7        5         9         0         1
  DEL PEAK 33(20P12.1) WILD-TYPE      23        3        31         2         0
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 33(20P12.1) MUTATED           0          4          7          5
  DEL PEAK 33(20P12.1) WILD-TYPE         4          3         18          9
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 33(20P12.1) MUTATED          6         3
  DEL PEAK 33(20P12.1) WILD-TYPE       12         4
D55V3, multiclass
            clus
vv           DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  STAGE I                               7                             23
  STAGE II                              5                              3
  STAGE IIA                             9                             31
  STAGE IIB                             0                              2
  STAGE IIC                             1                              0
  STAGE III                             0                              4
  STAGE IIIA                            4                              3
  STAGE IIIB                            7                             18
  STAGE IIIC                            5                              9
  STAGE IV                              6                             12
  STAGE IVA                             3                              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 33(20P12.1) MUTATED    2  9 33  5
  DEL PEAK 33(20P12.1) WILD-TYPE  7 19 79  9
D55V4, multiclass
    clus
vv   DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  T1                            2                              7
  T2                            9                             19
  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 33(20P12.1) MUTATED   24 13 12
  DEL PEAK 33(20P12.1) WILD-TYPE 60 32 21
D55V5, multiclass
    clus
vv   DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  N0                           24                             60
  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"
D55V6, binary
                                cls
clus                              0  1
  DEL PEAK 33(20P12.1) MUTATED   38  8
  DEL PEAK 33(20P12.1) WILD-TYPE 87 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     38    8
  DEL PEAK 33(20P12.1) WILD-TYPE   87   16
   clus
vv  DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  0                           38                             87
  1                            8                             16
[1] 2 2
[1] FALSE
D55V7, binary
                                cls
clus                              0  1
  DEL PEAK 33(20P12.1) MUTATED   25 24
  DEL PEAK 33(20P12.1) WILD-TYPE 51 65
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     25   24
  DEL PEAK 33(20P12.1) WILD-TYPE   51   65
        clus
vv       DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  FEMALE                           25                             51
  MALE                             24                             65
[1] 2 2
[1] FALSE
D55V8, binary
                                cls
clus                              0  1
  DEL PEAK 33(20P12.1) MUTATED   31  4
  DEL PEAK 33(20P12.1) WILD-TYPE 81 16
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     31    4
  DEL PEAK 33(20P12.1) WILD-TYPE   81   16
     clus
vv    DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(20P12.1) WILD-TYPE
  NO                            31                             81
  YES                            4                             16
[1] 2 2
[1] FALSE
D55V9, binary
                                cls
clus                               0   1
  DEL PEAK 33(20P12.1) MUTATED    43   5
  DEL PEAK 33(20P12.1) WILD-TYPE 103   8
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 33(20P12.1) MUTATED     43    5
  DEL PEAK 33(20P12.1) WILD-TYPE  103    8
                                clus
vv                               DEL PEAK 33(20P12.1) MUTATED
  RECTAL ADENOCARCINOMA                                    43
  RECTAL MUCINOUS ADENOCARCINOMA                            5
                                clus
vv                               DEL PEAK 33(20P12.1) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     103
  RECTAL MUCINOUS ADENOCARCINOMA                              8
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 33(20P12.1) MUTATED   36  1  5  1
  DEL PEAK 33(20P12.1) WILD-TYPE 87  1  7  3
D55V10, multiclass
    clus
vv   DEL PEAK 33(20P12.1) MUTATED DEL PEAK 33(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"
D55V11, continuous

Clustering(56) Variable = DEL PEAK 34(21Q11.2) MUTATION ANALYSIS
D56V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 34(21Q11.2) MUTATED   55 14
  DEL PEAK 34(21Q11.2) WILD-TYPE 76 13
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                            69                             89 
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                            14                             13 
$`DEL PEAK 34(21Q11.2) MUTATED`
TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A01N TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2687 
       17.03        17.03        31.00        18.28        26.43        46.92 
TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6655 
       39.48        17.23        37.97        29.98        24.36        20.02 
TCGA-AF-6672 TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3575 TCGA-AG-3581 
       24.59        86.63        11.84        36.03        12.00         7.07 
TCGA-AG-3582 TCGA-AG-3584 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3593 TCGA-AG-3599 
       36.03        24.00        46.03        34.03        34.03        12.03 
TCGA-AG-3609 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3881 TCGA-AG-3882 TCGA-AG-3896 
       19.99        20.98        29.98        19.04        19.99         1.02 
TCGA-AG-3898 TCGA-AG-3909 TCGA-AG-4001 TCGA-AG-4005 TCGA-AG-A020 TCGA-AG-A026 
       48.03        19.99        36.03        14.04         1.02         1.94 
TCGA-AG-A02G TCGA-AG-A02N TCGA-AG-A02X TCGA-AH-6544 TCGA-AH-6643 TCGA-CI-6621 
       38.96        61.97        41.00        38.56        43.20        13.78 
TCGA-CI-6624 TCGA-DC-4745 TCGA-DC-6155 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6682 
       48.20        21.01        13.97        51.98        10.98        25.05 
TCGA-DC-6683 TCGA-DY-A0XA TCGA-DY-A1DD TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5830 
       25.05       126.44        57.24        51.48        32.61         3.48 
TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
        4.18        20.55        20.91        15.85        17.69        16.34 
TCGA-EI-6881 TCGA-EI-7002 TCGA-EI-7004 TCGA-F5-6571 TCGA-F5-6810 TCGA-F5-6811 
       16.41        11.97         8.45        42.35         0.39        32.19 
TCGA-F5-6812 TCGA-F5-6814 TCGA-F5-6863 
       36.49        37.18        11.87 

$`DEL PEAK 34(21Q11.2) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-A00H TCGA-AG-A014 
       10.39         8.02        13.94        19.99        25.97        15.95 
TCGA-AG-A015 TCGA-AG-A023 TCGA-BM-6198 TCGA-G5-6235 TCGA-AF-2691 TCGA-AF-2692 
       36.03        51.98        21.24        55.76        43.04        13.55 
TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-A56L TCGA-AG-3578 TCGA-AG-3583 
       34.49        37.74        16.83        65.98        32.02        20.05 
TCGA-AG-3586 TCGA-AG-3592 TCGA-AG-3594 TCGA-AG-3598 TCGA-AG-3600 TCGA-AG-3605 
        1.02        34.03         2.01        50.04         6.05         0.99 
TCGA-AG-3608 TCGA-AG-3726 TCGA-AG-3727 TCGA-AG-3731 TCGA-AG-3732 TCGA-AG-3742 
       15.95         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-3901 TCGA-AG-3902 TCGA-AG-3999 TCGA-AG-4007 TCGA-AG-4021 
       14.01        25.02        32.02        28.04         1.02         3.98 
TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A00Y TCGA-AG-A011 
       46.03        20.98        13.94         6.02        23.01        37.02 
TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6644 
        9.07         1.02        49.97        38.04         2.50        27.55 
TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 TCGA-CI-6620 TCGA-CI-6622 TCGA-CI-6623 
       26.43        19.46         6.05        33.17        44.78        47.44 
TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-4749 TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 
       78.12         7.17        25.05        26.04        31.00        12.00 
TCGA-DC-6156 TCGA-DC-6160 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A1DC TCGA-DY-A1DE 
       31.00        44.02        25.97        12.62        41.36       129.27 
TCGA-DY-A1DF TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6514 TCGA-EI-6882 
       24.13        19.96        17.00        18.28        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-F5-6702 TCGA-F5-6813 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       28.57        19.66        38.14        12.46        47.08 

  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                          0.39                           0.99 
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                        126.44                         129.27 
  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE 
                         24.00                          20.05 
[1] "0.4 - 126.4 (24.0)" "1.0 - 129.3 (20.1)"
[1] "hr=" "1.2"
D56V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 34(21Q11.2) MUTATED        11        6        16         1         0
  DEL PEAK 34(21Q11.2) WILD-TYPE      19        2        24         1         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 34(21Q11.2) MUTATED           2          5         13          4
  DEL PEAK 34(21Q11.2) WILD-TYPE         2          2         12         10
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 34(21Q11.2) MUTATED          8         2
  DEL PEAK 34(21Q11.2) WILD-TYPE       10         5
D56V3, multiclass
            clus
vv           DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  STAGE I                              11                             19
  STAGE II                              6                              2
  STAGE IIA                            16                             24
  STAGE IIB                             1                              1
  STAGE IIC                             0                              1
  STAGE III                             2                              2
  STAGE IIIA                            5                              2
  STAGE IIIB                           13                             12
  STAGE IIIC                            4                             10
  STAGE IV                              8                             10
  STAGE IVA                             2                              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 34(21Q11.2) MUTATED    1 16 49  6
  DEL PEAK 34(21Q11.2) WILD-TYPE  8 12 63  8
D56V4, multiclass
    clus
vv   DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  T1                            1                              8
  T2                           16                             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 34(21Q11.2) MUTATED   35 24 13
  DEL PEAK 34(21Q11.2) WILD-TYPE 49 21 20
D56V5, multiclass
    clus
vv   DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  N0                           35                             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"
D56V6, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED   57  9
  DEL PEAK 34(21Q11.2) WILD-TYPE 68 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     57    9
  DEL PEAK 34(21Q11.2) WILD-TYPE   68   15
   clus
vv  DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  0                           57                             68
  1                            9                             15
[1] 2 2
[1] FALSE
D56V7, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED   32 41
  DEL PEAK 34(21Q11.2) WILD-TYPE 44 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     32   41
  DEL PEAK 34(21Q11.2) WILD-TYPE   44   48
        clus
vv       DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  FEMALE                           32                             44
  MALE                             41                             48
[1] 2 2
[1] FALSE
D56V8, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED   50  8
  DEL PEAK 34(21Q11.2) WILD-TYPE 62 12
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     50    8
  DEL PEAK 34(21Q11.2) WILD-TYPE   62   12
     clus
vv    DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(21Q11.2) WILD-TYPE
  NO                            50                             62
  YES                            8                             12
[1] 2 2
[1] FALSE
D56V9, binary
                                cls
clus                              0  1
  DEL PEAK 34(21Q11.2) MUTATED   66  3
  DEL PEAK 34(21Q11.2) WILD-TYPE 80 10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 34(21Q11.2) MUTATED     66    3
  DEL PEAK 34(21Q11.2) WILD-TYPE   80   10
                                clus
vv                               DEL PEAK 34(21Q11.2) MUTATED
  RECTAL ADENOCARCINOMA                                    66
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 34(21Q11.2) WILD-TYPE
  RECTAL ADENOCARCINOMA                                      80
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 34(21Q11.2) MUTATED   55  1  4  0
  DEL PEAK 34(21Q11.2) WILD-TYPE 68  1  8  4
D56V10, multiclass
    clus
vv   DEL PEAK 34(21Q11.2) MUTATED DEL PEAK 34(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"
D56V11, continuous

Clustering(57) Variable = DEL PEAK 35(22Q13.31) MUTATION ANALYSIS
D57V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 35(22Q13.31) MUTATED   50 13
  DEL PEAK 35(22Q13.31) WILD-TYPE 81 14
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                             63                              95 
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                             13                              14 
$`DEL PEAK 35(22Q13.31) MUTATED`
TCGA-AG-3611 TCGA-AG-A00H TCGA-BM-6198 TCGA-G5-6233 TCGA-G5-6641 TCGA-AF-2692 
       13.94        25.97        21.24        18.28        26.43        13.55 
TCGA-AF-2693 TCGA-AF-4110 TCGA-AF-6136 TCGA-AF-6672 TCGA-AF-A56L TCGA-AG-3575 
       37.97        29.98        24.36        24.59        65.98        12.00 
TCGA-AG-3578 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 TCGA-AG-3584 TCGA-AG-3591 
       32.02         7.07        36.03        20.05        24.00        34.03 
TCGA-AG-3593 TCGA-AG-3725 TCGA-AG-3728 TCGA-AG-3731 TCGA-AG-3882 TCGA-AG-3883 
       34.03        20.98        29.98        37.02        19.99         1.02 
TCGA-AG-3885 TCGA-AG-3896 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       17.95         1.02        19.99        28.04        36.03        14.04 
TCGA-AG-4021 TCGA-AG-A00Y TCGA-AG-A020 TCGA-AG-A026 TCGA-AG-A02G TCGA-AG-A02X 
        3.98        23.01         1.02         1.94        38.96        41.00 
TCGA-AH-6544 TCGA-AH-6644 TCGA-CI-6619 TCGA-CI-6621 TCGA-CI-6624 TCGA-DC-4745 
       38.56        27.55         6.05        13.78        48.20        21.01 
TCGA-DC-4749 TCGA-DC-5869 TCGA-DC-6155 TCGA-DC-6158 TCGA-DC-6160 TCGA-DC-6682 
       25.05        31.00        13.97        10.98        44.02        25.05 
TCGA-DC-6683 TCGA-DY-A1DC TCGA-DY-A1DE TCGA-DY-A1DG TCGA-DY-A1H8 TCGA-EF-5831 
       25.05        41.36       129.27        51.48        32.61         4.18 
TCGA-EI-6506 TCGA-EI-6508 TCGA-EI-6512 TCGA-EI-6881 TCGA-EI-7002 TCGA-F5-6702 
       20.55        20.91        17.69        16.41        11.97        28.57 
TCGA-F5-6810 TCGA-F5-6812 TCGA-F5-6863 
        0.39        36.49        11.87 

$`DEL PEAK 35(22Q13.31) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 TCGA-AG-A014 
       10.39         8.02        19.99        17.03        17.03        15.95 
TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6235 TCGA-AF-2687 TCGA-AF-2689 
       36.03        31.00        51.98        55.76        46.92        39.48 
TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 TCGA-AF-3911 TCGA-AF-5654 TCGA-AF-6655 
       17.23        43.04        34.49        37.74        16.83        20.02 
TCGA-AF-A56K TCGA-AF-A56N TCGA-AG-3574 TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3592 
       86.63        11.84        36.03         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-3732 TCGA-AG-3742 TCGA-AG-3878 
       19.99         7.99         0.99        32.98         0.99         0.99 
TCGA-AG-3881 TCGA-AG-3887 TCGA-AG-3892 TCGA-AG-3893 TCGA-AG-3894 TCGA-AG-3898 
       19.04        36.95        13.02        35.01        14.01        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-4007 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A008 
       25.02        32.02         1.02        46.03        20.98        13.94 
TCGA-AG-A00C TCGA-AG-A011 TCGA-AG-A016 TCGA-AG-A01J TCGA-AG-A025 TCGA-AG-A02N 
        6.02        37.02         9.07         1.02        49.97        61.97 
TCGA-AG-A032 TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6620 
       38.04         2.50        43.20        26.43        19.46        33.17 
TCGA-CI-6622 TCGA-CI-6623 TCGA-CL-5917 TCGA-CL-5918 TCGA-DC-5337 TCGA-DC-6154 
       44.78        47.44        78.12         7.17        26.04        12.00 
TCGA-DC-6156 TCGA-DC-6157 TCGA-DC-6681 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DD 
       31.00        51.98        25.97        12.62       126.44        57.24 
TCGA-DY-A1DF TCGA-EF-5830 TCGA-EI-6507 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 
       24.13         3.48        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        42.35        32.19 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        12.46        47.08 

  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                           0.39                            0.99 
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                         129.27                          126.44 
  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE 
                          24.00                           19.99 
[1] "0.4 - 129.3 (24.0)" "1.0 - 126.4 (20.0)"
[1] "hr=" "1.7"
D57V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE IIA STAGE IIB
  DEL PEAK 35(22Q13.31) MUTATED        10        2        15         0
  DEL PEAK 35(22Q13.31) WILD-TYPE      20        6        25         2
                                 vv
clus                              STAGE IIC STAGE III STAGE IIIA STAGE IIIB
  DEL PEAK 35(22Q13.31) MUTATED           0         2          4         14
  DEL PEAK 35(22Q13.31) WILD-TYPE         1         2          3         11
                                 vv
clus                              STAGE IIIC STAGE IV STAGE IVA
  DEL PEAK 35(22Q13.31) MUTATED            3       10         3
  DEL PEAK 35(22Q13.31) WILD-TYPE         11        8         4
D57V3, multiclass
            clus
vv           DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  STAGE I                               10                              20
  STAGE II                               2                               6
  STAGE IIA                             15                              25
  STAGE IIB                              0                               2
  STAGE IIC                              0                               1
  STAGE III                              2                               2
  STAGE IIIA                             4                               3
  STAGE IIIB                            14                              11
  STAGE IIIC                             3                              11
  STAGE IV                              10                               8
  STAGE IVA                              3                               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 35(22Q13.31) MUTATED    1 13 48  5
  DEL PEAK 35(22Q13.31) WILD-TYPE  8 15 64  9
D57V4, multiclass
    clus
vv   DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  T1                             1                               8
  T2                            13                              15
  T3                            48                              64
  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 35(22Q13.31) MUTATED   27 27 12
  DEL PEAK 35(22Q13.31) WILD-TYPE 57 18 21
D57V5, multiclass
    clus
vv   DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  N0                            27                              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"
D57V6, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.31) MUTATED   47 12
  DEL PEAK 35(22Q13.31) WILD-TYPE 78 12
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.31) MUTATED     47   12
  DEL PEAK 35(22Q13.31) WILD-TYPE   78   12
   clus
vv  DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  0                            47                              78
  1                            12                              12
[1] 2 2
[1] FALSE
D57V7, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.31) MUTATED   29 39
  DEL PEAK 35(22Q13.31) WILD-TYPE 47 50
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.31) MUTATED     29   39
  DEL PEAK 35(22Q13.31) WILD-TYPE   47   50
        clus
vv       DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  FEMALE                            29                              47
  MALE                              39                              50
[1] 2 2
[1] FALSE
D57V8, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.31) MUTATED   45  6
  DEL PEAK 35(22Q13.31) WILD-TYPE 67 14
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.31) MUTATED     45    6
  DEL PEAK 35(22Q13.31) WILD-TYPE   67   14
     clus
vv    DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(22Q13.31) WILD-TYPE
  NO                             45                              67
  YES                             6                              14
[1] 2 2
[1] FALSE
D57V9, binary
                                 cls
clus                               0  1
  DEL PEAK 35(22Q13.31) MUTATED   61  4
  DEL PEAK 35(22Q13.31) WILD-TYPE 85  9
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 35(22Q13.31) MUTATED     61    4
  DEL PEAK 35(22Q13.31) WILD-TYPE   85    9
                                clus
vv                               DEL PEAK 35(22Q13.31) MUTATED
  RECTAL ADENOCARCINOMA                                     61
  RECTAL MUCINOUS ADENOCARCINOMA                             4
                                clus
vv                               DEL PEAK 35(22Q13.31) WILD-TYPE
  RECTAL ADENOCARCINOMA                                       85
  RECTAL MUCINOUS ADENOCARCINOMA                               9
[1] 2 2
[1] FALSE
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 35(22Q13.31) MUTATED   46  1  7  1
  DEL PEAK 35(22Q13.31) WILD-TYPE 77  1  5  3
D57V10, multiclass
    clus
vv   DEL PEAK 35(22Q13.31) MUTATED DEL PEAK 35(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"
D57V11, continuous

Clustering(58) Variable = DEL PEAK 36(XP22.33) MUTATION ANALYSIS
D58V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 36(XP22.33) MUTATED    28   4
  DEL PEAK 36(XP22.33) WILD-TYPE 103  23
  DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE 
                            32                            126 
  DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE 
                             4                             23 
$`DEL PEAK 36(XP22.33) MUTATED`
TCGA-AG-A00H TCGA-BM-6198 TCGA-AF-2692 TCGA-AF-2693 TCGA-AF-A56N TCGA-AG-3575 
       25.97        21.24        13.55        37.97        11.84        12.00 
TCGA-AG-3578 TCGA-AG-3584 TCGA-AG-3593 TCGA-AG-3594 TCGA-AG-3600 TCGA-AG-3732 
       32.02        24.00        34.03         2.01         6.05        32.98 
TCGA-AG-3881 TCGA-AG-3893 TCGA-AG-4007 TCGA-AG-A008 TCGA-AG-A00C TCGA-AG-A02G 
       19.04        35.01         1.02        13.94         6.02        38.96 
TCGA-AG-A02X TCGA-AH-6544 TCGA-CI-6623 TCGA-CL-5917 TCGA-DC-4745 TCGA-DC-6155 
       41.00        38.56        47.44        78.12        21.01        13.97 
TCGA-DC-6156 TCGA-DC-6160 TCGA-DY-A1DE TCGA-DY-A1H8 TCGA-EI-7002 TCGA-F5-6465 
       31.00        44.02       129.27        32.61        11.97        49.51 
TCGA-F5-6571 TCGA-F5-6810 
       42.35         0.39 

$`DEL PEAK 36(XP22.33) WILD-TYPE`
TCGA-AF-3913 TCGA-AG-3580 TCGA-AG-3611 TCGA-AG-3612 TCGA-AG-3890 TCGA-AG-4008 
       10.39         8.02        13.94        19.99        17.03        17.03 
TCGA-AG-A014 TCGA-AG-A015 TCGA-AG-A01N TCGA-AG-A023 TCGA-G5-6233 TCGA-G5-6235 
       15.95        36.03        31.00        51.98        18.28        55.76 
TCGA-G5-6641 TCGA-AF-2687 TCGA-AF-2689 TCGA-AF-2690 TCGA-AF-2691 TCGA-AF-3400 
       26.43        46.92        39.48        17.23        43.04        34.49 
TCGA-AF-3911 TCGA-AF-4110 TCGA-AF-5654 TCGA-AF-6136 TCGA-AF-6655 TCGA-AF-6672 
       37.74        29.98        16.83        24.36        20.02        24.59 
TCGA-AF-A56K TCGA-AF-A56L TCGA-AG-3574 TCGA-AG-3581 TCGA-AG-3582 TCGA-AG-3583 
       86.63        65.98        36.03         7.07        36.03        20.05 
TCGA-AG-3586 TCGA-AG-3587 TCGA-AG-3591 TCGA-AG-3592 TCGA-AG-3598 TCGA-AG-3599 
        1.02        46.03        34.03        34.03        50.04        12.03 
TCGA-AG-3605 TCGA-AG-3608 TCGA-AG-3609 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-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-3892 TCGA-AG-3894 TCGA-AG-3896 TCGA-AG-3898 
       17.95        36.95        13.02        14.01         1.02        48.03 
TCGA-AG-3901 TCGA-AG-3902 TCGA-AG-3909 TCGA-AG-3999 TCGA-AG-4001 TCGA-AG-4005 
       25.02        32.02        19.99        28.04        36.03        14.04 
TCGA-AG-4021 TCGA-AG-4022 TCGA-AG-A002 TCGA-AG-A00Y TCGA-AG-A011 TCGA-AG-A016 
        3.98        46.03        20.98        23.01        37.02         9.07 
TCGA-AG-A01J TCGA-AG-A020 TCGA-AG-A025 TCGA-AG-A026 TCGA-AG-A02N TCGA-AG-A032 
        1.02         1.02        49.97         1.94        61.97        38.04 
TCGA-AH-6547 TCGA-AH-6643 TCGA-AH-6644 TCGA-AH-6897 TCGA-AH-6903 TCGA-CI-6619 
        2.50        43.20        27.55        26.43        19.46         6.05 
TCGA-CI-6620 TCGA-CI-6621 TCGA-CI-6622 TCGA-CI-6624 TCGA-CL-5918 TCGA-DC-4749 
       33.17        13.78        44.78        48.20         7.17        25.05 
TCGA-DC-5337 TCGA-DC-5869 TCGA-DC-6154 TCGA-DC-6157 TCGA-DC-6158 TCGA-DC-6681 
       26.04        31.00        12.00        51.98        10.98        25.97 
TCGA-DC-6682 TCGA-DC-6683 TCGA-DT-5265 TCGA-DY-A0XA TCGA-DY-A1DC TCGA-DY-A1DD 
       25.05        25.05        12.62       126.44        41.36        57.24 
TCGA-DY-A1DF TCGA-DY-A1DG TCGA-EF-5830 TCGA-EF-5831 TCGA-EI-6506 TCGA-EI-6507 
       24.13        51.48         3.48         4.18        20.55        19.96 
TCGA-EI-6508 TCGA-EI-6509 TCGA-EI-6510 TCGA-EI-6511 TCGA-EI-6512 TCGA-EI-6513 
       20.91        17.00        18.28        15.85        17.69        16.34 
TCGA-EI-6514 TCGA-EI-6881 TCGA-EI-6882 TCGA-EI-6883 TCGA-EI-6884 TCGA-EI-6885 
       16.31        16.41         8.61        11.51        10.78        13.64 
TCGA-EI-6917 TCGA-EI-7004 TCGA-F5-6464 TCGA-F5-6702 TCGA-F5-6811 TCGA-F5-6812 
       17.46         8.45         9.96        28.57        32.19        36.49 
TCGA-F5-6813 TCGA-F5-6814 TCGA-F5-6861 TCGA-F5-6863 TCGA-F5-6864 TCGA-G5-6572 
       19.66        37.18        38.14        11.87        12.46        47.08 

  DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE 
                          0.39                           0.99 
  DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE 
                        129.27                         126.44 
  DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE 
                        28.485                         20.300 
[1] "0.4 - 129.3 (28.5)" "1.0 - 126.4 (20.3)"
[1] "hr=" "1.7"
D58V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE IIA STAGE IIB STAGE IIC
  DEL PEAK 36(XP22.33) MUTATED         6        1        11         0         0
  DEL PEAK 36(XP22.33) WILD-TYPE      24        7        29         2         1
                                vv
clus                             STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  DEL PEAK 36(XP22.33) MUTATED           0          2          4          3
  DEL PEAK 36(XP22.33) WILD-TYPE         4          5         21         11
                                vv
clus                             STAGE IV STAGE IVA
  DEL PEAK 36(XP22.33) MUTATED          4         1
  DEL PEAK 36(XP22.33) WILD-TYPE       14         6
D58V3, multiclass
            clus
vv           DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE
  STAGE I                               6                             24
  STAGE II                              1                              7
  STAGE IIA                            11                             29
  STAGE IIB                             0                              2
  STAGE IIC                             0                              1
  STAGE III                             0                              4
  STAGE IIIA                            2                              5
  STAGE IIIB                            4                             21
  STAGE IIIC                            3                             11
  STAGE IV                              4                             14
  STAGE IVA                             1                              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 36(XP22.33) MUTATED    1  8 22  2
  DEL PEAK 36(XP22.33) WILD-TYPE  8 20 90 12
D58V4, multiclass
    clus
vv   DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE
  T1                            1                              8
  T2                            8                             20
  T3                           22                             90
  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 36(XP22.33) MUTATED   18  8  7
  DEL PEAK 36(XP22.33) WILD-TYPE 66 37 26
D58V5, multiclass
    clus
vv   DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE
  N0                           18                             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"
D58V6, binary
                                cls
clus                               0   1
  DEL PEAK 36(XP22.33) MUTATED    24   6
  DEL PEAK 36(XP22.33) WILD-TYPE 101  18
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XP22.33) MUTATED     24    6
  DEL PEAK 36(XP22.33) WILD-TYPE  101   18
   clus
vv  DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE
  0                           24                            101
  1                            6                             18
[1] 2 2
[1] FALSE
D58V7, binary
                                cls
clus                              0  1
  DEL PEAK 36(XP22.33) MUTATED   17 17
  DEL PEAK 36(XP22.33) WILD-TYPE 59 72
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XP22.33) MUTATED     17   17
  DEL PEAK 36(XP22.33) WILD-TYPE   59   72
        clus
vv       DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE
  FEMALE                           17                             59
  MALE                             17                             72
[1] 2 2
[1] FALSE
D58V8, binary
                                cls
clus                              0  1
  DEL PEAK 36(XP22.33) MUTATED   21  5
  DEL PEAK 36(XP22.33) WILD-TYPE 91 15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XP22.33) MUTATED     21    5
  DEL PEAK 36(XP22.33) WILD-TYPE   91   15
     clus
vv    DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(XP22.33) WILD-TYPE
  NO                            21                             91
  YES                            5                             15
[1] 2 2
[1] FALSE
D58V9, binary
                                cls
clus                               0   1
  DEL PEAK 36(XP22.33) MUTATED    28   3
  DEL PEAK 36(XP22.33) WILD-TYPE 118  10
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 36(XP22.33) MUTATED     28    3
  DEL PEAK 36(XP22.33) WILD-TYPE  118   10
                                clus
vv                               DEL PEAK 36(XP22.33) MUTATED
  RECTAL ADENOCARCINOMA                                    28
  RECTAL MUCINOUS ADENOCARCINOMA                            3
                                clus
vv                               DEL PEAK 36(XP22.33) WILD-TYPE
  RECTAL ADENOCARCINOMA                                     118
  RECTAL MUCINOUS ADENOCARCINOMA                             10
[1] 2 2
[1] FALSE
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 36(XP22.33) MUTATED   24  0  3  1
  DEL PEAK 36(XP22.33) WILD-TYPE 99  2  9  3
D58V10, multiclass
    clus
vv   DEL PEAK 36(XP22.33) MUTATED DEL PEAK 36(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"
D58V11, continuous
