[1] "terrence_modification_tag"
[1] TRUE
[1] "nver"         "-nVNozzle.R1"
[1] "nfn"                                 "/xchip/tcga/Tools/Nozzle/v1.current"
[1] "Nozzle.R1"
[1] "successfully load Nozzle.R1"
[1] "ofn"        "-oTPAAD-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/PAAD-TP/10006103/PAAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/PAAD-TP/10013781/transformed.cor.cli.txt"

nPatients in clinical file=93, in cluster file=102, common to both=86
[1] 47 86
[1] "AMP PEAK  1(1P34.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            5                            81 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            5                            81 
[1] "AMP PEAK  2(1P12) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                         13                          73 
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                         13                          73 
[1] "AMP PEAK  3(6P21.31) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE 
                             5                             81 
  AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE 
                             5                             81 
[1] "AMP PEAK  4(7Q22.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE 
                           25                            61 
  AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE 
                           25                            61 
[1] "AMP PEAK  5(8Q24.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                            35                             51 
  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                            35                             51 
[1] "AMP PEAK  6(9P13.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE 
                           10                            76 
  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE 
                           10                            76 
[1] "AMP PEAK  7(11P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE 
                            12                             74 
  AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE 
                            12                             74 
[1] "AMP PEAK  8(12P13.33) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                             12                              74 
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                             12                              74 
[1] "AMP PEAK  9(12P12.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE 
                            17                             69 
  AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE 
                            17                             69 
[1] "AMP PEAK 10(12P11.21) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE 
                             14                              72 
  AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE 
                             14                              72 
[1] "AMP PEAK 11(12Q15) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE 
                          10                           76 
  AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE 
                          10                           76 
[1] "AMP PEAK 12(17P11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE 
                             3                             83 
  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE 
                             3                             83 
[1] "AMP PEAK 13(17Q21.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE 
                             11                              75 
  AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE 
                             11                              75 
[1] "AMP PEAK 14(18Q11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE 
                            27                             59 
  AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE 
                            27                             59 
[1] "AMP PEAK 15(19Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE 
                            21                             65 
  AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE 
                            21                             65 
[1] "AMP PEAK 16(20Q13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE 
                            26                             60 
  AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE 
                            26                             60 
[1] "AMP PEAK 17(XP22.11) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE 
                             5                             81 
  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE 
                             5                             81 
[1] "AMP PEAK 18(XQ27.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE 
                            9                            77 
  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE 
                            9                            77 
[1] "DEL PEAK  1(1P36.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            23                             63 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            23                             63 
[1] "DEL PEAK  2(1P36.11) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            28                             58 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            28                             58 
[1] "DEL PEAK  3(1P21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE 
                           20                            66 
  DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE 
                           20                            66 
[1] "DEL PEAK  4(1Q42.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE 
                            4                            82 
  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE 
                            4                            82 
[1] "DEL PEAK  5(2P23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE 
                           11                            75 
  DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE 
                           11                            75 
[1] "DEL PEAK  6(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                            3                            83 
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                            3                            83 
[1] "DEL PEAK  7(3P24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                           20                            66 
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                           20                            66 
[1] "DEL PEAK  8(4Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                           15                            71 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                           15                            71 
[1] "DEL PEAK  9(5Q14.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE 
                           20                            66 
  DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE 
                           20                            66 
[1] "DEL PEAK 10(6P25.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE 
                           33                            53 
  DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE 
                           33                            53 
[1] "DEL PEAK 11(7Q36.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE 
                            8                            78 
  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE 
                            8                            78 
[1] "DEL PEAK 12(8P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE 
                           26                            60 
  DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE 
                           26                            60 
[1] "DEL PEAK 13(8Q12.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE 
                            8                            78 
  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE 
                            8                            78 
[1] "DEL PEAK 14(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                           54                            32 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                           54                            32 
[1] "DEL PEAK 15(9Q22.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE 
                            22                             64 
  DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE 
                            22                             64 
[1] "DEL PEAK 16(10Q23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE 
                            13                             73 
  DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE 
                            13                             73 
[1] "DEL PEAK 17(11P15.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE 
                            15                             71 
  DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE 
                            15                             71 
[1] "DEL PEAK 18(12P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE 
                            11                             75 
  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE 
                            11                             75 
[1] "DEL PEAK 19(12Q12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE 
                           8                           78 
  DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE 
                           8                           78 
[1] "DEL PEAK 20(12Q24.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             20                              66 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             20                              66 
[1] "DEL PEAK 21(15Q15.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE 
                            17                             69 
  DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE 
                            17                             69 
[1] "DEL PEAK 22(16Q23.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE 
                             4                             82 
  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE 
                             4                             82 
[1] "DEL PEAK 23(17Q22) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE 
                          24                           62 
  DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE 
                          24                           62 
[1] "DEL PEAK 24(18P11.32) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE 
                             30                              56 
  DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE 
                             30                              56 
[1] "DEL PEAK 25(18Q21.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                            59                             27 
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                            59                             27 
[1] "DEL PEAK 26(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE 
                            16                             70 
  DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE 
                            16                             70 
[1] "DEL PEAK 27(19Q13.41) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE 
                             11                              75 
  DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE 
                             11                              75 
[1] "DEL PEAK 28(21Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE 
                            32                             54 
  DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE 
                            32                             54 
[1] "DEL PEAK 29(22Q13.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE 
                             28                              58 
  DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE 
                             28                              58 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "RADIATIONTHERAPY"                      
[14] "HISTOLOGICALTYPE"                      
[15] "RADIATIONS.RADIATION.REGIMENINDICATION"
[16] "NUMBERPACKYEARSSMOKED"                 
[17] "YEAROFTOBACCOSMOKINGONSET"             
[18] "COMPLETENESS.OF.RESECTION"             
[19] "NUMBER.OF.LYMPH.NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 86 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-F2-6879 TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-7276 TCGA-F2-A44G TCGA-F2-A44H 
          NA          295          360           NA          153          586 
TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-FZ-5920 
           4          385          449            1          166           NA 
TCGA-FZ-5922 TCGA-FZ-5923 TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
          NA           NA          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7920 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
          28           20           NA            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8005 
         361            8           19           24           21           NA 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8637 TCGA-HZ-8638 
          28           16            3            5           NA           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A49I TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          23           29           NA          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7645 TCGA-IB-7646 TCGA-IB-7647 
          13           33          347           NA           NA           NA 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7887 
          NA           NA          476          851           NA           NA 
TCGA-IB-7888 TCGA-IB-7889 TCGA-IB-7890 TCGA-IB-7891 TCGA-IB-7893 TCGA-IB-7897 
          NA           NA           NA          488           NA           NA 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SQ TCGA-IB-A5SS 
          17          522          329          300           NA           NA 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7LX TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
           8           NA           NA          181          164          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-S4-A8RP 
          35          584          110          247          416           NA 
TCGA-US-A774 TCGA-US-A776 TCGA-US-A779 TCGA-US-A77E TCGA-US-A77G TCGA-US-A77J 
          NA          844           NA           NA           NA           NA 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 
Variable 1:'AGE':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 16:'NUMBERPACKYEARSSMOKED':	nDistinctValues=17,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER.OF.LYMPH.NODES':	nDistinctValues=13,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                       "NEOPLASM.DISEASESTAGE"    
 [3] "PATHOLOGY.T.STAGE"         "PATHOLOGY.N.STAGE"        
 [5] "PATHOLOGY.M.STAGE"         "GENDER"                   
 [7] "HISTOLOGICAL.TYPE"         "NUMBERPACKYEARSSMOKED"    
 [9] "COMPLETENESS.OF.RESECTION" "NUMBER.OF.LYMPH.NODES"    
[11] "RACE"                     
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 86 columns, 1 survival variables, and 11 non-survival variables.
AGE, nv=35, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T1 T2 T3 T4 
 2  6 76  2 
[1] "table(vv)"
vv
T1+T2 T3+T4 
    8    78 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T1 T2 T3 T4 
 2  6 76  2 

$ClinVariableType
[1] "binary"

$Class0_nSamples
[1] 8

$Class1_nSamples
[1] 78

$Class0_label
[1] "T1+T2"

$Class1_label
[1] "T3+T4"


T1+T2 T3+T4 
    8    78 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=17, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
NUMBER.OF.LYMPH.NODES, nv=13, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1P34.2) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  1(1P34.2) MUTATED    3  0
  AMP PEAK  1(1P34.2) WILD-TYPE 47 11
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            3                            58 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                            0                            11 
$`AMP PEAK  1(1P34.2) MUTATED`
TCGA-HZ-7289 TCGA-HZ-7925 TCGA-US-A776 
         240          361          844 

$`AMP PEAK  1(1P34.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
          28           20            4            8          369            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          160         1834 

  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                          240                             1 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                          844                          1991 
  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE 
                          361                           165 
[1] "240.0 - 844.0 (361.0)" "1.0 - 1991.0 (165.0)" 
[1] "hr="     "7.6e+07"
D1V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AMP PEAK  1(1P34.2) MUTATED          0        0         1         3         0
  AMP PEAK  1(1P34.2) WILD-TYPE        2        4        13        58         2
                               vv
clus                            STAGE IV
  AMP PEAK  1(1P34.2) MUTATED          1
  AMP PEAK  1(1P34.2) WILD-TYPE        2
D1V3, multiclass
           clus
vv          AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            0                             4
  STAGE IIA                           1                            13
  STAGE IIB                           3                            58
  STAGE III                           0                             2
  STAGE IV                            1                             2
[1] 6 2
[1] 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(1P34.2) MUTATED       0     5
  AMP PEAK  1(1P34.2) WILD-TYPE     8    73
D1V4, multiclass
       clus
vv      AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  T1+T2                           0                             8
  T3+T4                           5                            73
[1] 2 2
[1] FALSE
D1V5, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED    1  4
  AMP PEAK  1(1P34.2) WILD-TYPE 20 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      1    4
  AMP PEAK  1(1P34.2) WILD-TYPE   20   60
   clus
vv  AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  0                           1                            20
  1                           4                            60
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  1(1P34.2) MUTATED    0  1  4
  AMP PEAK  1(1P34.2) WILD-TYPE 41  2 38
D1V6, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  M0                           0                            41
  M1                           1                             2
  MX                           4                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                             0  1
  AMP PEAK  1(1P34.2) MUTATED    1  4
  AMP PEAK  1(1P34.2) WILD-TYPE 43 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1P34.2) MUTATED      1    4
  AMP PEAK  1(1P34.2) WILD-TYPE   43   38
        clus
vv       AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  FEMALE                           1                            43
  MALE                             4                            38
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  1(1P34.2) MUTATED                                     3
  AMP PEAK  1(1P34.2) WILD-TYPE                                  71
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  1(1P34.2) MUTATED                                       1
  AMP PEAK  1(1P34.2) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  1(1P34.2) MUTATED                                                  1
  AMP PEAK  1(1P34.2) WILD-TYPE                                                2
D1V8, multiclass
                                                  clus
vv                                                 AMP PEAK  1(1P34.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           1
                                                  clus
vv                                                 AMP PEAK  1(1P34.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         71
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D1V9, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  1(1P34.2) MUTATED    4  0  0  1
  AMP PEAK  1(1P34.2) WILD-TYPE 51 25  1  1
D1V10, multiclass
    clus
vv   AMP PEAK  1(1P34.2) MUTATED AMP PEAK  1(1P34.2) WILD-TYPE
  R0                           4                            51
  R1                           0                            25
  R2                           0                             1
  RX                           1                             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"
D1V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1P34.2) MUTATED       0                         0     5
  AMP PEAK  1(1P34.2) WILD-TYPE     2                         6    69
D1V12, multiclass
                           clus
vv                          AMP PEAK  1(1P34.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               5
                           clus
vv                          AMP PEAK  1(1P34.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                69
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = AMP PEAK  2(1P12) MUTATION ANALYSIS
D2V1, survival
                             sevent
clus2                          0  1
  AMP PEAK  2(1P12) MUTATED    6  1
  AMP PEAK  2(1P12) WILD-TYPE 44 10
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                          7                          54 
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                          1                          10 
$`AMP PEAK  2(1P12) MUTATED`
TCGA-FB-A78T TCGA-HZ-7925 TCGA-HZ-8636 TCGA-IB-A6UG TCGA-LB-A8F3 TCGA-M8-A5N4 
           1          361            5         1968           35          584 
TCGA-US-A776 
         844 

$`AMP PEAK  2(1P12) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
          28           20            4            8          369            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         851         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
         300         1991            8          181          164          127 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         110          247          416         1955          160         1834 

  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                          1                           3 
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                       1968                        1991 
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                      361.0                       173.5 
[1] "1.0 - 1968.0 (361.0)" "3.0 - 1991.0 (173.5)"
[1] "hr=" "1.4"
D2V2, continuous
                             vv
clus                          STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AMP PEAK  2(1P12) MUTATED          0        0         4         7         0
  AMP PEAK  2(1P12) WILD-TYPE        2        4        10        54         2
                             vv
clus                          STAGE IV
  AMP PEAK  2(1P12) MUTATED          2
  AMP PEAK  2(1P12) WILD-TYPE        1
D2V3, multiclass
           clus
vv          AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE
  STAGE IA                          0                           2
  STAGE IB                          0                           4
  STAGE IIA                         4                          10
  STAGE IIB                         7                          54
  STAGE III                         0                           2
  STAGE IV                          2                           1
[1] 6 2
[1] 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(1P12) MUTATED       0    13
  AMP PEAK  2(1P12) WILD-TYPE     8    65
D2V4, multiclass
       clus
vv      AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE
  T1+T2                         0                           8
  T3+T4                        13                          65
[1] 2 2
[1] FALSE
D2V5, binary
                             cls
clus                           0  1
  AMP PEAK  2(1P12) MUTATED    5  8
  AMP PEAK  2(1P12) WILD-TYPE 16 56
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1P12) MUTATED      5    8
  AMP PEAK  2(1P12) WILD-TYPE   16   56
   clus
vv  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE
  0                         5                          16
  1                         8                          56
[1] 2 2
[1] FALSE
                             vv
clus                          M0 M1 MX
  AMP PEAK  2(1P12) MUTATED    7  2  4
  AMP PEAK  2(1P12) WILD-TYPE 34  1 38
D2V6, multiclass
    clus
vv   AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE
  M0                         7                          34
  M1                         2                           1
  MX                         4                          38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                             cls
clus                           0  1
  AMP PEAK  2(1P12) MUTATED    7  6
  AMP PEAK  2(1P12) WILD-TYPE 37 36
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK  2(1P12) MUTATED      7    6
  AMP PEAK  2(1P12) WILD-TYPE   37   36
        clus
vv       AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE
  FEMALE                         7                          37
  MALE                           6                          36
[1] 2 2
[1] FALSE
                             vv
clus                          PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  2(1P12) MUTATED                                    12
  AMP PEAK  2(1P12) WILD-TYPE                                  62
                             vv
clus                          PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  2(1P12) MUTATED                                       0
  AMP PEAK  2(1P12) WILD-TYPE                                     8
                             vv
clus                          PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  2(1P12) MUTATED                                                  1
  AMP PEAK  2(1P12) WILD-TYPE                                                2
D2V8, multiclass
                                                  clus
vv                                                 AMP PEAK  2(1P12) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                     12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                    0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                         1
                                                  clus
vv                                                 AMP PEAK  2(1P12) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       62
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           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"
D2V9, continuous
[1] "Remove cluster labels:"    "AMP PEAK  2(1P12) MUTATED"
clus
  AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE 
                          2                          24 
                 TCGA-F2-6880                  TCGA-FB-A4P5 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-FB-A5VM                  TCGA-FB-A7DR 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-H6-8124                  TCGA-H6-A45N 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-H8-A6C1                  TCGA-HZ-A77Q 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-IB-7644                  TCGA-IB-7649 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-IB-7651                  TCGA-IB-7885 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-IB-7886                  TCGA-IB-7887 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-IB-7891                  TCGA-IB-8126 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-IB-8127                  TCGA-IB-A5SS 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-IB-A7M4                  TCGA-LB-A7SX 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-OE-A75W                  TCGA-S4-A8RP 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                 TCGA-US-A774                  TCGA-YY-A8LH 
"AMP PEAK  2(1P12) WILD-TYPE" "AMP PEAK  2(1P12) WILD-TYPE" 
                             vv
clus                          R0 R1 R2 RX
  AMP PEAK  2(1P12) MUTATED   10  3  0  0
  AMP PEAK  2(1P12) WILD-TYPE 45 22  1  2
D2V10, multiclass
    clus
vv   AMP PEAK  2(1P12) MUTATED AMP PEAK  2(1P12) WILD-TYPE
  R0                        10                          45
  R1                         3                          22
  R2                         0                           1
  RX                         0                           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"
D2V11, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1P12) MUTATED       0                         2     9
  AMP PEAK  2(1P12) WILD-TYPE     2                         4    65
D2V12, multiclass
                           clus
vv                          AMP PEAK  2(1P12) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                             9
                           clus
vv                          AMP PEAK  2(1P12) WILD-TYPE
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           4
  WHITE                                              65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = AMP PEAK  3(6P21.31) MUTATION ANALYSIS
D3V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  3(6P21.31) MUTATED    4  0
  AMP PEAK  3(6P21.31) WILD-TYPE 46 11
  AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE 
                             4                             57 
  AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE 
                             0                             11 
$`AMP PEAK  3(6P21.31) MUTATED`
TCGA-HZ-8636 TCGA-HZ-A77O TCGA-LB-A8F3 TCGA-US-A776 
           5           11           35          844 

$`AMP PEAK  3(6P21.31) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
          16            3           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          46           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         164          127          584          110          247          416 
TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          160         1834 

  AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE 
                             5                              1 
  AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE 
                           844                           1991 
  AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE 
                            23                            194 
[1] "5.0 - 844.0 (23.0)"   "1.0 - 1991.0 (194.0)"
[1] "hr="     "2.6e+07"
D3V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  3(6P21.31) MUTATED          0        0         2         2
  AMP PEAK  3(6P21.31) WILD-TYPE        2        4        12        59
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK  3(6P21.31) MUTATED           0        1
  AMP PEAK  3(6P21.31) WILD-TYPE         2        2
D3V3, multiclass
           clus
vv          AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            2                             12
  STAGE IIB                            2                             59
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(6P21.31) MUTATED       1     4
  AMP PEAK  3(6P21.31) WILD-TYPE     7    74
D3V4, multiclass
       clus
vv      AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE
  T1+T2                            1                              7
  T3+T4                            4                             74
[1] 2 2
[1] FALSE
D3V5, binary
                                cls
clus                              0  1
  AMP PEAK  3(6P21.31) MUTATED    3  2
  AMP PEAK  3(6P21.31) WILD-TYPE 18 62
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(6P21.31) MUTATED      3    2
  AMP PEAK  3(6P21.31) WILD-TYPE   18   62
   clus
vv  AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE
  0                            3                             18
  1                            2                             62
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  3(6P21.31) MUTATED    0  1  4
  AMP PEAK  3(6P21.31) WILD-TYPE 41  2 38
D3V6, multiclass
    clus
vv   AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE
  M0                            0                             41
  M1                            1                              2
  MX                            4                             38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                                cls
clus                              0  1
  AMP PEAK  3(6P21.31) MUTATED    3  2
  AMP PEAK  3(6P21.31) WILD-TYPE 41 40
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(6P21.31) MUTATED      3    2
  AMP PEAK  3(6P21.31) WILD-TYPE   41   40
        clus
vv       AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE
  FEMALE                            3                             41
  MALE                              2                             40
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  3(6P21.31) MUTATED                                     4
  AMP PEAK  3(6P21.31) WILD-TYPE                                  70
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  3(6P21.31) MUTATED                                       0
  AMP PEAK  3(6P21.31) WILD-TYPE                                     8
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  3(6P21.31) MUTATED                                                  1
  AMP PEAK  3(6P21.31) WILD-TYPE                                                2
D3V8, multiclass
                                                  clus
vv                                                 AMP PEAK  3(6P21.31) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            1
                                                  clus
vv                                                 AMP PEAK  3(6P21.31) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          70
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D3V9, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  3(6P21.31) MUTATED    3  2  0  0
  AMP PEAK  3(6P21.31) WILD-TYPE 52 23  1  2
D3V10, multiclass
    clus
vv   AMP PEAK  3(6P21.31) MUTATED AMP PEAK  3(6P21.31) WILD-TYPE
  R0                            3                             52
  R1                            2                             23
  R2                            0                              1
  RX                            0                              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"
D3V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(6P21.31) MUTATED       0                         1     4
  AMP PEAK  3(6P21.31) WILD-TYPE     2                         5    70
D3V12, multiclass
                           clus
vv                          AMP PEAK  3(6P21.31) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                4
                           clus
vv                          AMP PEAK  3(6P21.31) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = AMP PEAK  4(7Q22.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  4(7Q22.1) MUTATED   16  2
  AMP PEAK  4(7Q22.1) WILD-TYPE 34  9
  AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE 
                           18                            43 
  AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE 
                            2                             9 
$`AMP PEAK  4(7Q22.1) MUTATED`
TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7926 TCGA-HZ-8636 TCGA-HZ-A4BH 
         385          392          240            8            5          194 
TCGA-HZ-A77O TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG 
          11          476         1975          522          300         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-US-A776 TCGA-YB-A89D 
         164          127          584          247          844          160 

$`AMP PEAK  4(7Q22.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 
           1          166          233          396           28           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 
           4            8          369          361           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
          21           28           16            3           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          29           46           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS 
        1989          851          488           17          329         1991 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A774 
           8          181           35          110          416         1955 
TCGA-YY-A8LH 
        1834 

  AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE 
                            5                             1 
  AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE 
                         1975                          1991 
  AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE 
                        273.5                         110.0 
[1] "5.0 - 1975.0 (273.5)" "1.0 - 1991.0 (110.0)"
[1] "hr=" "2.1"
D4V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AMP PEAK  4(7Q22.1) MUTATED          0        0         4        19         0
  AMP PEAK  4(7Q22.1) WILD-TYPE        2        4        10        42         2
                               vv
clus                            STAGE IV
  AMP PEAK  4(7Q22.1) MUTATED          2
  AMP PEAK  4(7Q22.1) WILD-TYPE        1
D4V3, multiclass
           clus
vv          AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            0                             4
  STAGE IIA                           4                            10
  STAGE IIB                          19                            42
  STAGE III                           0                             2
  STAGE IV                            2                             1
[1] 6 2
[1] 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(7Q22.1) MUTATED       1    24
  AMP PEAK  4(7Q22.1) WILD-TYPE     7    54
D4V4, multiclass
       clus
vv      AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE
  T1+T2                           1                             7
  T3+T4                          24                            54
[1] 2 2
[1] FALSE
D4V5, binary
                               cls
clus                             0  1
  AMP PEAK  4(7Q22.1) MUTATED    5 20
  AMP PEAK  4(7Q22.1) WILD-TYPE 16 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(7Q22.1) MUTATED      5   20
  AMP PEAK  4(7Q22.1) WILD-TYPE   16   44
   clus
vv  AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE
  0                           5                            16
  1                          20                            44
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  4(7Q22.1) MUTATED   12  2 11
  AMP PEAK  4(7Q22.1) WILD-TYPE 29  1 31
D4V6, multiclass
    clus
vv   AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE
  M0                          12                            29
  M1                           2                             1
  MX                          11                            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"
D4V7, binary
                               cls
clus                             0  1
  AMP PEAK  4(7Q22.1) MUTATED   11 14
  AMP PEAK  4(7Q22.1) WILD-TYPE 33 28
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(7Q22.1) MUTATED     11   14
  AMP PEAK  4(7Q22.1) WILD-TYPE   33   28
        clus
vv       AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE
  FEMALE                          11                            33
  MALE                            14                            28
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  4(7Q22.1) MUTATED                                    22
  AMP PEAK  4(7Q22.1) WILD-TYPE                                  52
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  4(7Q22.1) MUTATED                                       2
  AMP PEAK  4(7Q22.1) WILD-TYPE                                     6
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  4(7Q22.1) MUTATED                                                  1
  AMP PEAK  4(7Q22.1) WILD-TYPE                                                2
D4V8, multiclass
                                                  clus
vv                                                 AMP PEAK  4(7Q22.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           1
                                                  clus
vv                                                 AMP PEAK  4(7Q22.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         52
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D4V9, continuous
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  4(7Q22.1) MUTATED    9 11  1  2
  AMP PEAK  4(7Q22.1) WILD-TYPE 46 14  0  0
D4V10, multiclass
    clus
vv   AMP PEAK  4(7Q22.1) MUTATED AMP PEAK  4(7Q22.1) WILD-TYPE
  R0                           9                            46
  R1                          11                            14
  R2                           1                             0
  RX                           2                             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"
D4V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(7Q22.1) MUTATED       1                         2    20
  AMP PEAK  4(7Q22.1) WILD-TYPE     1                         4    54
D4V12, multiclass
                           clus
vv                          AMP PEAK  4(7Q22.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              20
                           clus
vv                          AMP PEAK  4(7Q22.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = AMP PEAK  5(8Q24.21) MUTATION ANALYSIS
D5V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  5(8Q24.21) MUTATED   20  4
  AMP PEAK  5(8Q24.21) WILD-TYPE 30  7
  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                            24                             37 
  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                             4                              7 
$`AMP PEAK  5(8Q24.21) MUTATED`
TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
         385          449            1          396          240           28 
TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A77O TCGA-IB-7649 
           4          361           28            5           11         1951 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG 
         476         1975          522          300         1991         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-US-A776 TCGA-YB-A89D 
         181          164          584          110          844          160 

$`AMP PEAK  5(8Q24.21) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A7DR 
         295          360          153          586            4          166 
TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
         392          233           20            8          369            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
          19           24           21           16            3           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q 
          23           29          194           46           13           33 
TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
         347         1989          851          488           17          329 
TCGA-IB-A5ST TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
           8          127           35          247          416         1955 
TCGA-YY-A8LH 
        1834 

  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                             1                              3 
  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                          1991                           1989 
  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE 
                         330.5                          127.0 
[1] "1.0 - 1991.0 (330.5)" "3.0 - 1989.0 (127.0)"
[1] "hr=" "3.1"
D5V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  5(8Q24.21) MUTATED          0        2         7        25
  AMP PEAK  5(8Q24.21) WILD-TYPE        2        2         7        36
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK  5(8Q24.21) MUTATED           0        1
  AMP PEAK  5(8Q24.21) WILD-TYPE         2        2
D5V3, multiclass
           clus
vv          AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             2                              2
  STAGE IIA                            7                              7
  STAGE IIB                           25                             36
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(8Q24.21) MUTATED       3    32
  AMP PEAK  5(8Q24.21) WILD-TYPE     5    46
D5V4, multiclass
       clus
vv      AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE
  T1+T2                            3                              5
  T3+T4                           32                             46
[1] 2 2
[1] FALSE
D5V5, binary
                                cls
clus                              0  1
  AMP PEAK  5(8Q24.21) MUTATED   10 25
  AMP PEAK  5(8Q24.21) WILD-TYPE 11 39
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8Q24.21) MUTATED     10   25
  AMP PEAK  5(8Q24.21) WILD-TYPE   11   39
   clus
vv  AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE
  0                           10                             11
  1                           25                             39
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  5(8Q24.21) MUTATED   20  1 14
  AMP PEAK  5(8Q24.21) WILD-TYPE 21  2 28
D5V6, multiclass
    clus
vv   AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE
  M0                           20                             21
  M1                            1                              2
  MX                           14                             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"
D5V7, binary
                                cls
clus                              0  1
  AMP PEAK  5(8Q24.21) MUTATED   16 19
  AMP PEAK  5(8Q24.21) WILD-TYPE 28 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  5(8Q24.21) MUTATED     16   19
  AMP PEAK  5(8Q24.21) WILD-TYPE   28   23
        clus
vv       AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE
  FEMALE                           16                             28
  MALE                             19                             23
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  5(8Q24.21) MUTATED                                    31
  AMP PEAK  5(8Q24.21) WILD-TYPE                                  43
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  5(8Q24.21) MUTATED                                       2
  AMP PEAK  5(8Q24.21) WILD-TYPE                                     6
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  5(8Q24.21) MUTATED                                                  1
  AMP PEAK  5(8Q24.21) WILD-TYPE                                                2
D5V8, multiclass
                                                  clus
vv                                                 AMP PEAK  5(8Q24.21) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        31
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            1
                                                  clus
vv                                                 AMP PEAK  5(8Q24.21) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          43
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D5V9, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  5(8Q24.21) MUTATED   20 12  1  1
  AMP PEAK  5(8Q24.21) WILD-TYPE 35 13  0  1
D5V10, multiclass
    clus
vv   AMP PEAK  5(8Q24.21) MUTATED AMP PEAK  5(8Q24.21) WILD-TYPE
  R0                           20                             35
  R1                           12                             13
  R2                            1                              0
  RX                            1                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(8Q24.21) MUTATED       1                         0    31
  AMP PEAK  5(8Q24.21) WILD-TYPE     1                         6    43
D5V12, multiclass
                           clus
vv                          AMP PEAK  5(8Q24.21) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               31
                           clus
vv                          AMP PEAK  5(8Q24.21) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 43
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = AMP PEAK  6(9P13.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                            0  1
  AMP PEAK  6(9P13.3) MUTATED    5  0
  AMP PEAK  6(9P13.3) WILD-TYPE 45 11
  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE 
                            5                            56 
  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE 
                            0                            11 
$`AMP PEAK  6(9P13.3) MUTATED`
TCGA-H8-A6C1 TCGA-HZ-7925 TCGA-HZ-8636 TCGA-IB-8126 TCGA-M8-A5N4 
         396          361            5           17          584 

$`AMP PEAK  6(9P13.3) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7289 
         449            1          166          392          233          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
          28           20            4            8          369            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
         851         1975          488          522          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
        1991            8         1968          181          164          127 
TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
          35          110          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE 
                            5                             1 
  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE 
                          584                          1991 
  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE 
                        361.0                         173.5 
[1] "5.0 - 584.0 (361.0)"  "1.0 - 1991.0 (173.5)"
[1] "hr="     "7.9e+07"
D6V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AMP PEAK  6(9P13.3) MUTATED          0        0         3         5         1
  AMP PEAK  6(9P13.3) WILD-TYPE        2        4        11        56         1
                               vv
clus                            STAGE IV
  AMP PEAK  6(9P13.3) MUTATED          1
  AMP PEAK  6(9P13.3) WILD-TYPE        2
D6V3, multiclass
           clus
vv          AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            0                             4
  STAGE IIA                           3                            11
  STAGE IIB                           5                            56
  STAGE III                           1                             1
  STAGE IV                            1                             2
[1] 6 2
[1] 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(9P13.3) MUTATED       0    10
  AMP PEAK  6(9P13.3) WILD-TYPE     8    68
D6V4, multiclass
       clus
vv      AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE
  T1+T2                           0                             8
  T3+T4                          10                            68
[1] 2 2
[1] FALSE
D6V5, binary
                               cls
clus                             0  1
  AMP PEAK  6(9P13.3) MUTATED    4  6
  AMP PEAK  6(9P13.3) WILD-TYPE 17 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(9P13.3) MUTATED      4    6
  AMP PEAK  6(9P13.3) WILD-TYPE   17   58
   clus
vv  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE
  0                           4                            17
  1                           6                            58
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK  6(9P13.3) MUTATED    5  1  4
  AMP PEAK  6(9P13.3) WILD-TYPE 36  2 38
D6V6, multiclass
    clus
vv   AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE
  M0                           5                            36
  M1                           1                             2
  MX                           4                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                             0  1
  AMP PEAK  6(9P13.3) MUTATED    4  6
  AMP PEAK  6(9P13.3) WILD-TYPE 40 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(9P13.3) MUTATED      4    6
  AMP PEAK  6(9P13.3) WILD-TYPE   40   36
        clus
vv       AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE
  FEMALE                           4                            40
  MALE                             6                            36
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  6(9P13.3) MUTATED                                     9
  AMP PEAK  6(9P13.3) WILD-TYPE                                  65
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  6(9P13.3) MUTATED                                       1
  AMP PEAK  6(9P13.3) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  6(9P13.3) MUTATED                                                  0
  AMP PEAK  6(9P13.3) WILD-TYPE                                                3
D6V8, multiclass
                                                  clus
vv                                                 AMP PEAK  6(9P13.3) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           0
                                                  clus
vv                                                 AMP PEAK  6(9P13.3) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D6V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK  6(9P13.3) MUTATED"
clus
  AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE 
                            2                            24 
                   TCGA-F2-6880                    TCGA-FB-A4P5 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-FB-A5VM                    TCGA-FB-A78T 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-FB-A7DR                    TCGA-H6-8124 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-H6-A45N                    TCGA-HZ-A77Q 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-IB-7644                    TCGA-IB-7649 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-IB-7651                    TCGA-IB-7885 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-IB-7886                    TCGA-IB-7887 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-IB-7891                    TCGA-IB-8127 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-IB-A5SS                    TCGA-IB-A6UG 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-IB-A7M4                    TCGA-LB-A7SX 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-OE-A75W                    TCGA-S4-A8RP 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                   TCGA-US-A774                    TCGA-YY-A8LH 
"AMP PEAK  6(9P13.3) WILD-TYPE" "AMP PEAK  6(9P13.3) WILD-TYPE" 
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK  6(9P13.3) MUTATED    6  4  0  0
  AMP PEAK  6(9P13.3) WILD-TYPE 49 21  1  2
D6V10, multiclass
    clus
vv   AMP PEAK  6(9P13.3) MUTATED AMP PEAK  6(9P13.3) WILD-TYPE
  R0                           6                            49
  R1                           4                            21
  R2                           0                             1
  RX                           0                             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"
D6V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(9P13.3) MUTATED       0                         1     8
  AMP PEAK  6(9P13.3) WILD-TYPE     2                         5    66
D6V12, multiclass
                           clus
vv                          AMP PEAK  6(9P13.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               8
                           clus
vv                          AMP PEAK  6(9P13.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = AMP PEAK  7(11P11.2) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  7(11P11.2) MUTATED    6  2
  AMP PEAK  7(11P11.2) WILD-TYPE 44  9
  AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE 
                             8                             53 
  AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE 
                             2                              9 
$`AMP PEAK  7(11P11.2) MUTATED`
TCGA-FB-A545 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-LB-A8F3 
         385         1975          522          300         1968           35 
TCGA-M8-A5N4 TCGA-US-A776 
         584          844 

$`AMP PEAK  7(11P11.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
        1989          476          851          488           17          329 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-OE-A75W 
        1991            8          181          164          127          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         247          416         1955          160         1834 

  AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE 
                            35                              1 
  AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE 
                          1975                           1991 
  AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE 
                           553                            160 
[1] "35.0 - 1975.0 (553.0)" "1.0 - 1991.0 (160.0)" 
[1] "hr=" "1.5"
D7V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  7(11P11.2) MUTATED          0        0         5         7
  AMP PEAK  7(11P11.2) WILD-TYPE        2        4         9        54
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK  7(11P11.2) MUTATED           0        0
  AMP PEAK  7(11P11.2) WILD-TYPE         2        3
D7V3, multiclass
           clus
vv          AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            5                              9
  STAGE IIB                            7                             54
  STAGE III                            0                              2
  STAGE IV                             0                              3
[1] 6 2
[1] 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(11P11.2) MUTATED       0    12
  AMP PEAK  7(11P11.2) WILD-TYPE     8    66
D7V4, multiclass
       clus
vv      AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE
  T1+T2                            0                              8
  T3+T4                           12                             66
[1] 2 2
[1] FALSE
D7V5, binary
                                cls
clus                              0  1
  AMP PEAK  7(11P11.2) MUTATED    5  7
  AMP PEAK  7(11P11.2) WILD-TYPE 16 57
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11P11.2) MUTATED      5    7
  AMP PEAK  7(11P11.2) WILD-TYPE   16   57
   clus
vv  AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE
  0                            5                             16
  1                            7                             57
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  7(11P11.2) MUTATED    9  0  3
  AMP PEAK  7(11P11.2) WILD-TYPE 32  3 39
D7V6, multiclass
    clus
vv   AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE
  M0                            9                             32
  M1                            0                              3
  MX                            3                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                                cls
clus                              0  1
  AMP PEAK  7(11P11.2) MUTATED    4  8
  AMP PEAK  7(11P11.2) WILD-TYPE 40 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(11P11.2) MUTATED      4    8
  AMP PEAK  7(11P11.2) WILD-TYPE   40   34
        clus
vv       AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE
  FEMALE                            4                             40
  MALE                              8                             34
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  7(11P11.2) MUTATED                                    11
  AMP PEAK  7(11P11.2) WILD-TYPE                                  63
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  7(11P11.2) MUTATED                                       0
  AMP PEAK  7(11P11.2) WILD-TYPE                                     8
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  7(11P11.2) MUTATED                                                  1
  AMP PEAK  7(11P11.2) WILD-TYPE                                                2
D7V8, multiclass
                                                  clus
vv                                                 AMP PEAK  7(11P11.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        11
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            1
                                                  clus
vv                                                 AMP PEAK  7(11P11.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          63
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D7V9, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  7(11P11.2) MUTATED    5  6  0  0
  AMP PEAK  7(11P11.2) WILD-TYPE 50 19  1  2
D7V10, multiclass
    clus
vv   AMP PEAK  7(11P11.2) MUTATED AMP PEAK  7(11P11.2) WILD-TYPE
  R0                            5                             50
  R1                            6                             19
  R2                            0                              1
  RX                            0                              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"
D7V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(11P11.2) MUTATED       0                         2     9
  AMP PEAK  7(11P11.2) WILD-TYPE     2                         4    65
D7V12, multiclass
                           clus
vv                          AMP PEAK  7(11P11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                                9
                           clus
vv                          AMP PEAK  7(11P11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = AMP PEAK  8(12P13.33) MUTATION ANALYSIS
D8V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK  8(12P13.33) MUTATED    6  1
  AMP PEAK  8(12P13.33) WILD-TYPE 44 10
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                              7                              54 
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                              1                              10 
$`AMP PEAK  8(12P13.33) MUTATED`
TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-A77O TCGA-IB-8127 TCGA-IB-A6UG TCGA-LB-A7SX 
         240            4           11          522         1968          127 
TCGA-US-A776 
         844 

$`AMP PEAK  8(12P13.33) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
         851         1975          488           17          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 
        1991            8          181          164           35          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         110          247          416         1955          160         1834 

  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                              4                               1 
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                           1968                            1991 
  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE 
                          240.0                           173.5 
[1] "4.0 - 1968.0 (240.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1.3"
D8V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  8(12P13.33) MUTATED          0        1         1        10
  AMP PEAK  8(12P13.33) WILD-TYPE        2        3        13        51
                                 vv
clus                              STAGE III STAGE IV
  AMP PEAK  8(12P13.33) MUTATED           0        0
  AMP PEAK  8(12P13.33) WILD-TYPE         2        3
D8V3, multiclass
           clus
vv          AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  STAGE IA                              0                               2
  STAGE IB                              1                               3
  STAGE IIA                             1                              13
  STAGE IIB                            10                              51
  STAGE III                             0                               2
  STAGE IV                              0                               3
[1] 6 2
[1] 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(12P13.33) MUTATED       2    10
  AMP PEAK  8(12P13.33) WILD-TYPE     6    68
D8V4, multiclass
       clus
vv      AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  T1+T2                             2                               6
  T3+T4                            10                              68
[1] 2 2
[1] FALSE
D8V5, binary
                                 cls
clus                               0  1
  AMP PEAK  8(12P13.33) MUTATED    2 10
  AMP PEAK  8(12P13.33) WILD-TYPE 19 54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.33) MUTATED      2   10
  AMP PEAK  8(12P13.33) WILD-TYPE   19   54
   clus
vv  AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  0                             2                              19
  1                            10                              54
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK  8(12P13.33) MUTATED    5  0  7
  AMP PEAK  8(12P13.33) WILD-TYPE 36  3 35
D8V6, multiclass
    clus
vv   AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  M0                             5                              36
  M1                             0                               3
  MX                             7                              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                 cls
clus                               0  1
  AMP PEAK  8(12P13.33) MUTATED    3  9
  AMP PEAK  8(12P13.33) WILD-TYPE 41 33
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK  8(12P13.33) MUTATED      3    9
  AMP PEAK  8(12P13.33) WILD-TYPE   41   33
        clus
vv       AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  FEMALE                             3                              41
  MALE                               9                              33
[1] 2 2
[1] FALSE
                                 vv
clus                              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  8(12P13.33) MUTATED                                     9
  AMP PEAK  8(12P13.33) WILD-TYPE                                  65
                                 vv
clus                              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  8(12P13.33) MUTATED                                       1
  AMP PEAK  8(12P13.33) WILD-TYPE                                     7
                                 vv
clus                              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  8(12P13.33) MUTATED                                                  1
  AMP PEAK  8(12P13.33) WILD-TYPE                                                2
D8V8, multiclass
                                                  clus
vv                                                 AMP PEAK  8(12P13.33) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             1
                                                  clus
vv                                                 AMP PEAK  8(12P13.33) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                           65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                          7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                               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"
D8V9, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK  8(12P13.33) MUTATED    6  5  0  1
  AMP PEAK  8(12P13.33) WILD-TYPE 49 20  1  1
D8V10, multiclass
    clus
vv   AMP PEAK  8(12P13.33) MUTATED AMP PEAK  8(12P13.33) WILD-TYPE
  R0                             6                              49
  R1                             5                              20
  R2                             0                               1
  RX                             1                               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"
D8V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(12P13.33) MUTATED       0                         1    10
  AMP PEAK  8(12P13.33) WILD-TYPE     2                         5    64
D8V12, multiclass
                           clus
vv                          AMP PEAK  8(12P13.33) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                10
                           clus
vv                          AMP PEAK  8(12P13.33) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = AMP PEAK  9(12P12.1) MUTATION ANALYSIS
D9V1, survival
                                sevent
clus2                             0  1
  AMP PEAK  9(12P12.1) MUTATED    8  2
  AMP PEAK  9(12P12.1) WILD-TYPE 42  9
  AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE 
                            10                             51 
  AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE 
                             2                              9 
$`AMP PEAK  9(12P12.1) MUTATED`
TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-HZ-A77O 
         240           20            4            5           46           11 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A6UG TCGA-L1-A7W4 
        1975          522         1968          164 

$`AMP PEAK  9(12P12.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
          28            8          369          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 
          24           21           28           16            3           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
          23           29          194           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          476          851          488           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-LB-A7SX 
         329          300         1991            8          181          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
          35          584          110          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

  AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE 
                             4                              1 
  AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE 
                          1975                           1991 
  AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE 
                           105                            194 
[1] "4.0 - 1975.0 (105.0)" "1.0 - 1991.0 (194.0)"
[1] "hr=" "1.2"
D9V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK  9(12P12.1) MUTATED          0        1         0        15
  AMP PEAK  9(12P12.1) WILD-TYPE        2        3        14        46
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK  9(12P12.1) MUTATED           0        1
  AMP PEAK  9(12P12.1) WILD-TYPE         2        2
D9V3, multiclass
           clus
vv          AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             1                              3
  STAGE IIA                            0                             14
  STAGE IIB                           15                             46
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(12P12.1) MUTATED       2    15
  AMP PEAK  9(12P12.1) WILD-TYPE     6    63
D9V4, multiclass
       clus
vv      AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE
  T1+T2                            2                              6
  T3+T4                           15                             63
[1] 2 2
[1] FALSE
D9V5, binary
                                cls
clus                              0  1
  AMP PEAK  9(12P12.1) MUTATED    2 15
  AMP PEAK  9(12P12.1) WILD-TYPE 19 49
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12P12.1) MUTATED      2   15
  AMP PEAK  9(12P12.1) WILD-TYPE   19   49
   clus
vv  AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE
  0                            2                             19
  1                           15                             49
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK  9(12P12.1) MUTATED    9  1  7
  AMP PEAK  9(12P12.1) WILD-TYPE 32  2 35
D9V6, multiclass
    clus
vv   AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE
  M0                            9                             32
  M1                            1                              2
  MX                            7                             35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                                cls
clus                              0  1
  AMP PEAK  9(12P12.1) MUTATED    5 12
  AMP PEAK  9(12P12.1) WILD-TYPE 39 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  9(12P12.1) MUTATED      5   12
  AMP PEAK  9(12P12.1) WILD-TYPE   39   30
        clus
vv       AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE
  FEMALE                            5                             39
  MALE                             12                             30
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK  9(12P12.1) MUTATED                                    14
  AMP PEAK  9(12P12.1) WILD-TYPE                                  60
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK  9(12P12.1) MUTATED                                       2
  AMP PEAK  9(12P12.1) WILD-TYPE                                     6
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK  9(12P12.1) MUTATED                                                  0
  AMP PEAK  9(12P12.1) WILD-TYPE                                                3
D9V8, multiclass
                                                  clus
vv                                                 AMP PEAK  9(12P12.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            0
                                                  clus
vv                                                 AMP PEAK  9(12P12.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          60
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D9V9, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK  9(12P12.1) MUTATED    6  9  1  1
  AMP PEAK  9(12P12.1) WILD-TYPE 49 16  0  1
D9V10, multiclass
    clus
vv   AMP PEAK  9(12P12.1) MUTATED AMP PEAK  9(12P12.1) WILD-TYPE
  R0                            6                             49
  R1                            9                             16
  R2                            1                              0
  RX                            1                              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"
D9V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(12P12.1) MUTATED       0                         1    15
  AMP PEAK  9(12P12.1) WILD-TYPE     2                         5    59
D9V12, multiclass
                           clus
vv                          AMP PEAK  9(12P12.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               15
                           clus
vv                          AMP PEAK  9(12P12.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = AMP PEAK 10(12P11.21) MUTATION ANALYSIS
D10V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 10(12P11.21) MUTATED    7  2
  AMP PEAK 10(12P11.21) WILD-TYPE 43  9
  AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE 
                              9                              52 
  AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE 
                              2                               9 
$`AMP PEAK 10(12P11.21) MUTATED`
TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
         240            4            5          194           46           11 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A6UG 
        1975          522         1968 

$`AMP PEAK 10(12P11.21) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
          91           23           29           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          476          851          488           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 
         329          300         1991            8          181          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         127           35          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE 
                              4                               1 
  AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE 
                           1975                            1991 
  AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE 
                          194.0                           173.5 
[1] "4.0 - 1975.0 (194.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1.2"
D10V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 10(12P11.21) MUTATED          0        1         0        12
  AMP PEAK 10(12P11.21) WILD-TYPE        2        3        14        49
                                 vv
clus                              STAGE III STAGE IV
  AMP PEAK 10(12P11.21) MUTATED           0        1
  AMP PEAK 10(12P11.21) WILD-TYPE         2        2
D10V3, multiclass
           clus
vv          AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE
  STAGE IA                              0                               2
  STAGE IB                              1                               3
  STAGE IIA                             0                              14
  STAGE IIB                            12                              49
  STAGE III                             0                               2
  STAGE IV                              1                               2
[1] 6 2
[1] 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(12P11.21) MUTATED       2    12
  AMP PEAK 10(12P11.21) WILD-TYPE     6    66
D10V4, multiclass
       clus
vv      AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE
  T1+T2                             2                               6
  T3+T4                            12                              66
[1] 2 2
[1] FALSE
D10V5, binary
                                 cls
clus                               0  1
  AMP PEAK 10(12P11.21) MUTATED    2 12
  AMP PEAK 10(12P11.21) WILD-TYPE 19 52
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P11.21) MUTATED      2   12
  AMP PEAK 10(12P11.21) WILD-TYPE   19   52
   clus
vv  AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE
  0                             2                              19
  1                            12                              52
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 10(12P11.21) MUTATED    6  1  7
  AMP PEAK 10(12P11.21) WILD-TYPE 35  2 35
D10V6, multiclass
    clus
vv   AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE
  M0                             6                              35
  M1                             1                               2
  MX                             7                              35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                                 cls
clus                               0  1
  AMP PEAK 10(12P11.21) MUTATED    3 11
  AMP PEAK 10(12P11.21) WILD-TYPE 41 31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 10(12P11.21) MUTATED      3   11
  AMP PEAK 10(12P11.21) WILD-TYPE   41   31
        clus
vv       AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE
  FEMALE                             3                              41
  MALE                              11                              31
[1] 2 2
[1] FALSE
                                 vv
clus                              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 10(12P11.21) MUTATED                                    12
  AMP PEAK 10(12P11.21) WILD-TYPE                                  62
                                 vv
clus                              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 10(12P11.21) MUTATED                                       2
  AMP PEAK 10(12P11.21) WILD-TYPE                                     6
                                 vv
clus                              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 10(12P11.21) MUTATED                                                  0
  AMP PEAK 10(12P11.21) WILD-TYPE                                                3
D10V8, multiclass
                                                  clus
vv                                                 AMP PEAK 10(12P11.21) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         12
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             0
                                                  clus
vv                                                 AMP PEAK 10(12P11.21) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                           62
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                          6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                               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"
D10V9, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 10(12P11.21) MUTATED    5  8  0  1
  AMP PEAK 10(12P11.21) WILD-TYPE 50 17  1  1
D10V10, multiclass
    clus
vv   AMP PEAK 10(12P11.21) MUTATED AMP PEAK 10(12P11.21) WILD-TYPE
  R0                             5                              50
  R1                             8                              17
  R2                             0                               1
  RX                             1                               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"
D10V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(12P11.21) MUTATED       0                         1    12
  AMP PEAK 10(12P11.21) WILD-TYPE     2                         5    62
D10V12, multiclass
                           clus
vv                          AMP PEAK 10(12P11.21) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                12
                           clus
vv                          AMP PEAK 10(12P11.21) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = AMP PEAK 11(12Q15) MUTATION ANALYSIS
D11V1, survival
                              sevent
clus2                           0  1
  AMP PEAK 11(12Q15) MUTATED    3  2
  AMP PEAK 11(12Q15) WILD-TYPE 47  9
  AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE 
                           5                           56 
  AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE 
                           2                            9 
$`AMP PEAK 11(12Q15) MUTATED`
TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-A4BK TCGA-IB-A5SS TCGA-IB-A6UG 
         392          240           46         1991         1968 

$`AMP PEAK 11(12Q15) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
         449            1          166          233          396           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77O 
           5           91           23           29          194           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         851         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
         300            8          181          164          127           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          110          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE 
                          46                            1 
  AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE 
                        1991                         1989 
  AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE 
                         392                          165 
[1] "46.0 - 1991.0 (392.0)" "1.0 - 1989.0 (165.0)" 
[1] "hr=" "3.7"
D11V2, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AMP PEAK 11(12Q15) MUTATED          0        0         0        10         0
  AMP PEAK 11(12Q15) WILD-TYPE        2        4        14        51         2
                              vv
clus                           STAGE IV
  AMP PEAK 11(12Q15) MUTATED          0
  AMP PEAK 11(12Q15) WILD-TYPE        3
D11V3, multiclass
           clus
vv          AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE
  STAGE IA                           0                            2
  STAGE IB                           0                            4
  STAGE IIA                          0                           14
  STAGE IIB                         10                           51
  STAGE III                          0                            2
  STAGE IV                           0                            3
[1] 6 2
[1] 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(12Q15) MUTATED       0    10
  AMP PEAK 11(12Q15) WILD-TYPE     8    68
D11V4, multiclass
       clus
vv      AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE
  T1+T2                          0                            8
  T3+T4                         10                           68
[1] 2 2
[1] FALSE
D11V5, binary
                              cls
clus                            0  1
  AMP PEAK 11(12Q15) MUTATED    0 10
  AMP PEAK 11(12Q15) WILD-TYPE 21 54
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 11(12Q15) MUTATED      0   10
  AMP PEAK 11(12Q15) WILD-TYPE   21   54
   clus
vv  AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE
  0                          0                           21
  1                         10                           54
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  AMP PEAK 11(12Q15) MUTATED    5  0  5
  AMP PEAK 11(12Q15) WILD-TYPE 36  3 37
D11V6, multiclass
    clus
vv   AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE
  M0                          5                           36
  M1                          0                            3
  MX                          5                           37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                              cls
clus                            0  1
  AMP PEAK 11(12Q15) MUTATED    2  8
  AMP PEAK 11(12Q15) WILD-TYPE 42 34
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 11(12Q15) MUTATED      2    8
  AMP PEAK 11(12Q15) WILD-TYPE   42   34
        clus
vv       AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE
  FEMALE                          2                           42
  MALE                            8                           34
[1] 2 2
[1] FALSE
                              vv
clus                           PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 11(12Q15) MUTATED                                     8
  AMP PEAK 11(12Q15) WILD-TYPE                                  66
                              vv
clus                           PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 11(12Q15) MUTATED                                       2
  AMP PEAK 11(12Q15) WILD-TYPE                                     6
                              vv
clus                           PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 11(12Q15) MUTATED                                                  0
  AMP PEAK 11(12Q15) WILD-TYPE                                                3
D11V8, multiclass
                                                  clus
vv                                                 AMP PEAK 11(12Q15) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                     2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                          0
                                                  clus
vv                                                 AMP PEAK 11(12Q15) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        66
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            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"
D11V9, continuous
                              vv
clus                           R0 R1 R2 RX
  AMP PEAK 11(12Q15) MUTATED    4  5  0  1
  AMP PEAK 11(12Q15) WILD-TYPE 51 20  1  1
D11V10, multiclass
    clus
vv   AMP PEAK 11(12Q15) MUTATED AMP PEAK 11(12Q15) WILD-TYPE
  R0                          4                           51
  R1                          5                           20
  R2                          0                            1
  RX                          1                            1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(12Q15) MUTATED       0                         1     9
  AMP PEAK 11(12Q15) WILD-TYPE     2                         5    65
D11V12, multiclass
                           clus
vv                          AMP PEAK 11(12Q15) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                              9
                           clus
vv                          AMP PEAK 11(12Q15) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = AMP PEAK 12(17P11.2) MUTATION ANALYSIS
D12V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 12(17P11.2) MUTATED    3  0
  AMP PEAK 12(17P11.2) WILD-TYPE 47 11
  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE 
                             3                             58 
  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE 
                             0                             11 
$`AMP PEAK 12(17P11.2) MUTATED`
TCGA-FB-A545 TCGA-HZ-8315 TCGA-LB-A8F3 
         385           28           35 

$`AMP PEAK 12(17P11.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 
           8           19           24           21           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         164          127          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE 
                            28                              1 
  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE 
                           385                           1991 
  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE 
                          35.0                          187.5 
[1] "28.0 - 385.0 (35.0)"  "1.0 - 1991.0 (187.5)"
[1] "hr="     "2.6e+07"
D12V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 12(17P11.2) MUTATED          0        0         2         1
  AMP PEAK 12(17P11.2) WILD-TYPE        2        4        12        60
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK 12(17P11.2) MUTATED           0        0
  AMP PEAK 12(17P11.2) WILD-TYPE         2        3
D12V3, multiclass
           clus
vv          AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            2                             12
  STAGE IIB                            1                             60
  STAGE III                            0                              2
  STAGE IV                             0                              3
[1] 6 2
[1] 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(17P11.2) MUTATED       0     3
  AMP PEAK 12(17P11.2) WILD-TYPE     8    75
D12V4, multiclass
       clus
vv      AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE
  T1+T2                            0                              8
  T3+T4                            3                             75
[1] 2 2
[1] FALSE
D12V5, binary
                                cls
clus                              0  1
  AMP PEAK 12(17P11.2) MUTATED    2  1
  AMP PEAK 12(17P11.2) WILD-TYPE 19 63
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(17P11.2) MUTATED      2    1
  AMP PEAK 12(17P11.2) WILD-TYPE   19   63
   clus
vv  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE
  0                            2                             19
  1                            1                             63
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 12(17P11.2) MUTATED    1  0  2
  AMP PEAK 12(17P11.2) WILD-TYPE 40  3 40
D12V6, multiclass
    clus
vv   AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE
  M0                            1                             40
  M1                            0                              3
  MX                            2                             40
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                                cls
clus                              0  1
  AMP PEAK 12(17P11.2) MUTATED    3  0
  AMP PEAK 12(17P11.2) WILD-TYPE 41 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 12(17P11.2) MUTATED      3    0
  AMP PEAK 12(17P11.2) WILD-TYPE   41   42
        clus
vv       AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE
  FEMALE                            3                             41
  MALE                              0                             42
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 12(17P11.2) MUTATED                                     3
  AMP PEAK 12(17P11.2) WILD-TYPE                                  71
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 12(17P11.2) MUTATED                                       0
  AMP PEAK 12(17P11.2) WILD-TYPE                                     8
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 12(17P11.2) MUTATED                                                  0
  AMP PEAK 12(17P11.2) WILD-TYPE                                                3
D12V8, multiclass
                                                  clus
vv                                                 AMP PEAK 12(17P11.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            0
                                                  clus
vv                                                 AMP PEAK 12(17P11.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          71
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D12V9, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 12(17P11.2) MUTATED    1  1  0  0
  AMP PEAK 12(17P11.2) WILD-TYPE 54 24  1  2
D12V10, multiclass
[1] "Remove cluster labels:"       "AMP PEAK 12(17P11.2) MUTATED"
clus
  AMP PEAK 12(17P11.2) MUTATED AMP PEAK 12(17P11.2) WILD-TYPE 
                             2                             81 
                    TCGA-F2-6879                     TCGA-F2-6880 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-F2-7273                     TCGA-F2-7276 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-F2-A44G                     TCGA-F2-A44H 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-FB-A4P5                     TCGA-FB-A5VM 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-FB-A78T                     TCGA-FB-A7DR 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-FZ-5920                     TCGA-FZ-5922 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-FZ-5923                     TCGA-H6-8124 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-H8-A6C1                     TCGA-HZ-7289 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-7918                     TCGA-HZ-7919 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-7920                     TCGA-HZ-7922 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-7923                     TCGA-HZ-7924 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-7925                     TCGA-HZ-7926 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-8001                     TCGA-HZ-8002 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-8003                     TCGA-HZ-8005 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-8317                     TCGA-HZ-8519 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-8636                     TCGA-HZ-8637 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-8638                     TCGA-HZ-A49G 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-A49H                     TCGA-HZ-A49I 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-A4BH                     TCGA-HZ-A4BK 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-A77O                     TCGA-HZ-A77P 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-HZ-A77Q                     TCGA-IB-7644 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-7645                     TCGA-IB-7646 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-7647                     TCGA-IB-7649 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-7651                     TCGA-IB-7652 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-7885                     TCGA-IB-7886 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-7887                     TCGA-IB-7888 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-7889                     TCGA-IB-7890 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-7891                     TCGA-IB-7893 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-7897                     TCGA-IB-8126 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-8127                     TCGA-IB-A5SO 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-A5SP                     TCGA-IB-A5SQ 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-A5SS                     TCGA-IB-A5ST 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-A6UG                     TCGA-IB-A7LX 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-IB-A7M4                     TCGA-L1-A7W4 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-LB-A7SX                     TCGA-M8-A5N4 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-OE-A75W                     TCGA-Q3-A5QY 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-S4-A8RP                     TCGA-US-A774 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-US-A776                     TCGA-US-A779 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-US-A77E                     TCGA-US-A77G 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-US-A77J                     TCGA-YB-A89D 
"AMP PEAK 12(17P11.2) WILD-TYPE" "AMP PEAK 12(17P11.2) WILD-TYPE" 
                    TCGA-YY-A8LH 
"AMP PEAK 12(17P11.2) WILD-TYPE" 
D12V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(17P11.2) MUTATED       0                         1     2
  AMP PEAK 12(17P11.2) WILD-TYPE     2                         5    72
D12V12, multiclass
                           clus
vv                          AMP PEAK 12(17P11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                2
                           clus
vv                          AMP PEAK 12(17P11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 72
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(13) Variable = AMP PEAK 13(17Q21.32) MUTATION ANALYSIS
D13V1, survival
                                 sevent
clus2                              0  1
  AMP PEAK 13(17Q21.32) MUTATED    9  0
  AMP PEAK 13(17Q21.32) WILD-TYPE 41 11
  AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE 
                              9                              52 
  AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE 
                              0                              11 
$`AMP PEAK 13(17Q21.32) MUTATED`
TCGA-FB-A545 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-A4BH TCGA-IB-7891 
         385          396          240            4          194          488 
TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-M8-A5N4 
         181           35          584 

$`AMP PEAK 13(17Q21.32) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7919 
           1          166          392          233           28           20 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q 
          23           29           46           11           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
         347         1951         1989          476          851         1975 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST 
          17          522          329          300         1991            8 
TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
        1968          164          127          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE 
                              4                               1 
  AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE 
                            584                            1991 
  AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE 
                            240                             162 
[1] "4.0 - 584.0 (240.0)"  "1.0 - 1991.0 (162.0)"
[1] "hr="   "9e+07"
D13V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 13(17Q21.32) MUTATED          0        0         4         7
  AMP PEAK 13(17Q21.32) WILD-TYPE        2        4        10        54
                                 vv
clus                              STAGE III STAGE IV
  AMP PEAK 13(17Q21.32) MUTATED           0        0
  AMP PEAK 13(17Q21.32) WILD-TYPE         2        3
D13V3, multiclass
           clus
vv          AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE
  STAGE IA                              0                               2
  STAGE IB                              0                               4
  STAGE IIA                             4                              10
  STAGE IIB                             7                              54
  STAGE III                             0                               2
  STAGE IV                              0                               3
[1] 6 2
[1] 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(17Q21.32) MUTATED       0    11
  AMP PEAK 13(17Q21.32) WILD-TYPE     8    67
D13V4, multiclass
       clus
vv      AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE
  T1+T2                             0                               8
  T3+T4                            11                              67
[1] 2 2
[1] FALSE
D13V5, binary
                                 cls
clus                               0  1
  AMP PEAK 13(17Q21.32) MUTATED    4  7
  AMP PEAK 13(17Q21.32) WILD-TYPE 17 57
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(17Q21.32) MUTATED      4    7
  AMP PEAK 13(17Q21.32) WILD-TYPE   17   57
   clus
vv  AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE
  0                             4                              17
  1                             7                              57
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  AMP PEAK 13(17Q21.32) MUTATED    5  0  6
  AMP PEAK 13(17Q21.32) WILD-TYPE 36  3 36
D13V6, multiclass
    clus
vv   AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE
  M0                             5                              36
  M1                             0                               3
  MX                             6                              36
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V7, binary
                                 cls
clus                               0  1
  AMP PEAK 13(17Q21.32) MUTATED    4  7
  AMP PEAK 13(17Q21.32) WILD-TYPE 40 35
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  AMP PEAK 13(17Q21.32) MUTATED      4    7
  AMP PEAK 13(17Q21.32) WILD-TYPE   40   35
        clus
vv       AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE
  FEMALE                             4                              40
  MALE                               7                              35
[1] 2 2
[1] FALSE
                                 vv
clus                              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 13(17Q21.32) MUTATED                                     9
  AMP PEAK 13(17Q21.32) WILD-TYPE                                  65
                                 vv
clus                              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 13(17Q21.32) MUTATED                                       2
  AMP PEAK 13(17Q21.32) WILD-TYPE                                     6
                                 vv
clus                              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 13(17Q21.32) MUTATED                                                  0
  AMP PEAK 13(17Q21.32) WILD-TYPE                                                3
D13V8, multiclass
                                                  clus
vv                                                 AMP PEAK 13(17Q21.32) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             0
                                                  clus
vv                                                 AMP PEAK 13(17Q21.32) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                           65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                          6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                               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"
D13V9, continuous
                                 vv
clus                              R0 R1 R2 RX
  AMP PEAK 13(17Q21.32) MUTATED    6  3  0  1
  AMP PEAK 13(17Q21.32) WILD-TYPE 49 22  1  1
D13V10, multiclass
    clus
vv   AMP PEAK 13(17Q21.32) MUTATED AMP PEAK 13(17Q21.32) WILD-TYPE
  R0                             6                              49
  R1                             3                              22
  R2                             0                               1
  RX                             1                               1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 13(17Q21.32) MUTATED       0                         1     9
  AMP PEAK 13(17Q21.32) WILD-TYPE     2                         5    65
D13V12, multiclass
                           clus
vv                          AMP PEAK 13(17Q21.32) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                 9
                           clus
vv                          AMP PEAK 13(17Q21.32) WILD-TYPE
  ASIAN                                                   2
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(14) Variable = AMP PEAK 14(18Q11.2) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 14(18Q11.2) MUTATED   17  5
  AMP PEAK 14(18Q11.2) WILD-TYPE 33  6
  AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE 
                            22                             39 
  AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE 
                             5                              6 
$`AMP PEAK 14(18Q11.2) MUTATED`
TCGA-F2-A44G TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7919 
         153          385            1          392          396           20 
TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7644 TCGA-IB-7649 
         361            5           46           11          347         1951 
TCGA-IB-7886 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A6UG 
        1975           17          522          329          300         1968 
TCGA-IB-A7M4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-YY-A8LH 
         181          110          247         1834 

$`AMP PEAK 14(18Q11.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A7DR 
         295          360          586            4          449          166 
TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         233          240           28            4            8          369 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P 
           3           91           23           29          194           13 
TCGA-HZ-A77Q TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-A5SS 
          33         1989          476          851          488         1991 
TCGA-IB-A5ST TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-Q3-A5QY 
           8          164          127           35          584          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
        1955          844          160 

  AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE 
                             1                              3 
  AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE 
                          1975                           1991 
  AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE 
                         314.5                          160.0 
[1] "1.0 - 1975.0 (314.5)" "3.0 - 1991.0 (160.0)"
[1] "hr=" "1.7"
D14V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 14(18Q11.2) MUTATED          0        0         4        19
  AMP PEAK 14(18Q11.2) WILD-TYPE        2        4        10        42
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK 14(18Q11.2) MUTATED           1        3
  AMP PEAK 14(18Q11.2) WILD-TYPE         1        0
D14V3, multiclass
           clus
vv          AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            4                             10
  STAGE IIB                           19                             42
  STAGE III                            1                              1
  STAGE IV                             3                              0
[1] 6 2
[1] 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(18Q11.2) MUTATED       1    26
  AMP PEAK 14(18Q11.2) WILD-TYPE     7    52
D14V4, multiclass
       clus
vv      AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE
  T1+T2                            1                              7
  T3+T4                           26                             52
[1] 2 2
[1] FALSE
D14V5, binary
                                cls
clus                              0  1
  AMP PEAK 14(18Q11.2) MUTATED    5 22
  AMP PEAK 14(18Q11.2) WILD-TYPE 16 42
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(18Q11.2) MUTATED      5   22
  AMP PEAK 14(18Q11.2) WILD-TYPE   16   42
   clus
vv  AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE
  0                            5                             16
  1                           22                             42
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 14(18Q11.2) MUTATED   15  3  9
  AMP PEAK 14(18Q11.2) WILD-TYPE 26  0 33
D14V6, multiclass
    clus
vv   AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE
  M0                           15                             26
  M1                            3                              0
  MX                            9                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                              0  1
  AMP PEAK 14(18Q11.2) MUTATED   12 15
  AMP PEAK 14(18Q11.2) WILD-TYPE 32 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 14(18Q11.2) MUTATED     12   15
  AMP PEAK 14(18Q11.2) WILD-TYPE   32   27
        clus
vv       AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE
  FEMALE                           12                             32
  MALE                             15                             27
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 14(18Q11.2) MUTATED                                    24
  AMP PEAK 14(18Q11.2) WILD-TYPE                                  50
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 14(18Q11.2) MUTATED                                       2
  AMP PEAK 14(18Q11.2) WILD-TYPE                                     6
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 14(18Q11.2) MUTATED                                                  0
  AMP PEAK 14(18Q11.2) WILD-TYPE                                                3
D14V8, multiclass
                                                  clus
vv                                                 AMP PEAK 14(18Q11.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            0
                                                  clus
vv                                                 AMP PEAK 14(18Q11.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          50
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D14V9, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 14(18Q11.2) MUTATED   14 11  0  0
  AMP PEAK 14(18Q11.2) WILD-TYPE 41 14  1  2
D14V10, multiclass
    clus
vv   AMP PEAK 14(18Q11.2) MUTATED AMP PEAK 14(18Q11.2) WILD-TYPE
  R0                           14                             41
  R1                           11                             14
  R2                            0                              1
  RX                            0                              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"
D14V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 14(18Q11.2) MUTATED       0                         0    26
  AMP PEAK 14(18Q11.2) WILD-TYPE     2                         6    48
D14V12, multiclass
                           clus
vv                          AMP PEAK 14(18Q11.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               26
                           clus
vv                          AMP PEAK 14(18Q11.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(15) Variable = AMP PEAK 15(19Q13.2) MUTATION ANALYSIS
D15V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 15(19Q13.2) MUTATED   15  3
  AMP PEAK 15(19Q13.2) WILD-TYPE 35  8
  AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE 
                            18                             43 
  AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE 
                             3                              8 
$`AMP PEAK 15(19Q13.2) MUTATED`
TCGA-FB-A545 TCGA-FB-A7DR TCGA-H6-8124 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-8001 
         385          166          392           28            4           19 
TCGA-HZ-A4BH TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS 
         194         1975          488          522          300         1991 
TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-PZ-A5RE TCGA-US-A776 TCGA-YB-A89D 
        1968          164          127          247          844          160 

$`AMP PEAK 15(19Q13.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7923 
           1          233          396          240           20            8 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         369          361            8           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST 
        1989          476          851           17          329            8 
TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A774 
         181           35          584          110          416         1955 
TCGA-YY-A8LH 
        1834 

  AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE 
                             4                              1 
  AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE 
                          1991                           1989 
  AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE 
                         273.5                          110.0 
[1] "4.0 - 1991.0 (273.5)" "1.0 - 1989.0 (110.0)"
[1] "hr=" "4.1"
D15V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 15(19Q13.2) MUTATED          0        0         4        16
  AMP PEAK 15(19Q13.2) WILD-TYPE        2        4        10        45
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK 15(19Q13.2) MUTATED           1        0
  AMP PEAK 15(19Q13.2) WILD-TYPE         1        3
D15V3, multiclass
           clus
vv          AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            4                             10
  STAGE IIB                           16                             45
  STAGE III                            1                              1
  STAGE IV                             0                              3
[1] 6 2
[1] 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(19Q13.2) MUTATED       0    21
  AMP PEAK 15(19Q13.2) WILD-TYPE     8    57
D15V4, multiclass
       clus
vv      AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE
  T1+T2                            0                              8
  T3+T4                           21                             57
[1] 2 2
[1] FALSE
D15V5, binary
                                cls
clus                              0  1
  AMP PEAK 15(19Q13.2) MUTATED    4 16
  AMP PEAK 15(19Q13.2) WILD-TYPE 17 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(19Q13.2) MUTATED      4   16
  AMP PEAK 15(19Q13.2) WILD-TYPE   17   48
   clus
vv  AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE
  0                            4                             17
  1                           16                             48
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 15(19Q13.2) MUTATED   13  0  8
  AMP PEAK 15(19Q13.2) WILD-TYPE 28  3 34
D15V6, multiclass
    clus
vv   AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE
  M0                           13                             28
  M1                            0                              3
  MX                            8                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                                cls
clus                              0  1
  AMP PEAK 15(19Q13.2) MUTATED    7 14
  AMP PEAK 15(19Q13.2) WILD-TYPE 37 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 15(19Q13.2) MUTATED      7   14
  AMP PEAK 15(19Q13.2) WILD-TYPE   37   28
        clus
vv       AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE
  FEMALE                            7                             37
  MALE                             14                             28
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 15(19Q13.2) MUTATED                                    19
  AMP PEAK 15(19Q13.2) WILD-TYPE                                  55
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 15(19Q13.2) MUTATED                                       0
  AMP PEAK 15(19Q13.2) WILD-TYPE                                     8
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 15(19Q13.2) MUTATED                                                  2
  AMP PEAK 15(19Q13.2) WILD-TYPE                                                1
D15V8, multiclass
                                                  clus
vv                                                 AMP PEAK 15(19Q13.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            2
                                                  clus
vv                                                 AMP PEAK 15(19Q13.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          55
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V9, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 15(19Q13.2) MUTATED   11  7  1  0
  AMP PEAK 15(19Q13.2) WILD-TYPE 44 18  0  2
D15V10, multiclass
    clus
vv   AMP PEAK 15(19Q13.2) MUTATED AMP PEAK 15(19Q13.2) WILD-TYPE
  R0                           11                             44
  R1                            7                             18
  R2                            1                              0
  RX                            0                              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
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 15(19Q13.2) MUTATED       1                         2    18
  AMP PEAK 15(19Q13.2) WILD-TYPE     1                         4    56
D15V12, multiclass
                           clus
vv                          AMP PEAK 15(19Q13.2) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               18
                           clus
vv                          AMP PEAK 15(19Q13.2) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 56
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(16) Variable = AMP PEAK 16(20Q13.2) MUTATION ANALYSIS
D16V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 16(20Q13.2) MUTATED   17  1
  AMP PEAK 16(20Q13.2) WILD-TYPE 33 10
  AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE 
                            18                             43 
  AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE 
                             1                             10 
$`AMP PEAK 16(20Q13.2) MUTATED`
TCGA-FB-A545 TCGA-FB-A5VM TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-A4BK 
         385          449          240           28            4           46 
TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7M4 
          11           33         1975          522          300          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-YB-A89D TCGA-YY-A8LH 
         164          127           35          584          160         1834 

$`AMP PEAK 16(20Q13.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A78T 
         295          360          153          586            4            1 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7923 
         166          392          233          396           20            8 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
         369          361            8           19           24           21 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
          28           16            3            5           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          29          194           13          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS 
         476          851          488           17          329         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
           8         1968          110          247          416         1955 
TCGA-US-A776 
         844 

  AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE 
                             4                              1 
  AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE 
                          1975                           1991 
  AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE 
                         172.5                          194.0 
[1] "4.0 - 1975.0 (172.5)" "1.0 - 1991.0 (194.0)"
[1] "hr=" "2.9"
D16V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 16(20Q13.2) MUTATED          0        2         3        21
  AMP PEAK 16(20Q13.2) WILD-TYPE        2        2        11        40
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK 16(20Q13.2) MUTATED           0        0
  AMP PEAK 16(20Q13.2) WILD-TYPE         2        3
D16V3, multiclass
           clus
vv          AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             2                              2
  STAGE IIA                            3                             11
  STAGE IIB                           21                             40
  STAGE III                            0                              2
  STAGE IV                             0                              3
[1] 6 2
[1] 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(20Q13.2) MUTATED       3    23
  AMP PEAK 16(20Q13.2) WILD-TYPE     5    55
D16V4, multiclass
       clus
vv      AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE
  T1+T2                            3                              5
  T3+T4                           23                             55
[1] 2 2
[1] FALSE
D16V5, binary
                                cls
clus                              0  1
  AMP PEAK 16(20Q13.2) MUTATED    5 21
  AMP PEAK 16(20Q13.2) WILD-TYPE 16 43
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(20Q13.2) MUTATED      5   21
  AMP PEAK 16(20Q13.2) WILD-TYPE   16   43
   clus
vv  AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE
  0                            5                             16
  1                           21                             43
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 16(20Q13.2) MUTATED   12  0 14
  AMP PEAK 16(20Q13.2) WILD-TYPE 29  3 28
D16V6, multiclass
    clus
vv   AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE
  M0                           12                             29
  M1                            0                              3
  MX                           14                             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"
D16V7, binary
                                cls
clus                              0  1
  AMP PEAK 16(20Q13.2) MUTATED   11 15
  AMP PEAK 16(20Q13.2) WILD-TYPE 33 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 16(20Q13.2) MUTATED     11   15
  AMP PEAK 16(20Q13.2) WILD-TYPE   33   27
        clus
vv       AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE
  FEMALE                           11                             33
  MALE                             15                             27
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 16(20Q13.2) MUTATED                                    21
  AMP PEAK 16(20Q13.2) WILD-TYPE                                  53
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 16(20Q13.2) MUTATED                                       4
  AMP PEAK 16(20Q13.2) WILD-TYPE                                     4
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 16(20Q13.2) MUTATED                                                  0
  AMP PEAK 16(20Q13.2) WILD-TYPE                                                3
D16V8, multiclass
                                                  clus
vv                                                 AMP PEAK 16(20Q13.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        21
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            0
                                                  clus
vv                                                 AMP PEAK 16(20Q13.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          53
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D16V9, continuous
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 16(20Q13.2) MUTATED   13 10  1  1
  AMP PEAK 16(20Q13.2) WILD-TYPE 42 15  0  1
D16V10, multiclass
    clus
vv   AMP PEAK 16(20Q13.2) MUTATED AMP PEAK 16(20Q13.2) WILD-TYPE
  R0                           13                             42
  R1                           10                             15
  R2                            1                              0
  RX                            1                              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"
D16V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 16(20Q13.2) MUTATED       0                         2    22
  AMP PEAK 16(20Q13.2) WILD-TYPE     2                         4    52
D16V12, multiclass
                           clus
vv                          AMP PEAK 16(20Q13.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               22
                           clus
vv                          AMP PEAK 16(20Q13.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(17) Variable = AMP PEAK 17(XP22.11) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                             0  1
  AMP PEAK 17(XP22.11) MUTATED    4  0
  AMP PEAK 17(XP22.11) WILD-TYPE 46 11
  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE 
                             4                             57 
  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE 
                             0                             11 
$`AMP PEAK 17(XP22.11) MUTATED`
TCGA-F2-6880 TCGA-HZ-7925 TCGA-LB-A7SX TCGA-US-A776 
         295          361          127          844 

$`AMP PEAK 17(XP22.11) WILD-TYPE`
TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         360          153          586            4          385          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
          28           20            4            8          369            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK 
           5           91           23           29          194           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 
         476          851         1975          488           17          522 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         164           35          584          110          247          416 
TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          160         1834 

  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE 
                           127                              1 
  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE 
                           844                           1991 
  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE 
                           328                            166 
[1] "127.0 - 844.0 (328.0)" "1.0 - 1991.0 (166.0)" 
[1] "hr="     "7.6e+07"
D17V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  AMP PEAK 17(XP22.11) MUTATED          0        0         1         4
  AMP PEAK 17(XP22.11) WILD-TYPE        2        4        13        57
                                vv
clus                             STAGE III STAGE IV
  AMP PEAK 17(XP22.11) MUTATED           0        0
  AMP PEAK 17(XP22.11) WILD-TYPE         2        3
D17V3, multiclass
           clus
vv          AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            1                             13
  STAGE IIB                            4                             57
  STAGE III                            0                              2
  STAGE IV                             0                              3
[1] 6 2
[1] 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(XP22.11) MUTATED       0     5
  AMP PEAK 17(XP22.11) WILD-TYPE     8    73
D17V4, multiclass
       clus
vv      AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE
  T1+T2                            0                              8
  T3+T4                            5                             73
[1] 2 2
[1] FALSE
D17V5, binary
                                cls
clus                              0  1
  AMP PEAK 17(XP22.11) MUTATED    1  4
  AMP PEAK 17(XP22.11) WILD-TYPE 20 60
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(XP22.11) MUTATED      1    4
  AMP PEAK 17(XP22.11) WILD-TYPE   20   60
   clus
vv  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE
  0                            1                             20
  1                            4                             60
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  AMP PEAK 17(XP22.11) MUTATED    2  0  3
  AMP PEAK 17(XP22.11) WILD-TYPE 39  3 39
D17V6, multiclass
    clus
vv   AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE
  M0                            2                             39
  M1                            0                              3
  MX                            3                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                              0  1
  AMP PEAK 17(XP22.11) MUTATED    1  4
  AMP PEAK 17(XP22.11) WILD-TYPE 43 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK 17(XP22.11) MUTATED      1    4
  AMP PEAK 17(XP22.11) WILD-TYPE   43   38
        clus
vv       AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE
  FEMALE                            1                             43
  MALE                              4                             38
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 17(XP22.11) MUTATED                                     4
  AMP PEAK 17(XP22.11) WILD-TYPE                                  70
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 17(XP22.11) MUTATED                                       0
  AMP PEAK 17(XP22.11) WILD-TYPE                                     8
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 17(XP22.11) MUTATED                                                  1
  AMP PEAK 17(XP22.11) WILD-TYPE                                                2
D17V8, multiclass
                                                  clus
vv                                                 AMP PEAK 17(XP22.11) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         4
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            1
                                                  clus
vv                                                 AMP PEAK 17(XP22.11) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          70
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D17V9, continuous
[1] "Remove cluster labels:"       "AMP PEAK 17(XP22.11) MUTATED"
clus
  AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE 
                             2                             24 
                    TCGA-FB-A4P5                     TCGA-FB-A5VM 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-FB-A78T                     TCGA-FB-A7DR 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-H6-8124                     TCGA-H6-A45N 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-H8-A6C1                     TCGA-HZ-A77Q 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-IB-7644                     TCGA-IB-7649 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-IB-7651                     TCGA-IB-7885 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-IB-7886                     TCGA-IB-7887 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-IB-7891                     TCGA-IB-8126 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-IB-8127                     TCGA-IB-A5SS 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-IB-A6UG                     TCGA-IB-A7M4 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-OE-A75W                     TCGA-S4-A8RP 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                    TCGA-US-A774                     TCGA-YY-A8LH 
"AMP PEAK 17(XP22.11) WILD-TYPE" "AMP PEAK 17(XP22.11) WILD-TYPE" 
                                vv
clus                             R0 R1 R2 RX
  AMP PEAK 17(XP22.11) MUTATED    4  1  0  0
  AMP PEAK 17(XP22.11) WILD-TYPE 51 24  1  2
D17V10, multiclass
    clus
vv   AMP PEAK 17(XP22.11) MUTATED AMP PEAK 17(XP22.11) WILD-TYPE
  R0                            4                             51
  R1                            1                             24
  R2                            0                              1
  RX                            0                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 17(XP22.11) MUTATED       0                         1     4
  AMP PEAK 17(XP22.11) WILD-TYPE     2                         5    70
D17V12, multiclass
                           clus
vv                          AMP PEAK 17(XP22.11) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                                4
                           clus
vv                          AMP PEAK 17(XP22.11) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(18) Variable = AMP PEAK 18(XQ27.1) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                            0  1
  AMP PEAK 18(XQ27.1) MUTATED    5  1
  AMP PEAK 18(XQ27.1) WILD-TYPE 45 10
  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE 
                            6                            55 
  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE 
                            1                            10 
$`AMP PEAK 18(XQ27.1) MUTATED`
TCGA-FB-A78T TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-8001 TCGA-IB-7652 TCGA-IB-A6UG 
           1          240           28           19          476         1968 

$`AMP PEAK 18(XQ27.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 
         449          166          392          233          396           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8002 
           4            8          369          361            8           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
          23           29          194           46           11           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 
          33          347         1951         1989          851         1975 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
         488           17          522          329          300         1991 
TCGA-IB-A5ST TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 
           8          181          164          127           35          584 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         110          247          416         1955          844          160 
TCGA-YY-A8LH 
        1834 

  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE 
                            1                             3 
  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE 
                         1968                          1991 
  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE 
                          134                           181 
[1] "1.0 - 1968.0 (134.0)" "3.0 - 1991.0 (181.0)"
[1] "hr=" "1.1"
D18V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  AMP PEAK 18(XQ27.1) MUTATED          0        0         0         8         1
  AMP PEAK 18(XQ27.1) WILD-TYPE        2        4        14        53         1
                               vv
clus                            STAGE IV
  AMP PEAK 18(XQ27.1) MUTATED          0
  AMP PEAK 18(XQ27.1) WILD-TYPE        3
D18V3, multiclass
           clus
vv          AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            0                             4
  STAGE IIA                           0                            14
  STAGE IIB                           8                            53
  STAGE III                           1                             1
  STAGE IV                            0                             3
[1] 6 2
[1] 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(XQ27.1) MUTATED       0     9
  AMP PEAK 18(XQ27.1) WILD-TYPE     8    69
D18V4, multiclass
       clus
vv      AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE
  T1+T2                           0                             8
  T3+T4                           9                            69
[1] 2 2
[1] FALSE
D18V5, binary
                               cls
clus                             0  1
  AMP PEAK 18(XQ27.1) MUTATED    1  8
  AMP PEAK 18(XQ27.1) WILD-TYPE 20 56
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(XQ27.1) MUTATED      1    8
  AMP PEAK 18(XQ27.1) WILD-TYPE   20   56
   clus
vv  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE
  0                           1                            20
  1                           8                            56
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  AMP PEAK 18(XQ27.1) MUTATED    5  0  4
  AMP PEAK 18(XQ27.1) WILD-TYPE 36  3 38
D18V6, multiclass
    clus
vv   AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE
  M0                           5                            36
  M1                           0                             3
  MX                           4                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                               cls
clus                             0  1
  AMP PEAK 18(XQ27.1) MUTATED    3  6
  AMP PEAK 18(XQ27.1) WILD-TYPE 41 36
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 18(XQ27.1) MUTATED      3    6
  AMP PEAK 18(XQ27.1) WILD-TYPE   41   36
        clus
vv       AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE
  FEMALE                           3                            41
  MALE                             6                            36
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  AMP PEAK 18(XQ27.1) MUTATED                                     7
  AMP PEAK 18(XQ27.1) WILD-TYPE                                  67
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  AMP PEAK 18(XQ27.1) MUTATED                                       1
  AMP PEAK 18(XQ27.1) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  AMP PEAK 18(XQ27.1) MUTATED                                                  0
  AMP PEAK 18(XQ27.1) WILD-TYPE                                                3
D18V8, multiclass
                                                  clus
vv                                                 AMP PEAK 18(XQ27.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        7
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           0
                                                  clus
vv                                                 AMP PEAK 18(XQ27.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         67
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D18V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK 18(XQ27.1) MUTATED"
clus
  AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE 
                            2                            24 
                   TCGA-F2-6880                    TCGA-FB-A4P5 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-FB-A5VM                    TCGA-FB-A7DR 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-H6-8124                    TCGA-H6-A45N 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-H8-A6C1                    TCGA-HZ-A77Q 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-IB-7644                    TCGA-IB-7649 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-IB-7651                    TCGA-IB-7885 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-IB-7886                    TCGA-IB-7887 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-IB-7891                    TCGA-IB-8126 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-IB-8127                    TCGA-IB-A5SS 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-IB-A7M4                    TCGA-LB-A7SX 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-OE-A75W                    TCGA-S4-A8RP 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                   TCGA-US-A774                    TCGA-YY-A8LH 
"AMP PEAK 18(XQ27.1) WILD-TYPE" "AMP PEAK 18(XQ27.1) WILD-TYPE" 
                               vv
clus                            R0 R1 R2 RX
  AMP PEAK 18(XQ27.1) MUTATED    6  2  0  1
  AMP PEAK 18(XQ27.1) WILD-TYPE 49 23  1  1
D18V10, multiclass
    clus
vv   AMP PEAK 18(XQ27.1) MUTATED AMP PEAK 18(XQ27.1) WILD-TYPE
  R0                           6                            49
  R1                           2                            23
  R2                           0                             1
  RX                           1                             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
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 18(XQ27.1) MUTATED       1                         0     8
  AMP PEAK 18(XQ27.1) WILD-TYPE     1                         6    66
D18V12, multiclass
                           clus
vv                          AMP PEAK 18(XQ27.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               8
                           clus
vv                          AMP PEAK 18(XQ27.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(19) Variable = DEL PEAK  1(1P36.32) MUTATION ANALYSIS
D19V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  1(1P36.32) MUTATED   12  3
  DEL PEAK  1(1P36.32) WILD-TYPE 38  8
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                            15                             46 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             3                              8 
$`DEL PEAK  1(1P36.32) MUTATED`
TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-A77O TCGA-IB-7651 
           1          166          240           28           11         1989 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-LB-A8F3 
        1975          522          300         1968          181           35 
TCGA-M8-A5N4 TCGA-US-A776 TCGA-YY-A8LH 
         584          844         1834 

$`DEL PEAK  1(1P36.32) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7922 
         449          392          233          396           20            4 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q 
          23           29          194           46           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
         347         1951          476          851          488           17 
TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-OE-A75W 
         329         1991            8          164          127          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D 
         247          416         1955          160 

  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                             1                              3 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                          1989                           1991 
  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE 
                         300.0                          156.5 
[1] "1.0 - 1989.0 (300.0)" "3.0 - 1991.0 (156.5)"
[1] "hr=" "2.1"
D19V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  1(1P36.32) MUTATED          0        0         6        16
  DEL PEAK  1(1P36.32) WILD-TYPE        2        4         8        45
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK  1(1P36.32) MUTATED           0        1
  DEL PEAK  1(1P36.32) WILD-TYPE         2        2
D19V3, multiclass
           clus
vv          DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            6                              8
  STAGE IIB                           16                             45
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(1P36.32) MUTATED       1    22
  DEL PEAK  1(1P36.32) WILD-TYPE     7    56
D19V4, multiclass
       clus
vv      DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  T1+T2                            1                              7
  T3+T4                           22                             56
[1] 2 2
[1] FALSE
D19V5, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    5 17
  DEL PEAK  1(1P36.32) WILD-TYPE 16 47
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      5   17
  DEL PEAK  1(1P36.32) WILD-TYPE   16   47
   clus
vv  DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  0                            5                             16
  1                           17                             47
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK  1(1P36.32) MUTATED   13  1  9
  DEL PEAK  1(1P36.32) WILD-TYPE 28  2 33
D19V6, multiclass
    clus
vv   DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  M0                           13                             28
  M1                            1                              2
  MX                            9                             33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V7, binary
                                cls
clus                              0  1
  DEL PEAK  1(1P36.32) MUTATED    8 15
  DEL PEAK  1(1P36.32) WILD-TYPE 36 27
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.32) MUTATED      8   15
  DEL PEAK  1(1P36.32) WILD-TYPE   36   27
        clus
vv       DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  FEMALE                            8                             36
  MALE                             15                             27
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  1(1P36.32) MUTATED                                    20
  DEL PEAK  1(1P36.32) WILD-TYPE                                  54
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  1(1P36.32) MUTATED                                       1
  DEL PEAK  1(1P36.32) WILD-TYPE                                     7
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  1(1P36.32) MUTATED                                                  2
  DEL PEAK  1(1P36.32) WILD-TYPE                                                1
D19V8, multiclass
                                                  clus
vv                                                 DEL PEAK  1(1P36.32) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            2
                                                  clus
vv                                                 DEL PEAK  1(1P36.32) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          54
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  1(1P36.32) MUTATED   15  7  0  1
  DEL PEAK  1(1P36.32) WILD-TYPE 40 18  1  1
D19V10, multiclass
    clus
vv   DEL PEAK  1(1P36.32) MUTATED DEL PEAK  1(1P36.32) WILD-TYPE
  R0                           15                             40
  R1                            7                             18
  R2                            0                              1
  RX                            1                              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
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.32) MUTATED       1                         2    19
  DEL PEAK  1(1P36.32) WILD-TYPE     1                         4    55
D19V12, multiclass
                           clus
vv                          DEL PEAK  1(1P36.32) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               19
                           clus
vv                          DEL PEAK  1(1P36.32) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 55
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(20) Variable = DEL PEAK  2(1P36.11) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                             0  1
  DEL PEAK  2(1P36.11) MUTATED   15  4
  DEL PEAK  2(1P36.11) WILD-TYPE 35  7
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                            19                             42 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                             4                              7 
$`DEL PEAK  2(1P36.11) MUTATED`
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7925 
           1          166          396          240           28          361 
TCGA-HZ-A77O TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
          11         1989          476         1975          522          300 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-US-A776 
        1991         1968          181           35          110          844 
TCGA-YY-A8LH 
        1834 

$`DEL PEAK  2(1P36.11) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 
         449          392          233           20            4            8 
TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         369            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
         194           46           13           33          347         1951 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-L1-A7W4 
         851          488           17          329            8          164 
TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D 
         127          584          247          416         1955          160 

  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                             1                              3 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                          1991                           1955 
  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE 
                           361                            140 
[1] "1.0 - 1991.0 (361.0)" "3.0 - 1955.0 (140.0)"
[1] "hr="     "2.3e+09"
D20V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK  2(1P36.11) MUTATED          0        0         8        19
  DEL PEAK  2(1P36.11) WILD-TYPE        2        4         6        42
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK  2(1P36.11) MUTATED           0        1
  DEL PEAK  2(1P36.11) WILD-TYPE         2        2
D20V3, multiclass
           clus
vv          DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            8                              6
  STAGE IIB                           19                             42
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(1P36.11) MUTATED       1    27
  DEL PEAK  2(1P36.11) WILD-TYPE     7    51
D20V4, multiclass
       clus
vv      DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  T1+T2                            1                              7
  T3+T4                           27                             51
[1] 2 2
[1] FALSE
D20V5, binary
                                cls
clus                              0  1
  DEL PEAK  2(1P36.11) MUTATED    7 20
  DEL PEAK  2(1P36.11) WILD-TYPE 14 44
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED      7   20
  DEL PEAK  2(1P36.11) WILD-TYPE   14   44
   clus
vv  DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  0                            7                             14
  1                           20                             44
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK  2(1P36.11) MUTATED   16  1 11
  DEL PEAK  2(1P36.11) WILD-TYPE 25  2 31
D20V6, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  M0                           16                             25
  M1                            1                              2
  MX                           11                             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"
D20V7, binary
                                cls
clus                              0  1
  DEL PEAK  2(1P36.11) MUTATED    9 19
  DEL PEAK  2(1P36.11) WILD-TYPE 35 23
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  2(1P36.11) MUTATED      9   19
  DEL PEAK  2(1P36.11) WILD-TYPE   35   23
        clus
vv       DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  FEMALE                            9                             35
  MALE                             19                             23
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  2(1P36.11) MUTATED                                    24
  DEL PEAK  2(1P36.11) WILD-TYPE                                  50
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  2(1P36.11) MUTATED                                       2
  DEL PEAK  2(1P36.11) WILD-TYPE                                     6
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  2(1P36.11) MUTATED                                                  2
  DEL PEAK  2(1P36.11) WILD-TYPE                                                1
D20V8, multiclass
                                                  clus
vv                                                 DEL PEAK  2(1P36.11) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            2
                                                  clus
vv                                                 DEL PEAK  2(1P36.11) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          50
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK  2(1P36.11) MUTATED   20  7  0  1
  DEL PEAK  2(1P36.11) WILD-TYPE 35 18  1  1
D20V10, multiclass
    clus
vv   DEL PEAK  2(1P36.11) MUTATED DEL PEAK  2(1P36.11) WILD-TYPE
  R0                           20                             35
  R1                            7                             18
  R2                            0                              1
  RX                            1                              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
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P36.11) MUTATED       2                         2    24
  DEL PEAK  2(1P36.11) WILD-TYPE     0                         4    50
D20V12, multiclass
                           clus
vv                          DEL PEAK  2(1P36.11) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               24
                           clus
vv                          DEL PEAK  2(1P36.11) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 50
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(21) Variable = DEL PEAK  3(1P21.2) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  3(1P21.2) MUTATED   12  4
  DEL PEAK  3(1P21.2) WILD-TYPE 38  7
  DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE 
                           16                            45 
  DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE 
                            4                             7 
$`DEL PEAK  3(1P21.2) MUTATED`
TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-A77O TCGA-IB-7651 
           1          166          240           28           11         1989 
TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A6UG TCGA-IB-A7M4 
         476         1975          522         1991         1968          181 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-YY-A8LH 
         164           35          110         1834 

$`DEL PEAK  3(1P21.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7922 
         449          392          233          396           20            4 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q 
          23           29          194           46           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO 
         347         1951          851          488           17          329 
TCGA-IB-A5SP TCGA-IB-A5ST TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY 
         300            8          127          584          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
        1955          844          160 

  DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE 
                            1                             3 
  DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE 
                         1991                          1955 
  DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE 
                        210.5                         160.0 
[1] "1.0 - 1991.0 (210.5)" "3.0 - 1955.0 (160.0)"
[1] "hr="     "7.8e+08"
D21V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK  3(1P21.2) MUTATED          0        0         3        17         0
  DEL PEAK  3(1P21.2) WILD-TYPE        2        4        11        44         2
                               vv
clus                            STAGE IV
  DEL PEAK  3(1P21.2) MUTATED          0
  DEL PEAK  3(1P21.2) WILD-TYPE        3
D21V3, multiclass
           clus
vv          DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            0                             4
  STAGE IIA                           3                            11
  STAGE IIB                          17                            44
  STAGE III                           0                             2
  STAGE IV                            0                             3
[1] 6 2
[1] 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(1P21.2) MUTATED       1    19
  DEL PEAK  3(1P21.2) WILD-TYPE     7    59
D21V4, multiclass
       clus
vv      DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE
  T1+T2                           1                             7
  T3+T4                          19                            59
[1] 2 2
[1] FALSE
D21V5, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P21.2) MUTATED    2 17
  DEL PEAK  3(1P21.2) WILD-TYPE 19 47
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P21.2) MUTATED      2   17
  DEL PEAK  3(1P21.2) WILD-TYPE   19   47
   clus
vv  DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE
  0                           2                            19
  1                          17                            47
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  3(1P21.2) MUTATED   13  0  7
  DEL PEAK  3(1P21.2) WILD-TYPE 28  3 35
D21V6, multiclass
    clus
vv   DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE
  M0                          13                            28
  M1                           0                             3
  MX                           7                            35
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                               cls
clus                             0  1
  DEL PEAK  3(1P21.2) MUTATED    8 12
  DEL PEAK  3(1P21.2) WILD-TYPE 36 30
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(1P21.2) MUTATED      8   12
  DEL PEAK  3(1P21.2) WILD-TYPE   36   30
        clus
vv       DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE
  FEMALE                           8                            36
  MALE                            12                            30
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  3(1P21.2) MUTATED                                    18
  DEL PEAK  3(1P21.2) WILD-TYPE                                  56
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  3(1P21.2) MUTATED                                       1
  DEL PEAK  3(1P21.2) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  3(1P21.2) MUTATED                                                  1
  DEL PEAK  3(1P21.2) WILD-TYPE                                                2
D21V8, multiclass
                                                  clus
vv                                                 DEL PEAK  3(1P21.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           1
                                                  clus
vv                                                 DEL PEAK  3(1P21.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         56
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D21V9, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  3(1P21.2) MUTATED   12  6  1  1
  DEL PEAK  3(1P21.2) WILD-TYPE 43 19  0  1
D21V10, multiclass
    clus
vv   DEL PEAK  3(1P21.2) MUTATED DEL PEAK  3(1P21.2) WILD-TYPE
  R0                          12                            43
  R1                           6                            19
  R2                           1                             0
  RX                           1                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1P21.2) MUTATED       2                         2    16
  DEL PEAK  3(1P21.2) WILD-TYPE     0                         4    58
D21V12, multiclass
                           clus
vv                          DEL PEAK  3(1P21.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              16
                           clus
vv                          DEL PEAK  3(1P21.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(22) Variable = DEL PEAK  4(1Q42.2) MUTATION ANALYSIS
D22V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  4(1Q42.2) MUTATED    2  0
  DEL PEAK  4(1Q42.2) WILD-TYPE 48 11
  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE 
                            2                            59 
  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE 
                            0                            11 
$`DEL PEAK  4(1Q42.2) MUTATED`
TCGA-IB-A5SP TCGA-IB-A7M4 
         300          181 

$`DEL PEAK  4(1Q42.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         240           28           20            4            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          16            3            5           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
         194           46           11           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 
        1951         1989          476          851         1975          488 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
          17          522          329         1991            8         1968 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         164          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE 
                          181                             1 
  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE 
                          300                          1991 
  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE 
                        240.5                         166.0 
[1] "181.0 - 300.0 (240.5)" "1.0 - 1991.0 (166.0)" 
[1] "Remove cluster labels:"      "DEL PEAK  4(1Q42.2) MUTATED"
D22V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK  4(1Q42.2) MUTATED          0        0         1         3         0
  DEL PEAK  4(1Q42.2) WILD-TYPE        2        4        13        58         2
                               vv
clus                            STAGE IV
  DEL PEAK  4(1Q42.2) MUTATED          0
  DEL PEAK  4(1Q42.2) WILD-TYPE        3
D22V3, multiclass
           clus
vv          DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            0                             4
  STAGE IIA                           1                            13
  STAGE IIB                           3                            58
  STAGE III                           0                             2
  STAGE IV                            0                             3
[1] 6 2
[1] 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(1Q42.2) MUTATED       0     4
  DEL PEAK  4(1Q42.2) WILD-TYPE     8    74
D22V4, multiclass
       clus
vv      DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE
  T1+T2                           0                             8
  T3+T4                           4                            74
[1] 2 2
[1] FALSE
D22V5, binary
                               cls
clus                             0  1
  DEL PEAK  4(1Q42.2) MUTATED    1  3
  DEL PEAK  4(1Q42.2) WILD-TYPE 20 61
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1Q42.2) MUTATED      1    3
  DEL PEAK  4(1Q42.2) WILD-TYPE   20   61
   clus
vv  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE
  0                           1                            20
  1                           3                            61
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  4(1Q42.2) MUTATED    1  0  3
  DEL PEAK  4(1Q42.2) WILD-TYPE 40  3 39
D22V6, multiclass
    clus
vv   DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE
  M0                           1                            40
  M1                           0                             3
  MX                           3                            39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                               cls
clus                             0  1
  DEL PEAK  4(1Q42.2) MUTATED    0  4
  DEL PEAK  4(1Q42.2) WILD-TYPE 44 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(1Q42.2) MUTATED      0    4
  DEL PEAK  4(1Q42.2) WILD-TYPE   44   38
        clus
vv       DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE
  FEMALE                           0                            44
  MALE                             4                            38
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  4(1Q42.2) MUTATED                                     3
  DEL PEAK  4(1Q42.2) WILD-TYPE                                  71
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  4(1Q42.2) MUTATED                                       1
  DEL PEAK  4(1Q42.2) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  4(1Q42.2) MUTATED                                                  0
  DEL PEAK  4(1Q42.2) WILD-TYPE                                                3
D22V8, multiclass
                                                  clus
vv                                                 DEL PEAK  4(1Q42.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        3
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           0
                                                  clus
vv                                                 DEL PEAK  4(1Q42.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         71
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D22V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK  4(1Q42.2) MUTATED"
clus
  DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE 
                            1                            25 
                   TCGA-F2-6880                    TCGA-FB-A4P5 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-FB-A5VM                    TCGA-FB-A78T 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-FB-A7DR                    TCGA-H6-8124 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-H6-A45N                    TCGA-H8-A6C1 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-HZ-A77Q                    TCGA-IB-7644 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-IB-7649                    TCGA-IB-7651 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-IB-7885                    TCGA-IB-7886 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-IB-7887                    TCGA-IB-7891 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-IB-8126                    TCGA-IB-8127 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-IB-A5SS                    TCGA-IB-A6UG 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-LB-A7SX                    TCGA-OE-A75W 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-S4-A8RP                    TCGA-US-A774 
"DEL PEAK  4(1Q42.2) WILD-TYPE" "DEL PEAK  4(1Q42.2) WILD-TYPE" 
                   TCGA-YY-A8LH 
"DEL PEAK  4(1Q42.2) WILD-TYPE" 
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  4(1Q42.2) MUTATED    1  3  0  0
  DEL PEAK  4(1Q42.2) WILD-TYPE 54 22  1  2
D22V10, multiclass
    clus
vv   DEL PEAK  4(1Q42.2) MUTATED DEL PEAK  4(1Q42.2) WILD-TYPE
  R0                           1                            54
  R1                           3                            22
  R2                           0                             1
  RX                           0                             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"
D22V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(1Q42.2) MUTATED       0                         0     4
  DEL PEAK  4(1Q42.2) WILD-TYPE     2                         6    70
D22V12, multiclass
                           clus
vv                          DEL PEAK  4(1Q42.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               4
                           clus
vv                          DEL PEAK  4(1Q42.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                70
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(23) Variable = DEL PEAK  5(2P23.3) MUTATION ANALYSIS
D23V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  5(2P23.3) MUTATED    6  0
  DEL PEAK  5(2P23.3) WILD-TYPE 44 11
  DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE 
                            6                            55 
  DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE 
                            0                            11 
$`DEL PEAK  5(2P23.3) MUTATED`
TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-IB-7652 TCGA-OE-A75W TCGA-US-A776 
         392          396          240          476          110          844 

$`DEL PEAK  5(2P23.3) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7919 
         449            1          166          233           28           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
           4            8          369          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          24           21           28           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 
          13           33          347         1951         1989          851 
TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        1975          488           17          522          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
        1991            8         1968          181          164          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D 
          35          584          247          416         1955          160 
TCGA-YY-A8LH 
        1834 

  DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE 
                          110                             1 
  DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE 
                          844                          1991 
  DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE 
                          394                           164 
[1] "110.0 - 844.0 (394.0)" "1.0 - 1991.0 (164.0)" 
[1] "hr="     "8.7e+07"
D23V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK  5(2P23.3) MUTATED          0        1         4         6         0
  DEL PEAK  5(2P23.3) WILD-TYPE        2        3        10        55         2
                               vv
clus                            STAGE IV
  DEL PEAK  5(2P23.3) MUTATED          0
  DEL PEAK  5(2P23.3) WILD-TYPE        3
D23V3, multiclass
           clus
vv          DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            1                             3
  STAGE IIA                           4                            10
  STAGE IIB                           6                            55
  STAGE III                           0                             2
  STAGE IV                            0                             3
[1] 6 2
[1] 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(2P23.3) MUTATED       1    10
  DEL PEAK  5(2P23.3) WILD-TYPE     7    68
D23V4, multiclass
       clus
vv      DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE
  T1+T2                           1                             7
  T3+T4                          10                            68
[1] 2 2
[1] FALSE
D23V5, binary
                               cls
clus                             0  1
  DEL PEAK  5(2P23.3) MUTATED    5  6
  DEL PEAK  5(2P23.3) WILD-TYPE 16 58
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2P23.3) MUTATED      5    6
  DEL PEAK  5(2P23.3) WILD-TYPE   16   58
   clus
vv  DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE
  0                           5                            16
  1                           6                            58
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  5(2P23.3) MUTATED    7  0  4
  DEL PEAK  5(2P23.3) WILD-TYPE 34  3 38
D23V6, multiclass
    clus
vv   DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE
  M0                           7                            34
  M1                           0                             3
  MX                           4                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                               cls
clus                             0  1
  DEL PEAK  5(2P23.3) MUTATED    4  7
  DEL PEAK  5(2P23.3) WILD-TYPE 40 35
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(2P23.3) MUTATED      4    7
  DEL PEAK  5(2P23.3) WILD-TYPE   40   35
        clus
vv       DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE
  FEMALE                           4                            40
  MALE                             7                            35
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  5(2P23.3) MUTATED                                     8
  DEL PEAK  5(2P23.3) WILD-TYPE                                  66
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  5(2P23.3) MUTATED                                       2
  DEL PEAK  5(2P23.3) WILD-TYPE                                     6
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  5(2P23.3) MUTATED                                                  1
  DEL PEAK  5(2P23.3) WILD-TYPE                                                2
D23V8, multiclass
                                                  clus
vv                                                 DEL PEAK  5(2P23.3) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           1
                                                  clus
vv                                                 DEL PEAK  5(2P23.3) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         66
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D23V9, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  5(2P23.3) MUTATED    6  4  0  1
  DEL PEAK  5(2P23.3) WILD-TYPE 49 21  1  1
D23V10, multiclass
    clus
vv   DEL PEAK  5(2P23.3) MUTATED DEL PEAK  5(2P23.3) WILD-TYPE
  R0                           6                            49
  R1                           4                            21
  R2                           0                             1
  RX                           1                             1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(2P23.3) MUTATED       1                         1     8
  DEL PEAK  5(2P23.3) WILD-TYPE     1                         5    66
D23V12, multiclass
                           clus
vv                          DEL PEAK  5(2P23.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               8
                           clus
vv                          DEL PEAK  5(2P23.3) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(24) Variable = DEL PEAK  6(2Q37.3) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  6(2Q37.3) MUTATED    3  0
  DEL PEAK  6(2Q37.3) WILD-TYPE 47 11
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                            3                            58 
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                            0                            11 
$`DEL PEAK  6(2Q37.3) MUTATED`
TCGA-H6-8124 TCGA-L1-A7W4 TCGA-US-A776 
         392          164          844 

$`DEL PEAK  6(2Q37.3) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          166          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH 
           3            5           91           23           29          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1989          476          851         1975          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         522          329          300         1991            8         1968 
TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
         181          127           35          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          160         1834 

  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                          164                             1 
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                          844                          1991 
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                        392.0                         173.5 
[1] "164.0 - 844.0 (392.0)" "1.0 - 1991.0 (173.5)" 
[1] "hr="     "7.5e+07"
D24V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK  6(2Q37.3) MUTATED          0        0         1         2         0
  DEL PEAK  6(2Q37.3) WILD-TYPE        2        4        13        59         2
                               vv
clus                            STAGE IV
  DEL PEAK  6(2Q37.3) MUTATED          0
  DEL PEAK  6(2Q37.3) WILD-TYPE        3
D24V3, multiclass
           clus
vv          DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            0                             4
  STAGE IIA                           1                            13
  STAGE IIB                           2                            59
  STAGE III                           0                             2
  STAGE IV                            0                             3
[1] 6 2
[1] 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(2Q37.3) MUTATED       0     3
  DEL PEAK  6(2Q37.3) WILD-TYPE     8    75
D24V4, multiclass
       clus
vv      DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE
  T1+T2                           0                             8
  T3+T4                           3                            75
[1] 2 2
[1] FALSE
D24V5, binary
                               cls
clus                             0  1
  DEL PEAK  6(2Q37.3) MUTATED    1  2
  DEL PEAK  6(2Q37.3) WILD-TYPE 20 62
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.3) MUTATED      1    2
  DEL PEAK  6(2Q37.3) WILD-TYPE   20   62
   clus
vv  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE
  0                           1                            20
  1                           2                            62
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  6(2Q37.3) MUTATED    2  0  1
  DEL PEAK  6(2Q37.3) WILD-TYPE 39  3 41
D24V6, multiclass
    clus
vv   DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE
  M0                           2                            39
  M1                           0                             3
  MX                           1                            41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                               cls
clus                             0  1
  DEL PEAK  6(2Q37.3) MUTATED    2  1
  DEL PEAK  6(2Q37.3) WILD-TYPE 42 41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(2Q37.3) MUTATED      2    1
  DEL PEAK  6(2Q37.3) WILD-TYPE   42   41
        clus
vv       DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE
  FEMALE                           2                            42
  MALE                             1                            41
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  6(2Q37.3) MUTATED                                     2
  DEL PEAK  6(2Q37.3) WILD-TYPE                                  72
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  6(2Q37.3) MUTATED                                       0
  DEL PEAK  6(2Q37.3) WILD-TYPE                                     8
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  6(2Q37.3) MUTATED                                                  1
  DEL PEAK  6(2Q37.3) WILD-TYPE                                                2
D24V8, multiclass
                                                  clus
vv                                                 DEL PEAK  6(2Q37.3) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           1
                                                  clus
vv                                                 DEL PEAK  6(2Q37.3) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         72
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D24V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK  6(2Q37.3) MUTATED"
clus
  DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE 
                            1                            25 
                   TCGA-F2-6880                    TCGA-FB-A4P5 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-FB-A5VM                    TCGA-FB-A78T 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-FB-A7DR                    TCGA-H6-A45N 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-H8-A6C1                    TCGA-HZ-A77Q 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-IB-7644                    TCGA-IB-7649 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-IB-7651                    TCGA-IB-7885 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-IB-7886                    TCGA-IB-7887 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-IB-7891                    TCGA-IB-8126 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-IB-8127                    TCGA-IB-A5SS 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-IB-A6UG                    TCGA-IB-A7M4 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-LB-A7SX                    TCGA-OE-A75W 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-S4-A8RP                    TCGA-US-A774 
"DEL PEAK  6(2Q37.3) WILD-TYPE" "DEL PEAK  6(2Q37.3) WILD-TYPE" 
                   TCGA-YY-A8LH 
"DEL PEAK  6(2Q37.3) WILD-TYPE" 
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  6(2Q37.3) MUTATED    2  0  1  0
  DEL PEAK  6(2Q37.3) WILD-TYPE 53 25  0  2
D24V10, multiclass
    clus
vv   DEL PEAK  6(2Q37.3) MUTATED DEL PEAK  6(2Q37.3) WILD-TYPE
  R0                           2                            53
  R1                           0                            25
  R2                           1                             0
  RX                           0                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(2Q37.3) MUTATED       0                         0     3
  DEL PEAK  6(2Q37.3) WILD-TYPE     2                         6    71
D24V12, multiclass
                           clus
vv                          DEL PEAK  6(2Q37.3) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               3
                           clus
vv                          DEL PEAK  6(2Q37.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(25) Variable = DEL PEAK  7(3P24.1) MUTATION ANALYSIS
D25V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  7(3P24.1) MUTATED   12  1
  DEL PEAK  7(3P24.1) WILD-TYPE 38 10
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                           13                            48 
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                            1                            10 
$`DEL PEAK  7(3P24.1) MUTATED`
TCGA-F2-A44H TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-A4BK TCGA-HZ-A77O 
         586           28            4          361           46           11 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 
        1975          522          300          127           35          584 
TCGA-YY-A8LH 
        1834 

$`DEL PEAK  7(3P24.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
           1          166          392          233          396          240 
TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
          20            8          369            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
          23           29          194           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          476          851          488           17 
TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 
         329         1991            8         1968          181          164 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         110          247          416         1955          844          160 

  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                            4                             1 
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                         1975                          1991 
  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE 
                        300.0                         173.5 
[1] "4.0 - 1975.0 (300.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "2.5"
D25V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK  7(3P24.1) MUTATED          0        1         4        15         0
  DEL PEAK  7(3P24.1) WILD-TYPE        2        3        10        46         2
                               vv
clus                            STAGE IV
  DEL PEAK  7(3P24.1) MUTATED          0
  DEL PEAK  7(3P24.1) WILD-TYPE        3
D25V3, multiclass
           clus
vv          DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            1                             3
  STAGE IIA                           4                            10
  STAGE IIB                          15                            46
  STAGE III                           0                             2
  STAGE IV                            0                             3
[1] 6 2
[1] 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(3P24.1) MUTATED       2    18
  DEL PEAK  7(3P24.1) WILD-TYPE     6    60
D25V4, multiclass
       clus
vv      DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  T1+T2                           2                             6
  T3+T4                          18                            60
[1] 2 2
[1] FALSE
D25V5, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P24.1) MUTATED    5 15
  DEL PEAK  7(3P24.1) WILD-TYPE 16 49
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P24.1) MUTATED      5   15
  DEL PEAK  7(3P24.1) WILD-TYPE   16   49
   clus
vv  DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  0                           5                            16
  1                          15                            49
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  7(3P24.1) MUTATED   10  0 10
  DEL PEAK  7(3P24.1) WILD-TYPE 31  3 32
D25V6, multiclass
    clus
vv   DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  M0                          10                            31
  M1                           0                             3
  MX                          10                            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"
D25V7, binary
                               cls
clus                             0  1
  DEL PEAK  7(3P24.1) MUTATED    9 11
  DEL PEAK  7(3P24.1) WILD-TYPE 35 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P24.1) MUTATED      9   11
  DEL PEAK  7(3P24.1) WILD-TYPE   35   31
        clus
vv       DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  FEMALE                           9                            35
  MALE                            11                            31
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  7(3P24.1) MUTATED                                    19
  DEL PEAK  7(3P24.1) WILD-TYPE                                  55
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  7(3P24.1) MUTATED                                       1
  DEL PEAK  7(3P24.1) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  7(3P24.1) MUTATED                                                  0
  DEL PEAK  7(3P24.1) WILD-TYPE                                                3
D25V8, multiclass
                                                  clus
vv                                                 DEL PEAK  7(3P24.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           0
                                                  clus
vv                                                 DEL PEAK  7(3P24.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         55
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D25V9, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  7(3P24.1) MUTATED   10 10  0  0
  DEL PEAK  7(3P24.1) WILD-TYPE 45 15  1  2
D25V10, multiclass
    clus
vv   DEL PEAK  7(3P24.1) MUTATED DEL PEAK  7(3P24.1) WILD-TYPE
  R0                          10                            45
  R1                          10                            15
  R2                           0                             1
  RX                           0                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P24.1) MUTATED       0                         2    16
  DEL PEAK  7(3P24.1) WILD-TYPE     2                         4    58
D25V12, multiclass
                           clus
vv                          DEL PEAK  7(3P24.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              16
                           clus
vv                          DEL PEAK  7(3P24.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                58
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(26) Variable = DEL PEAK  8(4Q35.2) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  8(4Q35.2) MUTATED   10  1
  DEL PEAK  8(4Q35.2) WILD-TYPE 40 10
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                           11                            50 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                            1                            10 
$`DEL PEAK  8(4Q35.2) MUTATED`
TCGA-FB-A5VM TCGA-FB-A7DR TCGA-H8-A6C1 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-A49G 
         449          166          396            4          361           23 
TCGA-HZ-A4BH TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-A5SP TCGA-OE-A75W 
         194          476         1975          300          110 

$`DEL PEAK  8(4Q35.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
           1          392          233          240           28           20 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
           8          369            8           19           24           21 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H 
          28           16            3            5           91           29 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 
          46           11           13           33          347         1951 
TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
        1989          851          488           17          522          329 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
        1991            8         1968          181          164          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
          35          584          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                            4                             1 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                         1975                          1991 
  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE 
                          300                           162 
[1] "4.0 - 1975.0 (300.0)" "1.0 - 1991.0 (162.0)"
[1] "hr=" "2.3"
D26V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK  8(4Q35.2) MUTATED          0        1         4        10         0
  DEL PEAK  8(4Q35.2) WILD-TYPE        2        3        10        51         2
                               vv
clus                            STAGE IV
  DEL PEAK  8(4Q35.2) MUTATED          0
  DEL PEAK  8(4Q35.2) WILD-TYPE        3
D26V3, multiclass
           clus
vv          DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            1                             3
  STAGE IIA                           4                            10
  STAGE IIB                          10                            51
  STAGE III                           0                             2
  STAGE IV                            0                             3
[1] 6 2
[1] 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(4Q35.2) MUTATED       2    13
  DEL PEAK  8(4Q35.2) WILD-TYPE     6    65
D26V4, multiclass
       clus
vv      DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  T1+T2                           2                             6
  T3+T4                          13                            65
[1] 2 2
[1] FALSE
D26V5, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED    4 10
  DEL PEAK  8(4Q35.2) WILD-TYPE 17 54
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED      4   10
  DEL PEAK  8(4Q35.2) WILD-TYPE   17   54
   clus
vv  DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  0                           4                            17
  1                          10                            54
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  8(4Q35.2) MUTATED    7  0  8
  DEL PEAK  8(4Q35.2) WILD-TYPE 34  3 34
D26V6, multiclass
    clus
vv   DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  M0                           7                            34
  M1                           0                             3
  MX                           8                            34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                               cls
clus                             0  1
  DEL PEAK  8(4Q35.2) MUTATED    4 11
  DEL PEAK  8(4Q35.2) WILD-TYPE 40 31
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(4Q35.2) MUTATED      4   11
  DEL PEAK  8(4Q35.2) WILD-TYPE   40   31
        clus
vv       DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  FEMALE                           4                            40
  MALE                            11                            31
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  8(4Q35.2) MUTATED                                    13
  DEL PEAK  8(4Q35.2) WILD-TYPE                                  61
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  8(4Q35.2) MUTATED                                       1
  DEL PEAK  8(4Q35.2) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  8(4Q35.2) MUTATED                                                  1
  DEL PEAK  8(4Q35.2) WILD-TYPE                                                2
D26V8, multiclass
                                                  clus
vv                                                 DEL PEAK  8(4Q35.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           1
                                                  clus
vv                                                 DEL PEAK  8(4Q35.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         61
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D26V9, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  8(4Q35.2) MUTATED    9  6  0  0
  DEL PEAK  8(4Q35.2) WILD-TYPE 46 19  1  2
D26V10, multiclass
    clus
vv   DEL PEAK  8(4Q35.2) MUTATED DEL PEAK  8(4Q35.2) WILD-TYPE
  R0                           9                            46
  R1                           6                            19
  R2                           0                             1
  RX                           0                             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"
D26V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(4Q35.2) MUTATED       2                         1    12
  DEL PEAK  8(4Q35.2) WILD-TYPE     0                         5    62
D26V12, multiclass
                           clus
vv                          DEL PEAK  8(4Q35.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              12
                           clus
vv                          DEL PEAK  8(4Q35.2) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(27) Variable = DEL PEAK  9(5Q14.2) MUTATION ANALYSIS
D27V1, survival
                               sevent
clus2                            0  1
  DEL PEAK  9(5Q14.2) MUTATED   13  1
  DEL PEAK  9(5Q14.2) WILD-TYPE 37 10
  DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE 
                           14                            47 
  DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE 
                            1                            10 
$`DEL PEAK  9(5Q14.2) MUTATED`
TCGA-FB-A545 TCGA-FB-A5VM TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-A77O 
         385          449          240           28            4           11 
TCGA-IB-7652 TCGA-IB-8127 TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
         476          522         1968          181          164          127 
TCGA-M8-A5N4 TCGA-OE-A75W 
         584          110 

$`DEL PEAK  9(5Q14.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A78T 
         295          360          153          586            4            1 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7923 
         166          392          233          396           20            8 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
         369          361            8           19           24           21 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
          28           16            3            5           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
          29          194           46           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          851         1975          488           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A8F3 TCGA-PZ-A5RE 
         329          300         1991            8           35          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE 
                            4                             1 
  DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE 
                         1968                          1991 
  DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE 
                        210.5                         166.0 
[1] "4.0 - 1968.0 (210.5)" "1.0 - 1991.0 (166.0)"
[1] "hr=" "2.2"
D27V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK  9(5Q14.2) MUTATED          0        1         3        16         0
  DEL PEAK  9(5Q14.2) WILD-TYPE        2        3        11        45         2
                               vv
clus                            STAGE IV
  DEL PEAK  9(5Q14.2) MUTATED          0
  DEL PEAK  9(5Q14.2) WILD-TYPE        3
D27V3, multiclass
           clus
vv          DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            1                             3
  STAGE IIA                           3                            11
  STAGE IIB                          16                            45
  STAGE III                           0                             2
  STAGE IV                            0                             3
[1] 6 2
[1] 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(5Q14.2) MUTATED       2    18
  DEL PEAK  9(5Q14.2) WILD-TYPE     6    60
D27V4, multiclass
       clus
vv      DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE
  T1+T2                           2                             6
  T3+T4                          18                            60
[1] 2 2
[1] FALSE
D27V5, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q14.2) MUTATED    4 16
  DEL PEAK  9(5Q14.2) WILD-TYPE 17 48
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q14.2) MUTATED      4   16
  DEL PEAK  9(5Q14.2) WILD-TYPE   17   48
   clus
vv  DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE
  0                           4                            17
  1                          16                            48
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK  9(5Q14.2) MUTATED   10  0 10
  DEL PEAK  9(5Q14.2) WILD-TYPE 31  3 32
D27V6, multiclass
    clus
vv   DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE
  M0                          10                            31
  M1                           0                             3
  MX                          10                            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"
D27V7, binary
                               cls
clus                             0  1
  DEL PEAK  9(5Q14.2) MUTATED   10 10
  DEL PEAK  9(5Q14.2) WILD-TYPE 34 32
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(5Q14.2) MUTATED     10   10
  DEL PEAK  9(5Q14.2) WILD-TYPE   34   32
        clus
vv       DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE
  FEMALE                          10                            34
  MALE                            10                            32
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK  9(5Q14.2) MUTATED                                    19
  DEL PEAK  9(5Q14.2) WILD-TYPE                                  55
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK  9(5Q14.2) MUTATED                                       1
  DEL PEAK  9(5Q14.2) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK  9(5Q14.2) MUTATED                                                  0
  DEL PEAK  9(5Q14.2) WILD-TYPE                                                3
D27V8, multiclass
                                                  clus
vv                                                 DEL PEAK  9(5Q14.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       19
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           0
                                                  clus
vv                                                 DEL PEAK  9(5Q14.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         55
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D27V9, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK  9(5Q14.2) MUTATED   11  6  1  1
  DEL PEAK  9(5Q14.2) WILD-TYPE 44 19  0  1
D27V10, multiclass
    clus
vv   DEL PEAK  9(5Q14.2) MUTATED DEL PEAK  9(5Q14.2) WILD-TYPE
  R0                          11                            44
  R1                           6                            19
  R2                           1                             0
  RX                           1                             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"
D27V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(5Q14.2) MUTATED       1                         1    17
  DEL PEAK  9(5Q14.2) WILD-TYPE     1                         5    57
D27V12, multiclass
                           clus
vv                          DEL PEAK  9(5Q14.2) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              17
                           clus
vv                          DEL PEAK  9(5Q14.2) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(28) Variable = DEL PEAK 10(6P25.2) MUTATION ANALYSIS
D28V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 10(6P25.2) MUTATED   20  3
  DEL PEAK 10(6P25.2) WILD-TYPE 30  8
  DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE 
                           23                            38 
  DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE 
                            3                             8 
$`DEL PEAK 10(6P25.2) MUTATED`
TCGA-F2-A44H TCGA-FB-A545 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
         586          385          392          396          240           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-A4BK TCGA-HZ-A77O 
          20            4           19           28           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS 
          13           33         1975          522          300         1991 
TCGA-IB-A6UG TCGA-LB-A7SX TCGA-PZ-A5RE TCGA-YB-A89D TCGA-YY-A8LH 
        1968          127          247          160         1834 

$`DEL PEAK 10(6P25.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T 
         295          360          153            4          449            1 
TCGA-FB-A7DR TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
         166          233            8          369          361            8 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          24           21           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          23           29          194          347         1951         1989 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5ST 
         476          851          488           17          329            8 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY 
         181          164           35          584          110          416 
TCGA-US-A774 TCGA-US-A776 
        1955          844 

  DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE 
                            4                             1 
  DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE 
                         1991                          1989 
  DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE 
                        240.0                         173.5 
[1] "4.0 - 1991.0 (240.0)" "1.0 - 1989.0 (173.5)"
[1] "hr=" "4.4"
D28V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK 10(6P25.2) MUTATED          0        1         5        26         1
  DEL PEAK 10(6P25.2) WILD-TYPE        2        3         9        35         1
                               vv
clus                            STAGE IV
  DEL PEAK 10(6P25.2) MUTATED          0
  DEL PEAK 10(6P25.2) WILD-TYPE        3
D28V3, multiclass
           clus
vv          DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            1                             3
  STAGE IIA                           5                             9
  STAGE IIB                          26                            35
  STAGE III                           1                             1
  STAGE IV                            0                             3
[1] 6 2
[1] 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(6P25.2) MUTATED       2    31
  DEL PEAK 10(6P25.2) WILD-TYPE     6    47
D28V4, multiclass
       clus
vv      DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE
  T1+T2                           2                             6
  T3+T4                          31                            47
[1] 2 2
[1] FALSE
D28V5, binary
                               cls
clus                             0  1
  DEL PEAK 10(6P25.2) MUTATED    7 26
  DEL PEAK 10(6P25.2) WILD-TYPE 14 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.2) MUTATED      7   26
  DEL PEAK 10(6P25.2) WILD-TYPE   14   38
   clus
vv  DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE
  0                           7                            14
  1                          26                            38
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 10(6P25.2) MUTATED   18  0 15
  DEL PEAK 10(6P25.2) WILD-TYPE 23  3 27
D28V6, multiclass
    clus
vv   DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE
  M0                          18                            23
  M1                           0                             3
  MX                          15                            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"
D28V7, binary
                               cls
clus                             0  1
  DEL PEAK 10(6P25.2) MUTATED   15 18
  DEL PEAK 10(6P25.2) WILD-TYPE 29 24
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 10(6P25.2) MUTATED     15   18
  DEL PEAK 10(6P25.2) WILD-TYPE   29   24
        clus
vv       DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE
  FEMALE                          15                            29
  MALE                            18                            24
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 10(6P25.2) MUTATED                                    27
  DEL PEAK 10(6P25.2) WILD-TYPE                                  47
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 10(6P25.2) MUTATED                                       5
  DEL PEAK 10(6P25.2) WILD-TYPE                                     3
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 10(6P25.2) MUTATED                                                  0
  DEL PEAK 10(6P25.2) WILD-TYPE                                                3
D28V8, multiclass
                                                  clus
vv                                                 DEL PEAK 10(6P25.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       27
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           0
                                                  clus
vv                                                 DEL PEAK 10(6P25.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         47
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D28V9, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 10(6P25.2) MUTATED   19 11  0  1
  DEL PEAK 10(6P25.2) WILD-TYPE 36 14  1  1
D28V10, multiclass
    clus
vv   DEL PEAK 10(6P25.2) MUTATED DEL PEAK 10(6P25.2) WILD-TYPE
  R0                          19                            36
  R1                          11                            14
  R2                           0                             1
  RX                           1                             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"
D28V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6P25.2) MUTATED       0                         2    30
  DEL PEAK 10(6P25.2) WILD-TYPE     2                         4    44
D28V12, multiclass
                           clus
vv                          DEL PEAK 10(6P25.2) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              30
                           clus
vv                          DEL PEAK 10(6P25.2) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                44
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(29) Variable = DEL PEAK 11(7Q36.1) MUTATION ANALYSIS
D29V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 11(7Q36.1) MUTATED    5  0
  DEL PEAK 11(7Q36.1) WILD-TYPE 45 11
  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE 
                            5                            56 
  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE 
                            0                            11 
$`DEL PEAK 11(7Q36.1) MUTATED`
TCGA-H6-8124 TCGA-HZ-7922 TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-PZ-A5RE 
         392            4          194           11          247 

$`DEL PEAK 11(7Q36.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          166          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77P 
           5           91           23           29           46           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        1975          488           17          522          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
        1991            8         1968          181          164          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
          35          584          110          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE 
                            4                             1 
  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE 
                          392                          1991 
  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE 
                        194.0                         173.5 
[1] "4.0 - 392.0 (194.0)"  "1.0 - 1991.0 (173.5)"
[1] "hr="     "2.7e+07"
D29V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK 11(7Q36.1) MUTATED          0        1         0         7         0
  DEL PEAK 11(7Q36.1) WILD-TYPE        2        3        14        54         2
                               vv
clus                            STAGE IV
  DEL PEAK 11(7Q36.1) MUTATED          0
  DEL PEAK 11(7Q36.1) WILD-TYPE        3
D29V3, multiclass
           clus
vv          DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            1                             3
  STAGE IIA                           0                            14
  STAGE IIB                           7                            54
  STAGE III                           0                             2
  STAGE IV                            0                             3
[1] 6 2
[1] 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(7Q36.1) MUTATED       2     6
  DEL PEAK 11(7Q36.1) WILD-TYPE     6    72
D29V4, multiclass
       clus
vv      DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE
  T1+T2                           2                             6
  T3+T4                           6                            72
[1] 2 2
[1] FALSE
D29V5, binary
                               cls
clus                             0  1
  DEL PEAK 11(7Q36.1) MUTATED    1  7
  DEL PEAK 11(7Q36.1) WILD-TYPE 20 57
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.1) MUTATED      1    7
  DEL PEAK 11(7Q36.1) WILD-TYPE   20   57
   clus
vv  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE
  0                           1                            20
  1                           7                            57
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 11(7Q36.1) MUTATED    3  0  5
  DEL PEAK 11(7Q36.1) WILD-TYPE 38  3 37
D29V6, multiclass
    clus
vv   DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE
  M0                           3                            38
  M1                           0                             3
  MX                           5                            37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                               cls
clus                             0  1
  DEL PEAK 11(7Q36.1) MUTATED    4  4
  DEL PEAK 11(7Q36.1) WILD-TYPE 40 38
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(7Q36.1) MUTATED      4    4
  DEL PEAK 11(7Q36.1) WILD-TYPE   40   38
        clus
vv       DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE
  FEMALE                           4                            40
  MALE                             4                            38
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 11(7Q36.1) MUTATED                                     8
  DEL PEAK 11(7Q36.1) WILD-TYPE                                  66
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 11(7Q36.1) MUTATED                                       0
  DEL PEAK 11(7Q36.1) WILD-TYPE                                     8
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 11(7Q36.1) MUTATED                                                  0
  DEL PEAK 11(7Q36.1) WILD-TYPE                                                3
D29V8, multiclass
                                                  clus
vv                                                 DEL PEAK 11(7Q36.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           0
                                                  clus
vv                                                 DEL PEAK 11(7Q36.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         66
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D29V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK 11(7Q36.1) MUTATED"
clus
  DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE 
                            1                            25 
                   TCGA-F2-6880                    TCGA-FB-A4P5 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-FB-A5VM                    TCGA-FB-A78T 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-FB-A7DR                    TCGA-H6-A45N 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-H8-A6C1                    TCGA-HZ-A77Q 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-IB-7644                    TCGA-IB-7649 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-IB-7651                    TCGA-IB-7885 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-IB-7886                    TCGA-IB-7887 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-IB-7891                    TCGA-IB-8126 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-IB-8127                    TCGA-IB-A5SS 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-IB-A6UG                    TCGA-IB-A7M4 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-LB-A7SX                    TCGA-OE-A75W 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-S4-A8RP                    TCGA-US-A774 
"DEL PEAK 11(7Q36.1) WILD-TYPE" "DEL PEAK 11(7Q36.1) WILD-TYPE" 
                   TCGA-YY-A8LH 
"DEL PEAK 11(7Q36.1) WILD-TYPE" 
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 11(7Q36.1) MUTATED    5  2  0  0
  DEL PEAK 11(7Q36.1) WILD-TYPE 50 23  1  2
D29V10, multiclass
    clus
vv   DEL PEAK 11(7Q36.1) MUTATED DEL PEAK 11(7Q36.1) WILD-TYPE
  R0                           5                            50
  R1                           2                            23
  R2                           0                             1
  RX                           0                             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"
D29V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(7Q36.1) MUTATED       0                         0     7
  DEL PEAK 11(7Q36.1) WILD-TYPE     2                         6    67
D29V12, multiclass
                           clus
vv                          DEL PEAK 11(7Q36.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                               7
                           clus
vv                          DEL PEAK 11(7Q36.1) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             6
  WHITE                                                67
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(30) Variable = DEL PEAK 12(8P21.3) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 12(8P21.3) MUTATED   16  2
  DEL PEAK 12(8P21.3) WILD-TYPE 34  9
  DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE 
                           18                            43 
  DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE 
                            2                             9 
$`DEL PEAK 12(8P21.3) MUTATED`
TCGA-FB-A7DR TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7925 TCGA-HZ-8636 
         166          240           20            4          361            5 
TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A6UG 
          46           13          476         1975          522         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-US-A776 
         181          164           35          110          247          844 

$`DEL PEAK 12(8P21.3) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
         449            1          392          233          396           28 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
           8          369            8           19           24           21 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H 
          28           16            3           91           23           29 
TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
         194           11           33          347         1951         1989 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
         851          488           17          329          300         1991 
TCGA-IB-A5ST TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D 
           8          127          584          416         1955          160 
TCGA-YY-A8LH 
        1834 

  DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE 
                            4                             1 
  DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE 
                         1975                          1991 
  DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE 
                        173.5                         194.0 
[1] "4.0 - 1975.0 (173.5)" "1.0 - 1991.0 (194.0)"
[1] "hr=" "1.8"
D30V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK 12(8P21.3) MUTATED          0        1         4        20         0
  DEL PEAK 12(8P21.3) WILD-TYPE        2        3        10        41         2
                               vv
clus                            STAGE IV
  DEL PEAK 12(8P21.3) MUTATED          1
  DEL PEAK 12(8P21.3) WILD-TYPE        2
D30V3, multiclass
           clus
vv          DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            1                             3
  STAGE IIA                           4                            10
  STAGE IIB                          20                            41
  STAGE III                           0                             2
  STAGE IV                            1                             2
[1] 6 2
[1] 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(8P21.3) MUTATED       1    25
  DEL PEAK 12(8P21.3) WILD-TYPE     7    53
D30V4, multiclass
       clus
vv      DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE
  T1+T2                           1                             7
  T3+T4                          25                            53
[1] 2 2
[1] FALSE
D30V5, binary
                               cls
clus                             0  1
  DEL PEAK 12(8P21.3) MUTATED    5 20
  DEL PEAK 12(8P21.3) WILD-TYPE 16 44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P21.3) MUTATED      5   20
  DEL PEAK 12(8P21.3) WILD-TYPE   16   44
   clus
vv  DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE
  0                           5                            16
  1                          20                            44
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 12(8P21.3) MUTATED   13  1 12
  DEL PEAK 12(8P21.3) WILD-TYPE 28  2 30
D30V6, multiclass
    clus
vv   DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE
  M0                          13                            28
  M1                           1                             2
  MX                          12                            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"
D30V7, binary
                               cls
clus                             0  1
  DEL PEAK 12(8P21.3) MUTATED   10 16
  DEL PEAK 12(8P21.3) WILD-TYPE 34 26
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P21.3) MUTATED     10   16
  DEL PEAK 12(8P21.3) WILD-TYPE   34   26
        clus
vv       DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE
  FEMALE                          10                            34
  MALE                            16                            26
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 12(8P21.3) MUTATED                                    20
  DEL PEAK 12(8P21.3) WILD-TYPE                                  54
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 12(8P21.3) MUTATED                                       3
  DEL PEAK 12(8P21.3) WILD-TYPE                                     5
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 12(8P21.3) MUTATED                                                  2
  DEL PEAK 12(8P21.3) WILD-TYPE                                                1
D30V8, multiclass
                                                  clus
vv                                                 DEL PEAK 12(8P21.3) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           2
                                                  clus
vv                                                 DEL PEAK 12(8P21.3) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         54
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V9, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 12(8P21.3) MUTATED   12 11  1  1
  DEL PEAK 12(8P21.3) WILD-TYPE 43 14  0  1
D30V10, multiclass
    clus
vv   DEL PEAK 12(8P21.3) MUTATED DEL PEAK 12(8P21.3) WILD-TYPE
  R0                          12                            43
  R1                          11                            14
  R2                           1                             0
  RX                           1                             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"
D30V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(8P21.3) MUTATED       2                         1    22
  DEL PEAK 12(8P21.3) WILD-TYPE     0                         5    52
D30V12, multiclass
                           clus
vv                          DEL PEAK 12(8P21.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              22
                           clus
vv                          DEL PEAK 12(8P21.3) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                52
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(31) Variable = DEL PEAK 13(8Q12.1) MUTATION ANALYSIS
D31V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 13(8Q12.1) MUTATED    6  0
  DEL PEAK 13(8Q12.1) WILD-TYPE 44 11
  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE 
                            6                            55 
  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE 
                            0                            11 
$`DEL PEAK 13(8Q12.1) MUTATED`
TCGA-FB-A7DR TCGA-HZ-7925 TCGA-HZ-8636 TCGA-HZ-A4BK TCGA-LB-A8F3 TCGA-OE-A75W 
         166          361            5           46           35          110 

$`DEL PEAK 13(8Q12.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7926 
          28           20            4            8          369            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P 
          91           23           29          194           11           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        1975          488           17          522          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX 
        1991            8         1968          181          164          127 
TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         584          247          416         1955          844          160 
TCGA-YY-A8LH 
        1834 

  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE 
                            5                             1 
  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE 
                          361                          1991 
  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE 
                           78                           233 
[1] "5.0 - 361.0 (78.0)"   "1.0 - 1991.0 (233.0)"
[1] "hr="     "2.7e+07"
D31V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK 13(8Q12.1) MUTATED          0        0         3         4         0
  DEL PEAK 13(8Q12.1) WILD-TYPE        2        4        11        57         2
                               vv
clus                            STAGE IV
  DEL PEAK 13(8Q12.1) MUTATED          1
  DEL PEAK 13(8Q12.1) WILD-TYPE        2
D31V3, multiclass
           clus
vv          DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            0                             4
  STAGE IIA                           3                            11
  STAGE IIB                           4                            57
  STAGE III                           0                             2
  STAGE IV                            1                             2
[1] 6 2
[1] 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(8Q12.1) MUTATED       0     8
  DEL PEAK 13(8Q12.1) WILD-TYPE     8    70
D31V4, multiclass
       clus
vv      DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE
  T1+T2                           0                             8
  T3+T4                           8                            70
[1] 2 2
[1] FALSE
D31V5, binary
                               cls
clus                             0  1
  DEL PEAK 13(8Q12.1) MUTATED    3  4
  DEL PEAK 13(8Q12.1) WILD-TYPE 18 60
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8Q12.1) MUTATED      3    4
  DEL PEAK 13(8Q12.1) WILD-TYPE   18   60
   clus
vv  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE
  0                           3                            18
  1                           4                            60
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 13(8Q12.1) MUTATED    3  1  4
  DEL PEAK 13(8Q12.1) WILD-TYPE 38  2 38
D31V6, multiclass
    clus
vv   DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE
  M0                           3                            38
  M1                           1                             2
  MX                           4                            38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V7, binary
                               cls
clus                             0  1
  DEL PEAK 13(8Q12.1) MUTATED    3  5
  DEL PEAK 13(8Q12.1) WILD-TYPE 41 37
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 13(8Q12.1) MUTATED      3    5
  DEL PEAK 13(8Q12.1) WILD-TYPE   41   37
        clus
vv       DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE
  FEMALE                           3                            41
  MALE                             5                            37
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 13(8Q12.1) MUTATED                                     6
  DEL PEAK 13(8Q12.1) WILD-TYPE                                  68
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 13(8Q12.1) MUTATED                                       1
  DEL PEAK 13(8Q12.1) WILD-TYPE                                     7
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 13(8Q12.1) MUTATED                                                  1
  DEL PEAK 13(8Q12.1) WILD-TYPE                                                2
D31V8, multiclass
                                                  clus
vv                                                 DEL PEAK 13(8Q12.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        6
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           1
                                                  clus
vv                                                 DEL PEAK 13(8Q12.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         68
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D31V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK 13(8Q12.1) MUTATED"
clus
  DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE 
                            2                            24 
                   TCGA-F2-6880                    TCGA-FB-A4P5 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-FB-A5VM                    TCGA-FB-A78T 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-H6-8124                    TCGA-H6-A45N 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-H8-A6C1                    TCGA-HZ-A77Q 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-IB-7644                    TCGA-IB-7649 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-IB-7651                    TCGA-IB-7885 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-IB-7886                    TCGA-IB-7887 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-IB-7891                    TCGA-IB-8126 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-IB-8127                    TCGA-IB-A5SS 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-IB-A6UG                    TCGA-IB-A7M4 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-LB-A7SX                    TCGA-S4-A8RP 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                   TCGA-US-A774                    TCGA-YY-A8LH 
"DEL PEAK 13(8Q12.1) WILD-TYPE" "DEL PEAK 13(8Q12.1) WILD-TYPE" 
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 13(8Q12.1) MUTATED    5  3  0  0
  DEL PEAK 13(8Q12.1) WILD-TYPE 50 22  1  2
D31V10, multiclass
    clus
vv   DEL PEAK 13(8Q12.1) MUTATED DEL PEAK 13(8Q12.1) WILD-TYPE
  R0                           5                            50
  R1                           3                            22
  R2                           0                             1
  RX                           0                             2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D31V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(8Q12.1) MUTATED       1                         1     6
  DEL PEAK 13(8Q12.1) WILD-TYPE     1                         5    68
D31V12, multiclass
                           clus
vv                          DEL PEAK 13(8Q12.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                               6
                           clus
vv                          DEL PEAK 13(8Q12.1) WILD-TYPE
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             5
  WHITE                                                68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(32) Variable = DEL PEAK 14(9P21.3) MUTATION ANALYSIS
D32V1, survival
                               sevent
clus2                            0  1
  DEL PEAK 14(9P21.3) MUTATED   31  5
  DEL PEAK 14(9P21.3) WILD-TYPE 19  6
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                           36                            25 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                            5                             6 
$`DEL PEAK 14(9P21.3) MUTATED`
TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR 
         153          586          385          449            1          166 
TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 
         392          396          240           28           20            4 
TCGA-HZ-7925 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A4BK 
         361           28            5           23          194           46 
TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 
          11           33          347         1951          476          851 
TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A7M4 TCGA-L1-A7W4 
        1975          522          300         1991          181          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-YY-A8LH 
         127           35          584          110          247         1834 

$`DEL PEAK 14(9P21.3) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-FB-A4P5 TCGA-H6-A45N TCGA-HZ-7923 TCGA-HZ-7924 
         295          360            4          233            8          369 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 
           8           19           24           21           16            3 
TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A77P TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-8126 
          91           29           13         1989          488           17 
TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A6UG TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         329            8         1968          416         1955          844 
TCGA-YB-A89D 
         160 

  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                            1                             3 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                         1991                          1989 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          217                            91 
[1] "1.0 - 1991.0 (217.0)" "3.0 - 1989.0 (91.0)" 
[1] "hr=" "2.1"
D32V2, continuous
                               vv
clus                            STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK 14(9P21.3) MUTATED          0        2        10        39         0
  DEL PEAK 14(9P21.3) WILD-TYPE        2        2         4        22         2
                               vv
clus                            STAGE IV
  DEL PEAK 14(9P21.3) MUTATED          3
  DEL PEAK 14(9P21.3) WILD-TYPE        0
D32V3, multiclass
           clus
vv          DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  STAGE IA                            0                             2
  STAGE IB                            2                             2
  STAGE IIA                          10                             4
  STAGE IIB                          39                            22
  STAGE III                           0                             2
  STAGE IV                            3                             0
[1] 6 2
[1] 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(9P21.3) MUTATED       4    50
  DEL PEAK 14(9P21.3) WILD-TYPE     4    28
D32V4, multiclass
       clus
vv      DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  T1+T2                           4                             4
  T3+T4                          50                            28
[1] 2 2
[1] FALSE
D32V5, binary
                               cls
clus                             0  1
  DEL PEAK 14(9P21.3) MUTATED   12 41
  DEL PEAK 14(9P21.3) WILD-TYPE  9 23
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED     12   41
  DEL PEAK 14(9P21.3) WILD-TYPE    9   23
   clus
vv  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  0                          12                             9
  1                          41                            23
[1] 2 2
[1] FALSE
                               vv
clus                            M0 M1 MX
  DEL PEAK 14(9P21.3) MUTATED   28  3 23
  DEL PEAK 14(9P21.3) WILD-TYPE 13  0 19
D32V6, multiclass
    clus
vv   DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  M0                          28                            13
  M1                           3                             0
  MX                          23                            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"
D32V7, binary
                               cls
clus                             0  1
  DEL PEAK 14(9P21.3) MUTATED   28 26
  DEL PEAK 14(9P21.3) WILD-TYPE 16 16
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED     28   26
  DEL PEAK 14(9P21.3) WILD-TYPE   16   16
        clus
vv       DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  FEMALE                          28                            16
  MALE                            26                            16
[1] 2 2
[1] FALSE
                               vv
clus                            PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 14(9P21.3) MUTATED                                    47
  DEL PEAK 14(9P21.3) WILD-TYPE                                  27
                               vv
clus                            PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 14(9P21.3) MUTATED                                       5
  DEL PEAK 14(9P21.3) WILD-TYPE                                     3
                               vv
clus                            PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 14(9P21.3) MUTATED                                                  1
  DEL PEAK 14(9P21.3) WILD-TYPE                                                2
D32V8, multiclass
                                                  clus
vv                                                 DEL PEAK 14(9P21.3) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       47
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                      5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                           1
                                                  clus
vv                                                 DEL PEAK 14(9P21.3) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         27
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             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"
D32V9, continuous
                               vv
clus                            R0 R1 R2 RX
  DEL PEAK 14(9P21.3) MUTATED   29 21  1  1
  DEL PEAK 14(9P21.3) WILD-TYPE 26  4  0  1
D32V10, multiclass
    clus
vv   DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  R0                          29                            26
  R1                          21                             4
  R2                           1                             0
  RX                           1                             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"
D32V11, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P21.3) MUTATED       2                         3    45
  DEL PEAK 14(9P21.3) WILD-TYPE     0                         3    29
D32V12, multiclass
                           clus
vv                          DEL PEAK 14(9P21.3) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              45
                           clus
vv                          DEL PEAK 14(9P21.3) WILD-TYPE
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             3
  WHITE                                                29
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(33) Variable = DEL PEAK 15(9Q22.33) MUTATION ANALYSIS
D33V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 15(9Q22.33) MUTATED   13  2
  DEL PEAK 15(9Q22.33) WILD-TYPE 37  9
  DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE 
                            15                             46 
  DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE 
                             2                              9 
$`DEL PEAK 15(9Q22.33) MUTATED`
TCGA-F2-A44G TCGA-F2-A44H TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7922 
         153          586          392          396           28            4 
TCGA-HZ-A49G TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-IB-7649 TCGA-LB-A7SX 
          23          194           46           11         1951          127 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-YY-A8LH 
          35          584         1834 

$`DEL PEAK 15(9Q22.33) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T 
         295          360            4          385          449            1 
TCGA-FB-A7DR TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 
         166          233          240           20            8          369 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 
         361            8           19           24           21           28 
TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H TCGA-HZ-A77P 
          16            3            5           91           29           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 
          33          347         1989          476          851         1975 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS 
         488           17          522          329          300         1991 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-OE-A75W TCGA-PZ-A5RE 
           8         1968          181          164          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
         416         1955          844          160 

  DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE 
                             4                              1 
  DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE 
                          1951                           1991 
  DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE 
                           153                            207 
[1] "4.0 - 1951.0 (153.0)" "1.0 - 1991.0 (207.0)"
[1] "hr=" "1.7"
D33V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 15(9Q22.33) MUTATED          0        0         6        16
  DEL PEAK 15(9Q22.33) WILD-TYPE        2        4         8        45
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 15(9Q22.33) MUTATED           0        0
  DEL PEAK 15(9Q22.33) WILD-TYPE         2        3
D33V3, multiclass
           clus
vv          DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            6                              8
  STAGE IIB                           16                             45
  STAGE III                            0                              2
  STAGE IV                             0                              3
[1] 6 2
[1] 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(9Q22.33) MUTATED       2    20
  DEL PEAK 15(9Q22.33) WILD-TYPE     6    58
D33V4, multiclass
       clus
vv      DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE
  T1+T2                            2                              6
  T3+T4                           20                             58
[1] 2 2
[1] FALSE
D33V5, binary
                                cls
clus                              0  1
  DEL PEAK 15(9Q22.33) MUTATED    6 16
  DEL PEAK 15(9Q22.33) WILD-TYPE 15 48
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(9Q22.33) MUTATED      6   16
  DEL PEAK 15(9Q22.33) WILD-TYPE   15   48
   clus
vv  DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE
  0                            6                             15
  1                           16                             48
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 15(9Q22.33) MUTATED    9  0 13
  DEL PEAK 15(9Q22.33) WILD-TYPE 32  3 29
D33V6, multiclass
    clus
vv   DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE
  M0                            9                             32
  M1                            0                              3
  MX                           13                             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"
D33V7, binary
                                cls
clus                              0  1
  DEL PEAK 15(9Q22.33) MUTATED   13  9
  DEL PEAK 15(9Q22.33) WILD-TYPE 31 33
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(9Q22.33) MUTATED     13    9
  DEL PEAK 15(9Q22.33) WILD-TYPE   31   33
        clus
vv       DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE
  FEMALE                           13                             31
  MALE                              9                             33
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 15(9Q22.33) MUTATED                                    20
  DEL PEAK 15(9Q22.33) WILD-TYPE                                  54
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 15(9Q22.33) MUTATED                                       2
  DEL PEAK 15(9Q22.33) WILD-TYPE                                     6
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 15(9Q22.33) MUTATED                                                  0
  DEL PEAK 15(9Q22.33) WILD-TYPE                                                3
D33V8, multiclass
                                                  clus
vv                                                 DEL PEAK 15(9Q22.33) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        20
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            0
                                                  clus
vv                                                 DEL PEAK 15(9Q22.33) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          54
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D33V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 15(9Q22.33) MUTATED   14  8  0  0
  DEL PEAK 15(9Q22.33) WILD-TYPE 41 17  1  2
D33V10, multiclass
    clus
vv   DEL PEAK 15(9Q22.33) MUTATED DEL PEAK 15(9Q22.33) WILD-TYPE
  R0                           14                             41
  R1                            8                             17
  R2                            0                              1
  RX                            0                              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
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(9Q22.33) MUTATED       0                         2    17
  DEL PEAK 15(9Q22.33) WILD-TYPE     2                         4    57
D33V12, multiclass
                           clus
vv                          DEL PEAK 15(9Q22.33) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               17
                           clus
vv                          DEL PEAK 15(9Q22.33) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 57
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(34) Variable = DEL PEAK 16(10Q23.2) MUTATION ANALYSIS
D34V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 16(10Q23.2) MUTATED    8  0
  DEL PEAK 16(10Q23.2) WILD-TYPE 42 11
  DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE 
                             8                             53 
  DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE 
                             0                             11 
$`DEL PEAK 16(10Q23.2) MUTATED`
TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-A77O TCGA-HZ-A77Q 
         385          392          240           28           11           33 
TCGA-IB-7885 TCGA-US-A776 
         851          844 

$`DEL PEAK 16(10Q23.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7922 
           1          166          233          396           20            4 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 
          21           28           16            3            5           91 
TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-IB-7644 
          23           29          194           46           13          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1951         1989          476         1975          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG 
         522          329          300         1991            8         1968 
TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W 
         181          164          127           35          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         247          416         1955          160         1834 

  DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE 
                            11                              1 
  DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE 
                           851                           1991 
  DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE 
                         312.5                          166.0 
[1] "11.0 - 851.0 (312.5)" "1.0 - 1991.0 (166.0)"
[1] "hr="     "8.7e+07"
D34V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 16(10Q23.2) MUTATED          0        1         2        10
  DEL PEAK 16(10Q23.2) WILD-TYPE        2        3        12        51
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 16(10Q23.2) MUTATED           0        0
  DEL PEAK 16(10Q23.2) WILD-TYPE         2        3
D34V3, multiclass
           clus
vv          DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             1                              3
  STAGE IIA                            2                             12
  STAGE IIB                           10                             51
  STAGE III                            0                              2
  STAGE IV                             0                              3
[1] 6 2
[1] 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(10Q23.2) MUTATED       2    11
  DEL PEAK 16(10Q23.2) WILD-TYPE     6    67
D34V4, multiclass
       clus
vv      DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE
  T1+T2                            2                              6
  T3+T4                           11                             67
[1] 2 2
[1] FALSE
D34V5, binary
                                cls
clus                              0  1
  DEL PEAK 16(10Q23.2) MUTATED    3 10
  DEL PEAK 16(10Q23.2) WILD-TYPE 18 54
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10Q23.2) MUTATED      3   10
  DEL PEAK 16(10Q23.2) WILD-TYPE   18   54
   clus
vv  DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE
  0                            3                             18
  1                           10                             54
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 16(10Q23.2) MUTATED    8  0  5
  DEL PEAK 16(10Q23.2) WILD-TYPE 33  3 37
D34V6, multiclass
    clus
vv   DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE
  M0                            8                             33
  M1                            0                              3
  MX                            5                             37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D34V7, binary
                                cls
clus                              0  1
  DEL PEAK 16(10Q23.2) MUTATED    6  7
  DEL PEAK 16(10Q23.2) WILD-TYPE 38 35
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(10Q23.2) MUTATED      6    7
  DEL PEAK 16(10Q23.2) WILD-TYPE   38   35
        clus
vv       DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE
  FEMALE                            6                             38
  MALE                              7                             35
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 16(10Q23.2) MUTATED                                    10
  DEL PEAK 16(10Q23.2) WILD-TYPE                                  64
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 16(10Q23.2) MUTATED                                       2
  DEL PEAK 16(10Q23.2) WILD-TYPE                                     6
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 16(10Q23.2) MUTATED                                                  1
  DEL PEAK 16(10Q23.2) WILD-TYPE                                                2
D34V8, multiclass
                                                  clus
vv                                                 DEL PEAK 16(10Q23.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            1
                                                  clus
vv                                                 DEL PEAK 16(10Q23.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          64
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D34V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 16(10Q23.2) MUTATED    8  3  0  1
  DEL PEAK 16(10Q23.2) WILD-TYPE 47 22  1  1
D34V10, multiclass
    clus
vv   DEL PEAK 16(10Q23.2) MUTATED DEL PEAK 16(10Q23.2) WILD-TYPE
  R0                            8                             47
  R1                            3                             22
  R2                            0                              1
  RX                            1                              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"
D34V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(10Q23.2) MUTATED       0                         0    12
  DEL PEAK 16(10Q23.2) WILD-TYPE     2                         6    62
D34V12, multiclass
                           clus
vv                          DEL PEAK 16(10Q23.2) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                               12
                           clus
vv                          DEL PEAK 16(10Q23.2) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 62
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(35) Variable = DEL PEAK 17(11P15.4) MUTATION ANALYSIS
D35V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 17(11P15.4) MUTATED    9  1
  DEL PEAK 17(11P15.4) WILD-TYPE 41 10
  DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE 
                            10                             51 
  DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE 
                             1                             10 
$`DEL PEAK 17(11P15.4) MUTATED`
TCGA-F2-A44H TCGA-FB-A545 TCGA-HZ-7918 TCGA-HZ-A4BH TCGA-IB-7652 TCGA-IB-7885 
         586          385           28          194          476          851 
TCGA-IB-7886 TCGA-IB-8127 TCGA-LB-A7SX TCGA-M8-A5N4 
        1975          522          127          584 

$`DEL PEAK 17(11P15.4) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A5VM TCGA-FB-A78T 
         295          360          153            4          449            1 
TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7919 
         166          392          233          396          240           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
           4            8          369          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          24           21           28           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
          91           23           29           46           11           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-8126 
          33          347         1951         1989          488           17 
TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 
         329          300         1991            8         1968          181 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
         164           35          110          247          416         1955 
TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         844          160         1834 

  DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE 
                            28                              1 
  DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE 
                          1975                           1991 
  DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE 
                           499                            160 
[1] "28.0 - 1975.0 (499.0)" "1.0 - 1991.0 (160.0)" 
[1] "hr=" "2.6"
D35V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 17(11P15.4) MUTATED          0        0         2        13
  DEL PEAK 17(11P15.4) WILD-TYPE        2        4        12        48
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 17(11P15.4) MUTATED           0        0
  DEL PEAK 17(11P15.4) WILD-TYPE         2        3
D35V3, multiclass
           clus
vv          DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            2                             12
  STAGE IIB                           13                             48
  STAGE III                            0                              2
  STAGE IV                             0                              3
[1] 6 2
[1] 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(11P15.4) MUTATED       0    15
  DEL PEAK 17(11P15.4) WILD-TYPE     8    63
D35V4, multiclass
       clus
vv      DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE
  T1+T2                            0                              8
  T3+T4                           15                             63
[1] 2 2
[1] FALSE
D35V5, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.4) MUTATED    2 13
  DEL PEAK 17(11P15.4) WILD-TYPE 19 51
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.4) MUTATED      2   13
  DEL PEAK 17(11P15.4) WILD-TYPE   19   51
   clus
vv  DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE
  0                            2                             19
  1                           13                             51
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 17(11P15.4) MUTATED   12  0  3
  DEL PEAK 17(11P15.4) WILD-TYPE 29  3 39
D35V6, multiclass
    clus
vv   DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE
  M0                           12                             29
  M1                            0                              3
  MX                            3                             39
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V7, binary
                                cls
clus                              0  1
  DEL PEAK 17(11P15.4) MUTATED    9  6
  DEL PEAK 17(11P15.4) WILD-TYPE 35 36
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(11P15.4) MUTATED      9    6
  DEL PEAK 17(11P15.4) WILD-TYPE   35   36
        clus
vv       DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE
  FEMALE                            9                             35
  MALE                              6                             36
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 17(11P15.4) MUTATED                                    15
  DEL PEAK 17(11P15.4) WILD-TYPE                                  59
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 17(11P15.4) MUTATED                                       0
  DEL PEAK 17(11P15.4) WILD-TYPE                                     8
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 17(11P15.4) MUTATED                                                  0
  DEL PEAK 17(11P15.4) WILD-TYPE                                                3
D35V8, multiclass
                                                  clus
vv                                                 DEL PEAK 17(11P15.4) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        15
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            0
                                                  clus
vv                                                 DEL PEAK 17(11P15.4) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          59
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D35V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 17(11P15.4) MUTATED    7  7  0  0
  DEL PEAK 17(11P15.4) WILD-TYPE 48 18  1  2
D35V10, multiclass
    clus
vv   DEL PEAK 17(11P15.4) MUTATED DEL PEAK 17(11P15.4) WILD-TYPE
  R0                            7                             48
  R1                            7                             18
  R2                            0                              1
  RX                            0                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D35V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(11P15.4) MUTATED       1                         2    10
  DEL PEAK 17(11P15.4) WILD-TYPE     1                         4    64
D35V12, multiclass
                           clus
vv                          DEL PEAK 17(11P15.4) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               10
                           clus
vv                          DEL PEAK 17(11P15.4) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 64
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(36) Variable = DEL PEAK 18(12P12.3) MUTATION ANALYSIS
D36V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 18(12P12.3) MUTATED    6  1
  DEL PEAK 18(12P12.3) WILD-TYPE 44 10
  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE 
                             7                             54 
  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE 
                             1                             10 
$`DEL PEAK 18(12P12.3) MUTATED`
TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-IB-7886 TCGA-IB-A5SP 
         240           20            5          194         1975          300 
TCGA-LB-A7SX 
         127 

$`DEL PEAK 18(12P12.3) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 
         449            1          166          392          233          396 
TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P 
          91           23           29           46           11           13 
TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          33          347         1951         1989          476          851 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST 
         488           17          522          329         1991            8 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W 
        1968          181          164           35          584          110 
TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         247          416         1955          844          160         1834 

  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE 
                             5                              1 
  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE 
                          1975                           1991 
  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE 
                         194.0                          173.5 
[1] "5.0 - 1975.0 (194.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1.5"
D36V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 18(12P12.3) MUTATED          0        0         2         8
  DEL PEAK 18(12P12.3) WILD-TYPE        2        4        12        53
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 18(12P12.3) MUTATED           0        1
  DEL PEAK 18(12P12.3) WILD-TYPE         2        2
D36V3, multiclass
           clus
vv          DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            2                             12
  STAGE IIB                            8                             53
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(12P12.3) MUTATED       0    11
  DEL PEAK 18(12P12.3) WILD-TYPE     8    67
D36V4, multiclass
       clus
vv      DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE
  T1+T2                            0                              8
  T3+T4                           11                             67
[1] 2 2
[1] FALSE
D36V5, binary
                                cls
clus                              0  1
  DEL PEAK 18(12P12.3) MUTATED    3  8
  DEL PEAK 18(12P12.3) WILD-TYPE 18 56
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(12P12.3) MUTATED      3    8
  DEL PEAK 18(12P12.3) WILD-TYPE   18   56
   clus
vv  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE
  0                            3                             18
  1                            8                             56
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 18(12P12.3) MUTATED    6  1  4
  DEL PEAK 18(12P12.3) WILD-TYPE 35  2 38
D36V6, multiclass
    clus
vv   DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE
  M0                            6                             35
  M1                            1                              2
  MX                            4                             38
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D36V7, binary
                                cls
clus                              0  1
  DEL PEAK 18(12P12.3) MUTATED    3  8
  DEL PEAK 18(12P12.3) WILD-TYPE 41 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(12P12.3) MUTATED      3    8
  DEL PEAK 18(12P12.3) WILD-TYPE   41   34
        clus
vv       DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE
  FEMALE                            3                             41
  MALE                              8                             34
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 18(12P12.3) MUTATED                                     9
  DEL PEAK 18(12P12.3) WILD-TYPE                                  65
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 18(12P12.3) MUTATED                                       1
  DEL PEAK 18(12P12.3) WILD-TYPE                                     7
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 18(12P12.3) MUTATED                                                  0
  DEL PEAK 18(12P12.3) WILD-TYPE                                                3
D36V8, multiclass
                                                  clus
vv                                                 DEL PEAK 18(12P12.3) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         9
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            0
                                                  clus
vv                                                 DEL PEAK 18(12P12.3) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          65
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D36V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 18(12P12.3) MUTATED"
clus
  DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE 
                             2                             24 
                    TCGA-F2-6880                     TCGA-FB-A4P5 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-FB-A5VM                     TCGA-FB-A78T 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-FB-A7DR                     TCGA-H6-8124 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-H6-A45N                     TCGA-H8-A6C1 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-HZ-A77Q                     TCGA-IB-7644 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-IB-7649                     TCGA-IB-7651 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-IB-7885                     TCGA-IB-7887 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-IB-7891                     TCGA-IB-8126 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-IB-8127                     TCGA-IB-A5SS 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-IB-A6UG                     TCGA-IB-A7M4 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-OE-A75W                     TCGA-S4-A8RP 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                    TCGA-US-A774                     TCGA-YY-A8LH 
"DEL PEAK 18(12P12.3) WILD-TYPE" "DEL PEAK 18(12P12.3) WILD-TYPE" 
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 18(12P12.3) MUTATED    3  7  0  1
  DEL PEAK 18(12P12.3) WILD-TYPE 52 18  1  1
D36V10, multiclass
    clus
vv   DEL PEAK 18(12P12.3) MUTATED DEL PEAK 18(12P12.3) WILD-TYPE
  R0                            3                             52
  R1                            7                             18
  R2                            0                              1
  RX                            1                              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"
D36V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(12P12.3) MUTATED       0                         2     9
  DEL PEAK 18(12P12.3) WILD-TYPE     2                         4    65
D36V12, multiclass
                           clus
vv                          DEL PEAK 18(12P12.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                                9
                           clus
vv                          DEL PEAK 18(12P12.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 65
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(37) Variable = DEL PEAK 19(12Q12) MUTATION ANALYSIS
D37V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 19(12Q12) MUTATED    4  1
  DEL PEAK 19(12Q12) WILD-TYPE 46 10
  DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE 
                           5                           56 
  DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE 
                           1                           10 
$`DEL PEAK 19(12Q12) MUTATED`
TCGA-FB-A545 TCGA-H6-8124 TCGA-HZ-8636 TCGA-IB-7886 TCGA-LB-A7SX 
         385          392            5         1975          127 

$`DEL PEAK 19(12Q12) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 
           1          166          233          396          240           28 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          20            4            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
         851          488           17          522          329          300 
TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A8F3 
        1991            8         1968          181          164           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          110          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE 
                           5                            1 
  DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE 
                        1975                         1991 
  DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE 
                       385.0                        173.5 
[1] "5.0 - 1975.0 (385.0)" "1.0 - 1991.0 (173.5)"
[1] "hr=" "1.6"
D37V2, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK 19(12Q12) MUTATED          0        1         1         5         0
  DEL PEAK 19(12Q12) WILD-TYPE        2        3        13        56         2
                              vv
clus                           STAGE IV
  DEL PEAK 19(12Q12) MUTATED          1
  DEL PEAK 19(12Q12) WILD-TYPE        2
D37V3, multiclass
           clus
vv          DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE
  STAGE IA                           0                            2
  STAGE IB                           1                            3
  STAGE IIA                          1                           13
  STAGE IIB                          5                           56
  STAGE III                          0                            2
  STAGE IV                           1                            2
[1] 6 2
[1] 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(12Q12) MUTATED       1     7
  DEL PEAK 19(12Q12) WILD-TYPE     7    71
D37V4, multiclass
       clus
vv      DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE
  T1+T2                          1                            7
  T3+T4                          7                           71
[1] 2 2
[1] FALSE
D37V5, binary
                              cls
clus                            0  1
  DEL PEAK 19(12Q12) MUTATED    3  5
  DEL PEAK 19(12Q12) WILD-TYPE 18 59
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(12Q12) MUTATED      3    5
  DEL PEAK 19(12Q12) WILD-TYPE   18   59
   clus
vv  DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE
  0                          3                           18
  1                          5                           59
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  DEL PEAK 19(12Q12) MUTATED    6  1  1
  DEL PEAK 19(12Q12) WILD-TYPE 35  2 41
D37V6, multiclass
    clus
vv   DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE
  M0                          6                           35
  M1                          1                            2
  MX                          1                           41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V7, binary
                              cls
clus                            0  1
  DEL PEAK 19(12Q12) MUTATED    5  3
  DEL PEAK 19(12Q12) WILD-TYPE 39 39
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 19(12Q12) MUTATED      5    3
  DEL PEAK 19(12Q12) WILD-TYPE   39   39
        clus
vv       DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE
  FEMALE                          5                           39
  MALE                            3                           39
[1] 2 2
[1] FALSE
                              vv
clus                           PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 19(12Q12) MUTATED                                     8
  DEL PEAK 19(12Q12) WILD-TYPE                                  66
                              vv
clus                           PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 19(12Q12) MUTATED                                       0
  DEL PEAK 19(12Q12) WILD-TYPE                                     8
                              vv
clus                           PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 19(12Q12) MUTATED                                                  0
  DEL PEAK 19(12Q12) WILD-TYPE                                                3
D37V8, multiclass
                                                  clus
vv                                                 DEL PEAK 19(12Q12) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                       8
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                     0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                          0
                                                  clus
vv                                                 DEL PEAK 19(12Q12) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        66
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            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"
D37V9, continuous
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 19(12Q12) MUTATED    3  4  0  0
  DEL PEAK 19(12Q12) WILD-TYPE 52 21  1  2
D37V10, multiclass
    clus
vv   DEL PEAK 19(12Q12) MUTATED DEL PEAK 19(12Q12) WILD-TYPE
  R0                          3                           52
  R1                          4                           21
  R2                          0                            1
  RX                          0                            2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D37V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(12Q12) MUTATED       0                         1     6
  DEL PEAK 19(12Q12) WILD-TYPE     2                         5    68
D37V12, multiclass
                           clus
vv                          DEL PEAK 19(12Q12) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          1
  WHITE                                              6
                           clus
vv                          DEL PEAK 19(12Q12) WILD-TYPE
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            5
  WHITE                                               68
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(38) Variable = DEL PEAK 20(12Q24.33) MUTATION ANALYSIS
D38V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 20(12Q24.33) MUTATED   12  2
  DEL PEAK 20(12Q24.33) WILD-TYPE 38  9
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                             14                              47 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                              2                               9 
$`DEL PEAK 20(12Q24.33) MUTATED`
TCGA-FB-A7DR TCGA-H6-8124 TCGA-HZ-7289 TCGA-HZ-7922 TCGA-HZ-7926 TCGA-HZ-A77O 
         166          392          240            4            8           11 
TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SS TCGA-IB-A7M4 
         476          851         1975          522         1991          181 
TCGA-LB-A7SX TCGA-LB-A8F3 
         127           35 

$`DEL PEAK 20(12Q24.33) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 
         449            1          233          396           28           20 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
           8          369          361           19           24           21 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
          28           16            3            5           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
          29          194           46           13           33          347 
TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SP 
        1951         1989          488           17          329          300 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE 
           8         1968          164          584          110          247 
TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
         416         1955          844          160         1834 

  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                              4                               1 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                           1991                            1989 
  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE 
                          210.5                           164.0 
[1] "4.0 - 1991.0 (210.5)" "1.0 - 1989.0 (164.0)"
[1] "hr=" "5.9"
D38V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 20(12Q24.33) MUTATED          0        1         3        16
  DEL PEAK 20(12Q24.33) WILD-TYPE        2        3        11        45
                                 vv
clus                              STAGE III STAGE IV
  DEL PEAK 20(12Q24.33) MUTATED           0        0
  DEL PEAK 20(12Q24.33) WILD-TYPE         2        3
D38V3, multiclass
           clus
vv          DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  STAGE IA                              0                               2
  STAGE IB                              1                               3
  STAGE IIA                             3                              11
  STAGE IIB                            16                              45
  STAGE III                             0                               2
  STAGE IV                              0                               3
[1] 6 2
[1] 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(12Q24.33) MUTATED       2    18
  DEL PEAK 20(12Q24.33) WILD-TYPE     6    60
D38V4, multiclass
       clus
vv      DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  T1+T2                             2                               6
  T3+T4                            18                              60
[1] 2 2
[1] FALSE
D38V5, binary
                                 cls
clus                               0  1
  DEL PEAK 20(12Q24.33) MUTATED    3 16
  DEL PEAK 20(12Q24.33) WILD-TYPE 18 48
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED      3   16
  DEL PEAK 20(12Q24.33) WILD-TYPE   18   48
   clus
vv  DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  0                             3                              18
  1                            16                              48
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 20(12Q24.33) MUTATED   11  0  9
  DEL PEAK 20(12Q24.33) WILD-TYPE 30  3 33
D38V6, multiclass
    clus
vv   DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  M0                            11                              30
  M1                             0                               3
  MX                             9                              33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D38V7, binary
                                 cls
clus                               0  1
  DEL PEAK 20(12Q24.33) MUTATED    9 11
  DEL PEAK 20(12Q24.33) WILD-TYPE 35 31
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 20(12Q24.33) MUTATED      9   11
  DEL PEAK 20(12Q24.33) WILD-TYPE   35   31
        clus
vv       DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  FEMALE                             9                              35
  MALE                              11                              31
[1] 2 2
[1] FALSE
                                 vv
clus                              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 20(12Q24.33) MUTATED                                    18
  DEL PEAK 20(12Q24.33) WILD-TYPE                                  56
                                 vv
clus                              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 20(12Q24.33) MUTATED                                       1
  DEL PEAK 20(12Q24.33) WILD-TYPE                                     7
                                 vv
clus                              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 20(12Q24.33) MUTATED                                                  1
  DEL PEAK 20(12Q24.33) WILD-TYPE                                                2
D38V8, multiclass
                                                  clus
vv                                                 DEL PEAK 20(12Q24.33) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         18
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             1
                                                  clus
vv                                                 DEL PEAK 20(12Q24.33) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                           56
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                          7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                               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"
D38V9, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 20(12Q24.33) MUTATED   12  6  0  2
  DEL PEAK 20(12Q24.33) WILD-TYPE 43 19  1  0
D38V10, multiclass
    clus
vv   DEL PEAK 20(12Q24.33) MUTATED DEL PEAK 20(12Q24.33) WILD-TYPE
  R0                            12                              43
  R1                             6                              19
  R2                             0                               1
  RX                             2                               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"
D38V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(12Q24.33) MUTATED       2                         4    13
  DEL PEAK 20(12Q24.33) WILD-TYPE     0                         2    61
D38V12, multiclass
                           clus
vv                          DEL PEAK 20(12Q24.33) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                13
                           clus
vv                          DEL PEAK 20(12Q24.33) WILD-TYPE
  ASIAN                                                   0
  BLACK OR AFRICAN AMERICAN                               2
  WHITE                                                  61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(39) Variable = DEL PEAK 21(15Q15.1) MUTATION ANALYSIS
D39V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 21(15Q15.1) MUTATED   12  1
  DEL PEAK 21(15Q15.1) WILD-TYPE 38 10
  DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE 
                            13                             48 
  DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE 
                             1                             10 
$`DEL PEAK 21(15Q15.1) MUTATED`
TCGA-FB-A545 TCGA-FB-A7DR TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 TCGA-HZ-A4BK 
         385          166          240           28            4           46 
TCGA-IB-7644 TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A7M4 TCGA-LB-A7SX TCGA-M8-A5N4 
         347          522          300          181          127          584 
TCGA-US-A776 
         844 

$`DEL PEAK 21(15Q15.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 TCGA-HZ-7923 
           1          392          233          396           20            8 
TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 
         369          361            8           19           24           21 
TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G 
          28           16            3            5           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7649 
          29          194           11           13           33         1951 
TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1989          476          851         1975          488           17 
TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A8F3 
         329         1991            8         1968          164           35 
TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-YB-A89D TCGA-YY-A8LH 
         110          247          416         1955          160         1834 

  DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE 
                             4                              1 
  DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE 
                           844                           1991 
  DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE 
                           240                            162 
[1] "4.0 - 844.0 (240.0)"  "1.0 - 1991.0 (162.0)"
[1] "hr=" "1.2"
D39V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 21(15Q15.1) MUTATED          0        1         5        10
  DEL PEAK 21(15Q15.1) WILD-TYPE        2        3         9        51
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 21(15Q15.1) MUTATED           0        1
  DEL PEAK 21(15Q15.1) WILD-TYPE         2        2
D39V3, multiclass
           clus
vv          DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             1                              3
  STAGE IIA                            5                              9
  STAGE IIB                           10                             51
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(15Q15.1) MUTATED       1    16
  DEL PEAK 21(15Q15.1) WILD-TYPE     7    62
D39V4, multiclass
       clus
vv      DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE
  T1+T2                            1                              7
  T3+T4                           16                             62
[1] 2 2
[1] FALSE
D39V5, binary
                                cls
clus                              0  1
  DEL PEAK 21(15Q15.1) MUTATED    5 11
  DEL PEAK 21(15Q15.1) WILD-TYPE 16 53
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(15Q15.1) MUTATED      5   11
  DEL PEAK 21(15Q15.1) WILD-TYPE   16   53
   clus
vv  DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE
  0                            5                             16
  1                           11                             53
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 21(15Q15.1) MUTATED    8  1  8
  DEL PEAK 21(15Q15.1) WILD-TYPE 33  2 34
D39V6, multiclass
    clus
vv   DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE
  M0                            8                             33
  M1                            1                              2
  MX                            8                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V7, binary
                                cls
clus                              0  1
  DEL PEAK 21(15Q15.1) MUTATED    5 12
  DEL PEAK 21(15Q15.1) WILD-TYPE 39 30
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 21(15Q15.1) MUTATED      5   12
  DEL PEAK 21(15Q15.1) WILD-TYPE   39   30
        clus
vv       DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE
  FEMALE                            5                             39
  MALE                             12                             30
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 21(15Q15.1) MUTATED                                    13
  DEL PEAK 21(15Q15.1) WILD-TYPE                                  61
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 21(15Q15.1) MUTATED                                       2
  DEL PEAK 21(15Q15.1) WILD-TYPE                                     6
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 21(15Q15.1) MUTATED                                                  2
  DEL PEAK 21(15Q15.1) WILD-TYPE                                                1
D39V8, multiclass
                                                  clus
vv                                                 DEL PEAK 21(15Q15.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        13
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            2
                                                  clus
vv                                                 DEL PEAK 21(15Q15.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          61
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 21(15Q15.1) MUTATED    8  7  0  1
  DEL PEAK 21(15Q15.1) WILD-TYPE 47 18  1  1
D39V10, multiclass
    clus
vv   DEL PEAK 21(15Q15.1) MUTATED DEL PEAK 21(15Q15.1) WILD-TYPE
  R0                            8                             47
  R1                            7                             18
  R2                            0                              1
  RX                            1                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D39V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(15Q15.1) MUTATED       1                         1    13
  DEL PEAK 21(15Q15.1) WILD-TYPE     1                         5    61
D39V12, multiclass
                           clus
vv                          DEL PEAK 21(15Q15.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               13
                           clus
vv                          DEL PEAK 21(15Q15.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 61
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(40) Variable = DEL PEAK 22(16Q23.1) MUTATION ANALYSIS
D40V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 22(16Q23.1) MUTATED    3  0
  DEL PEAK 22(16Q23.1) WILD-TYPE 47 11
  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE 
                             3                             58 
  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE 
                             0                             11 
$`DEL PEAK 22(16Q23.1) MUTATED`
TCGA-FB-A7DR TCGA-HZ-7289 TCGA-HZ-7918 
         166          240           28 

$`DEL PEAK 22(16Q23.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7919 
         449            1          392          233          396           20 
TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 
           4            8          369          361            8           19 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 
          24           21           28           16            3            5 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O 
          91           23           29          194           46           11 
TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 
          13           33          347         1951         1989          476 
TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO 
         851         1975          488           17          522          329 
TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 
         300         1991            8         1968          181          164 
TCGA-LB-A7SX TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY 
         127           35          584          110          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D TCGA-YY-A8LH 
        1955          844          160         1834 

  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE 
                            28                              1 
  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE 
                           240                           1991 
  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE 
                         166.0                          187.5 
[1] "28.0 - 240.0 (166.0)" "1.0 - 1991.0 (187.5)"
[1] "hr="     "2.6e+07"
D40V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 22(16Q23.1) MUTATED          0        0         1         2
  DEL PEAK 22(16Q23.1) WILD-TYPE        2        4        13        59
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 22(16Q23.1) MUTATED           0        1
  DEL PEAK 22(16Q23.1) WILD-TYPE         2        2
D40V3, multiclass
           clus
vv          DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            1                             13
  STAGE IIB                            2                             59
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(16Q23.1) MUTATED       0     4
  DEL PEAK 22(16Q23.1) WILD-TYPE     8    74
D40V4, multiclass
       clus
vv      DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE
  T1+T2                            0                              8
  T3+T4                            4                             74
[1] 2 2
[1] FALSE
D40V5, binary
                                cls
clus                              0  1
  DEL PEAK 22(16Q23.1) MUTATED    0  3
  DEL PEAK 22(16Q23.1) WILD-TYPE 21 61
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(16Q23.1) MUTATED      0    3
  DEL PEAK 22(16Q23.1) WILD-TYPE   21   61
   clus
vv  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE
  0                            0                             21
  1                            3                             61
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 22(16Q23.1) MUTATED    2  1  1
  DEL PEAK 22(16Q23.1) WILD-TYPE 39  2 41
D40V6, multiclass
    clus
vv   DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE
  M0                            2                             39
  M1                            1                              2
  MX                            1                             41
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V7, binary
                                cls
clus                              0  1
  DEL PEAK 22(16Q23.1) MUTATED    0  4
  DEL PEAK 22(16Q23.1) WILD-TYPE 44 38
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(16Q23.1) MUTATED      0    4
  DEL PEAK 22(16Q23.1) WILD-TYPE   44   38
        clus
vv       DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE
  FEMALE                            0                             44
  MALE                              4                             38
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 22(16Q23.1) MUTATED                                     2
  DEL PEAK 22(16Q23.1) WILD-TYPE                                  72
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 22(16Q23.1) MUTATED                                       1
  DEL PEAK 22(16Q23.1) WILD-TYPE                                     7
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 22(16Q23.1) MUTATED                                                  1
  DEL PEAK 22(16Q23.1) WILD-TYPE                                                2
D40V8, multiclass
                                                  clus
vv                                                 DEL PEAK 22(16Q23.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         2
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            1
                                                  clus
vv                                                 DEL PEAK 22(16Q23.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          72
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D40V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 22(16Q23.1) MUTATED"
clus
  DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE 
                             1                             25 
                    TCGA-F2-6880                     TCGA-FB-A4P5 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-FB-A5VM                     TCGA-FB-A78T 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-H6-8124                     TCGA-H6-A45N 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-H8-A6C1                     TCGA-HZ-A77Q 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-IB-7644                     TCGA-IB-7649 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-IB-7651                     TCGA-IB-7885 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-IB-7886                     TCGA-IB-7887 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-IB-7891                     TCGA-IB-8126 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-IB-8127                     TCGA-IB-A5SS 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-IB-A6UG                     TCGA-IB-A7M4 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-LB-A7SX                     TCGA-OE-A75W 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-S4-A8RP                     TCGA-US-A774 
"DEL PEAK 22(16Q23.1) WILD-TYPE" "DEL PEAK 22(16Q23.1) WILD-TYPE" 
                    TCGA-YY-A8LH 
"DEL PEAK 22(16Q23.1) WILD-TYPE" 
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 22(16Q23.1) MUTATED    3  0  0  1
  DEL PEAK 22(16Q23.1) WILD-TYPE 52 25  1  1
D40V10, multiclass
    clus
vv   DEL PEAK 22(16Q23.1) MUTATED DEL PEAK 22(16Q23.1) WILD-TYPE
  R0                            3                             52
  R1                            0                             25
  R2                            0                              1
  RX                            1                              1
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D40V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(16Q23.1) MUTATED       1                         0     3
  DEL PEAK 22(16Q23.1) WILD-TYPE     1                         6    71
D40V12, multiclass
                           clus
vv                          DEL PEAK 22(16Q23.1) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            0
  WHITE                                                3
                           clus
vv                          DEL PEAK 22(16Q23.1) WILD-TYPE
  ASIAN                                                  1
  BLACK OR AFRICAN AMERICAN                              6
  WHITE                                                 71
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(41) Variable = DEL PEAK 23(17Q22) MUTATION ANALYSIS
D41V1, survival
                              sevent
clus2                           0  1
  DEL PEAK 23(17Q22) MUTATED   14  2
  DEL PEAK 23(17Q22) WILD-TYPE 36  9
  DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE 
                          16                           45 
  DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE 
                           2                            9 
$`DEL PEAK 23(17Q22) MUTATED`
TCGA-FB-A545 TCGA-HZ-7289 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH 
         385          240           20            4            5          194 
TCGA-HZ-A77O TCGA-IB-7644 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-8127 TCGA-IB-A5SP 
          11          347          476         1975          522          300 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-OE-A75W TCGA-YY-A8LH 
         164          127          110         1834 

$`DEL PEAK 23(17Q22) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7918 
           1          166          392          233          396           28 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
          21           28           16            3           91           23 
TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7649 TCGA-IB-7651 
          29           46           13           33         1951         1989 
TCGA-IB-7885 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST 
         851          488           17          329         1991            8 
TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-PZ-A5RE TCGA-Q3-A5QY 
        1968          181           35          584          247          416 
TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
        1955          844          160 

  DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE 
                           4                            1 
  DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE 
                        1975                         1991 
  DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE 
                         217                          166 
[1] "4.0 - 1975.0 (217.0)" "1.0 - 1991.0 (166.0)"
[1] "hr=" "1.2"
D41V2, continuous
                              vv
clus                           STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE III
  DEL PEAK 23(17Q22) MUTATED          0        0         3        19         0
  DEL PEAK 23(17Q22) WILD-TYPE        2        4        11        42         2
                              vv
clus                           STAGE IV
  DEL PEAK 23(17Q22) MUTATED          2
  DEL PEAK 23(17Q22) WILD-TYPE        1
D41V3, multiclass
           clus
vv          DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE
  STAGE IA                           0                            2
  STAGE IB                           0                            4
  STAGE IIA                          3                           11
  STAGE IIB                         19                           42
  STAGE III                          0                            2
  STAGE IV                           2                            1
[1] 6 2
[1] 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(17Q22) MUTATED       1    23
  DEL PEAK 23(17Q22) WILD-TYPE     7    55
D41V4, multiclass
       clus
vv      DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE
  T1+T2                          1                            7
  T3+T4                         23                           55
[1] 2 2
[1] FALSE
D41V5, binary
                              cls
clus                            0  1
  DEL PEAK 23(17Q22) MUTATED    4 20
  DEL PEAK 23(17Q22) WILD-TYPE 17 44
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(17Q22) MUTATED      4   20
  DEL PEAK 23(17Q22) WILD-TYPE   17   44
   clus
vv  DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE
  0                          4                           17
  1                         20                           44
[1] 2 2
[1] FALSE
                              vv
clus                           M0 M1 MX
  DEL PEAK 23(17Q22) MUTATED   13  2  9
  DEL PEAK 23(17Q22) WILD-TYPE 28  1 33
D41V6, multiclass
    clus
vv   DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE
  M0                         13                           28
  M1                          2                            1
  MX                          9                           33
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D41V7, binary
                              cls
clus                            0  1
  DEL PEAK 23(17Q22) MUTATED   13 11
  DEL PEAK 23(17Q22) WILD-TYPE 31 31
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  DEL PEAK 23(17Q22) MUTATED     13   11
  DEL PEAK 23(17Q22) WILD-TYPE   31   31
        clus
vv       DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE
  FEMALE                         13                           31
  MALE                           11                           31
[1] 2 2
[1] FALSE
                              vv
clus                           PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 23(17Q22) MUTATED                                    22
  DEL PEAK 23(17Q22) WILD-TYPE                                  52
                              vv
clus                           PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 23(17Q22) MUTATED                                       1
  DEL PEAK 23(17Q22) WILD-TYPE                                     7
                              vv
clus                           PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 23(17Q22) MUTATED                                                  0
  DEL PEAK 23(17Q22) WILD-TYPE                                                3
D41V8, multiclass
                                                  clus
vv                                                 DEL PEAK 23(17Q22) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                      22
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                     1
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                          0
                                                  clus
vv                                                 DEL PEAK 23(17Q22) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        52
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       7
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            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"
D41V9, continuous
                              vv
clus                           R0 R1 R2 RX
  DEL PEAK 23(17Q22) MUTATED    9 12  1  1
  DEL PEAK 23(17Q22) WILD-TYPE 46 13  0  1
D41V10, multiclass
    clus
vv   DEL PEAK 23(17Q22) MUTATED DEL PEAK 23(17Q22) WILD-TYPE
  R0                          9                           46
  R1                         12                           13
  R2                          1                            0
  RX                          1                            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"
D41V11, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(17Q22) MUTATED       1                         3    20
  DEL PEAK 23(17Q22) WILD-TYPE     1                         3    54
D41V12, multiclass
                           clus
vv                          DEL PEAK 23(17Q22) MUTATED
  ASIAN                                              1
  BLACK OR AFRICAN AMERICAN                          3
  WHITE                                             20
                           clus
vv                          DEL PEAK 23(17Q22) WILD-TYPE
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               54
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(42) Variable = DEL PEAK 24(18P11.32) MUTATION ANALYSIS
D42V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 24(18P11.32) MUTATED   19  5
  DEL PEAK 24(18P11.32) WILD-TYPE 31  6
  DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE 
                             24                              37 
  DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE 
                              5                               6 
$`DEL PEAK 24(18P11.32) MUTATED`
TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR 
         153          586          385          449            1          166 
TCGA-H6-A45N TCGA-HZ-7918 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-A49G 
         233           28            8           19           28           23 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7649 TCGA-IB-7885 
         194           46           13           33         1951          851 
TCGA-IB-7886 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A7M4 TCGA-M8-A5N4 TCGA-OE-A75W 
        1975          329         1991          181          584          110 

$`DEL PEAK 24(18P11.32) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-FB-A4P5 TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7289 
         295          360            4          392          396          240 
TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-8002 
          20            4            8          369          361           24 
TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49H 
          21           16            3            5           91           29 
TCGA-HZ-A77O TCGA-IB-7644 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7891 TCGA-IB-8126 
          11          347         1989          476          488           17 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A7SX 
         522          300            8         1968          164          127 
TCGA-LB-A8F3 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 TCGA-YB-A89D 
          35          247          416         1955          844          160 
TCGA-YY-A8LH 
        1834 

  DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE 
                              1                               3 
  DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE 
                           1991                            1989 
  DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE 
                          173.5                           240.0 
[1] "1.0 - 1991.0 (173.5)" "3.0 - 1989.0 (240.0)"
[1] "hr=" "1.2"
D42V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 24(18P11.32) MUTATED          0        3         5        21
  DEL PEAK 24(18P11.32) WILD-TYPE        2        1         9        40
                                 vv
clus                              STAGE III STAGE IV
  DEL PEAK 24(18P11.32) MUTATED           1        0
  DEL PEAK 24(18P11.32) WILD-TYPE         1        3
D42V3, multiclass
           clus
vv          DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE
  STAGE IA                              0                               2
  STAGE IB                              3                               1
  STAGE IIA                             5                               9
  STAGE IIB                            21                              40
  STAGE III                             1                               1
  STAGE IV                              0                               3
[1] 6 2
[1] 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(18P11.32) MUTATED       4    26
  DEL PEAK 24(18P11.32) WILD-TYPE     4    52
D42V4, multiclass
       clus
vv      DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE
  T1+T2                             4                               4
  T3+T4                            26                              52
[1] 2 2
[1] FALSE
D42V5, binary
                                 cls
clus                               0  1
  DEL PEAK 24(18P11.32) MUTATED    8 21
  DEL PEAK 24(18P11.32) WILD-TYPE 13 43
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(18P11.32) MUTATED      8   21
  DEL PEAK 24(18P11.32) WILD-TYPE   13   43
   clus
vv  DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE
  0                             8                              13
  1                            21                              43
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 24(18P11.32) MUTATED   17  0 13
  DEL PEAK 24(18P11.32) WILD-TYPE 24  3 29
D42V6, multiclass
    clus
vv   DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE
  M0                            17                              24
  M1                             0                               3
  MX                            13                              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"
D42V7, binary
                                 cls
clus                               0  1
  DEL PEAK 24(18P11.32) MUTATED   14 16
  DEL PEAK 24(18P11.32) WILD-TYPE 30 26
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 24(18P11.32) MUTATED     14   16
  DEL PEAK 24(18P11.32) WILD-TYPE   30   26
        clus
vv       DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE
  FEMALE                            14                              30
  MALE                              16                              26
[1] 2 2
[1] FALSE
                                 vv
clus                              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 24(18P11.32) MUTATED                                    25
  DEL PEAK 24(18P11.32) WILD-TYPE                                  49
                                 vv
clus                              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 24(18P11.32) MUTATED                                       4
  DEL PEAK 24(18P11.32) WILD-TYPE                                     4
                                 vv
clus                              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 24(18P11.32) MUTATED                                                  1
  DEL PEAK 24(18P11.32) WILD-TYPE                                                2
D42V8, multiclass
                                                  clus
vv                                                 DEL PEAK 24(18P11.32) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         25
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             1
                                                  clus
vv                                                 DEL PEAK 24(18P11.32) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                           49
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                          4
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                               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"
D42V9, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 24(18P11.32) MUTATED   19  8  0  1
  DEL PEAK 24(18P11.32) WILD-TYPE 36 17  1  1
D42V10, multiclass
    clus
vv   DEL PEAK 24(18P11.32) MUTATED DEL PEAK 24(18P11.32) WILD-TYPE
  R0                            19                              36
  R1                             8                              17
  R2                             0                               1
  RX                             1                               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"
D42V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(18P11.32) MUTATED       1                         1    25
  DEL PEAK 24(18P11.32) WILD-TYPE     1                         5    49
D42V12, multiclass
                           clus
vv                          DEL PEAK 24(18P11.32) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                25
                           clus
vv                          DEL PEAK 24(18P11.32) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  49
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(43) Variable = DEL PEAK 25(18Q21.2) MUTATION ANALYSIS
D43V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 25(18Q21.2) MUTATED   36  8
  DEL PEAK 25(18Q21.2) WILD-TYPE 14  3
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                            44                             17 
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                             8                              3 
$`DEL PEAK 25(18Q21.2) MUTATED`
TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A545 TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR 
         153          586          385          449            1          166 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7919 
         392          233          396          240           28           20 
TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8315 TCGA-HZ-8636 TCGA-HZ-A49G 
         361            8           19           28            5           23 
TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 
         194           46           11           13           33          347 
TCGA-IB-7649 TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 
        1951          476          851         1975          488           17 
TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5SS TCGA-IB-A6UG TCGA-IB-A7M4 
         522          329          300         1991         1968          181 
TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-US-A774 
         164          127          584          110          247         1955 
TCGA-US-A776 TCGA-YB-A89D 
         844          160 

$`DEL PEAK 25(18Q21.2) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-FB-A4P5 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 
         295          360            4            4            8          369 
TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49H 
          24           21           16            3           91           29 
TCGA-IB-7651 TCGA-IB-A5ST TCGA-LB-A8F3 TCGA-Q3-A5QY TCGA-YY-A8LH 
        1989            8           35          416         1834 

  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                             1                              3 
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                          1991                           1989 
  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE 
                         236.5                           29.0 
[1] "1.0 - 1991.0 (236.5)" "3.0 - 1989.0 (29.0)" 
[1] "hr=" "1.3"
D43V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 25(18Q21.2) MUTATED          0        3         9        42
  DEL PEAK 25(18Q21.2) WILD-TYPE        2        1         5        19
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 25(18Q21.2) MUTATED           2        3
  DEL PEAK 25(18Q21.2) WILD-TYPE         0        0
D43V3, multiclass
           clus
vv          DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             3                              1
  STAGE IIA                            9                              5
  STAGE IIB                           42                             19
  STAGE III                            2                              0
  STAGE IV                             3                              0
[1] 6 2
[1] 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(18Q21.2) MUTATED       5    54
  DEL PEAK 25(18Q21.2) WILD-TYPE     3    24
D43V4, multiclass
       clus
vv      DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  T1+T2                            5                              3
  T3+T4                           54                             24
[1] 2 2
[1] FALSE
D43V5, binary
                                cls
clus                              0  1
  DEL PEAK 25(18Q21.2) MUTATED   13 45
  DEL PEAK 25(18Q21.2) WILD-TYPE  8 19
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(18Q21.2) MUTATED     13   45
  DEL PEAK 25(18Q21.2) WILD-TYPE    8   19
   clus
vv  DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  0                           13                              8
  1                           45                             19
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 25(18Q21.2) MUTATED   31  3 25
  DEL PEAK 25(18Q21.2) WILD-TYPE 10  0 17
D43V6, multiclass
    clus
vv   DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  M0                           31                             10
  M1                            3                              0
  MX                           25                             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"
D43V7, binary
                                cls
clus                              0  1
  DEL PEAK 25(18Q21.2) MUTATED   28 31
  DEL PEAK 25(18Q21.2) WILD-TYPE 16 11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 25(18Q21.2) MUTATED     28   31
  DEL PEAK 25(18Q21.2) WILD-TYPE   16   11
        clus
vv       DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  FEMALE                           28                             16
  MALE                             31                             11
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 25(18Q21.2) MUTATED                                    50
  DEL PEAK 25(18Q21.2) WILD-TYPE                                  24
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 25(18Q21.2) MUTATED                                       6
  DEL PEAK 25(18Q21.2) WILD-TYPE                                     2
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 25(18Q21.2) MUTATED                                                  2
  DEL PEAK 25(18Q21.2) WILD-TYPE                                                1
D43V8, multiclass
                                                  clus
vv                                                 DEL PEAK 25(18Q21.2) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        50
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            2
                                                  clus
vv                                                 DEL PEAK 25(18Q21.2) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              1
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D43V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 25(18Q21.2) MUTATED   32 21  1  2
  DEL PEAK 25(18Q21.2) WILD-TYPE 23  4  0  0
D43V10, multiclass
    clus
vv   DEL PEAK 25(18Q21.2) MUTATED DEL PEAK 25(18Q21.2) WILD-TYPE
  R0                           32                             23
  R1                           21                              4
  R2                            1                              0
  RX                            2                              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"
D43V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 25(18Q21.2) MUTATED       2                         3    51
  DEL PEAK 25(18Q21.2) WILD-TYPE     0                         3    23
D43V12, multiclass
                           clus
vv                          DEL PEAK 25(18Q21.2) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               51
                           clus
vv                          DEL PEAK 25(18Q21.2) WILD-TYPE
  ASIAN                                                  0
  BLACK OR AFRICAN AMERICAN                              3
  WHITE                                                 23
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(44) Variable = DEL PEAK 26(19P13.3) MUTATION ANALYSIS
D44V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 26(19P13.3) MUTATED    9  2
  DEL PEAK 26(19P13.3) WILD-TYPE 41  9
  DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE 
                            11                             50 
  DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE 
                             2                              9 
$`DEL PEAK 26(19P13.3) MUTATED`
TCGA-H6-8124 TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A77O TCGA-IB-7885 
         392            4            5          194           11          851 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-US-A776 
        1991         1968          164          127          844 

$`DEL PEAK 26(19P13.3) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-FB-A7DR TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          166          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 
          28           20            8          369          361            8 
TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 
          19           24           21           28           16            3 
TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK TCGA-HZ-A77P TCGA-HZ-A77Q 
          91           23           29           46           13           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7886 TCGA-IB-7891 
         347         1951         1989          476         1975          488 
TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP TCGA-IB-A5ST TCGA-IB-A7M4 
          17          522          329          300            8          181 
TCGA-LB-A8F3 TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 
          35          584          110          247          416         1955 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE 
                             4                              1 
  DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE 
                          1991                           1989 
  DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE 
                         194.0                          173.5 
[1] "4.0 - 1991.0 (194.0)" "1.0 - 1989.0 (173.5)"
[1] "hr=" "4.3"
D44V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 26(19P13.3) MUTATED          0        0         1        14
  DEL PEAK 26(19P13.3) WILD-TYPE        2        4        13        47
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 26(19P13.3) MUTATED           0        1
  DEL PEAK 26(19P13.3) WILD-TYPE         2        2
D44V3, multiclass
           clus
vv          DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            1                             13
  STAGE IIB                           14                             47
  STAGE III                            0                              2
  STAGE IV                             1                              2
[1] 6 2
[1] 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(19P13.3) MUTATED       1    15
  DEL PEAK 26(19P13.3) WILD-TYPE     7    63
D44V4, multiclass
       clus
vv      DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE
  T1+T2                            1                              7
  T3+T4                           15                             63
[1] 2 2
[1] FALSE
D44V5, binary
                                cls
clus                              0  1
  DEL PEAK 26(19P13.3) MUTATED    2 14
  DEL PEAK 26(19P13.3) WILD-TYPE 19 50
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(19P13.3) MUTATED      2   14
  DEL PEAK 26(19P13.3) WILD-TYPE   19   50
   clus
vv  DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE
  0                            2                             19
  1                           14                             50
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 26(19P13.3) MUTATED    7  1  8
  DEL PEAK 26(19P13.3) WILD-TYPE 34  2 34
D44V6, multiclass
    clus
vv   DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE
  M0                            7                             34
  M1                            1                              2
  MX                            8                             34
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V7, binary
                                cls
clus                              0  1
  DEL PEAK 26(19P13.3) MUTATED    8  8
  DEL PEAK 26(19P13.3) WILD-TYPE 36 34
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 26(19P13.3) MUTATED      8    8
  DEL PEAK 26(19P13.3) WILD-TYPE   36   34
        clus
vv       DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE
  FEMALE                            8                             36
  MALE                              8                             34
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 26(19P13.3) MUTATED                                    14
  DEL PEAK 26(19P13.3) WILD-TYPE                                  60
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 26(19P13.3) MUTATED                                       0
  DEL PEAK 26(19P13.3) WILD-TYPE                                     8
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 26(19P13.3) MUTATED                                                  1
  DEL PEAK 26(19P13.3) WILD-TYPE                                                2
D44V8, multiclass
                                                  clus
vv                                                 DEL PEAK 26(19P13.3) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        14
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            1
                                                  clus
vv                                                 DEL PEAK 26(19P13.3) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          60
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D44V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 26(19P13.3) MUTATED    9  6  1  0
  DEL PEAK 26(19P13.3) WILD-TYPE 46 19  0  2
D44V10, multiclass
    clus
vv   DEL PEAK 26(19P13.3) MUTATED DEL PEAK 26(19P13.3) WILD-TYPE
  R0                            9                             46
  R1                            6                             19
  R2                            1                              0
  RX                            0                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D44V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 26(19P13.3) MUTATED       0                         1    15
  DEL PEAK 26(19P13.3) WILD-TYPE     2                         5    59
D44V12, multiclass
                           clus
vv                          DEL PEAK 26(19P13.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            1
  WHITE                                               15
                           clus
vv                          DEL PEAK 26(19P13.3) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              5
  WHITE                                                 59
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(45) Variable = DEL PEAK 27(19Q13.41) MUTATION ANALYSIS
D45V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 27(19Q13.41) MUTATED    4  1
  DEL PEAK 27(19Q13.41) WILD-TYPE 46 10
  DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE 
                              5                              56 
  DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE 
                              1                              10 
$`DEL PEAK 27(19Q13.41) MUTATED`
TCGA-FB-A7DR TCGA-HZ-A4BH TCGA-IB-7652 TCGA-IB-7885 TCGA-IB-A5SS 
         166          194          476          851         1991 

$`DEL PEAK 27(19Q13.41) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A545 
         295          360          153          586            4          385 
TCGA-FB-A5VM TCGA-FB-A78T TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 
         449            1          392          233          396          240 
TCGA-HZ-7918 TCGA-HZ-7919 TCGA-HZ-7922 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
          28           20            4            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8636 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A4BK 
           3            5           91           23           29           46 
TCGA-HZ-A77O TCGA-HZ-A77P TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 
          11           13           33          347         1951         1989 
TCGA-IB-7886 TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5SP 
        1975          488           17          522          329          300 
TCGA-IB-A5ST TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-LB-A7SX TCGA-LB-A8F3 
           8         1968          181          164          127           35 
TCGA-M8-A5N4 TCGA-OE-A75W TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          110          247          416         1955          844 
TCGA-YB-A89D TCGA-YY-A8LH 
         160         1834 

  DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE 
                            166                               1 
  DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE 
                           1991                            1989 
  DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE 
                            476                             162 
[1] "166.0 - 1991.0 (476.0)" "1.0 - 1989.0 (162.0)"  
[1] "hr="     "3.1e+08"
D45V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 27(19Q13.41) MUTATED          0        0         1        10
  DEL PEAK 27(19Q13.41) WILD-TYPE        2        4        13        51
                                 vv
clus                              STAGE III STAGE IV
  DEL PEAK 27(19Q13.41) MUTATED           0        0
  DEL PEAK 27(19Q13.41) WILD-TYPE         2        3
D45V3, multiclass
           clus
vv          DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE
  STAGE IA                              0                               2
  STAGE IB                              0                               4
  STAGE IIA                             1                              13
  STAGE IIB                            10                              51
  STAGE III                             0                               2
  STAGE IV                              0                               3
[1] 6 2
[1] 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(19Q13.41) MUTATED       0    11
  DEL PEAK 27(19Q13.41) WILD-TYPE     8    67
D45V4, multiclass
       clus
vv      DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE
  T1+T2                             0                               8
  T3+T4                            11                              67
[1] 2 2
[1] FALSE
D45V5, binary
                                 cls
clus                               0  1
  DEL PEAK 27(19Q13.41) MUTATED    0 10
  DEL PEAK 27(19Q13.41) WILD-TYPE 21 54
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(19Q13.41) MUTATED      0   10
  DEL PEAK 27(19Q13.41) WILD-TYPE   21   54
   clus
vv  DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE
  0                             0                              21
  1                            10                              54
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 27(19Q13.41) MUTATED    6  0  5
  DEL PEAK 27(19Q13.41) WILD-TYPE 35  3 37
D45V6, multiclass
    clus
vv   DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE
  M0                             6                              35
  M1                             0                               3
  MX                             5                              37
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D45V7, binary
                                 cls
clus                               0  1
  DEL PEAK 27(19Q13.41) MUTATED    3  8
  DEL PEAK 27(19Q13.41) WILD-TYPE 41 34
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 27(19Q13.41) MUTATED      3    8
  DEL PEAK 27(19Q13.41) WILD-TYPE   41   34
        clus
vv       DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE
  FEMALE                             3                              41
  MALE                               8                              34
[1] 2 2
[1] FALSE
                                 vv
clus                              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 27(19Q13.41) MUTATED                                    10
  DEL PEAK 27(19Q13.41) WILD-TYPE                                  64
                                 vv
clus                              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 27(19Q13.41) MUTATED                                       0
  DEL PEAK 27(19Q13.41) WILD-TYPE                                     8
                                 vv
clus                              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 27(19Q13.41) MUTATED                                                  1
  DEL PEAK 27(19Q13.41) WILD-TYPE                                                2
D45V8, multiclass
                                                  clus
vv                                                 DEL PEAK 27(19Q13.41) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         10
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        0
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             1
                                                  clus
vv                                                 DEL PEAK 27(19Q13.41) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                           64
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                          8
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                               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"
D45V9, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 27(19Q13.41) MUTATED    6  5  0  0
  DEL PEAK 27(19Q13.41) WILD-TYPE 49 20  1  2
D45V10, multiclass
    clus
vv   DEL PEAK 27(19Q13.41) MUTATED DEL PEAK 27(19Q13.41) WILD-TYPE
  R0                             6                              49
  R1                             5                              20
  R2                             0                               1
  RX                             0                               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
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 27(19Q13.41) MUTATED       2                         1     8
  DEL PEAK 27(19Q13.41) WILD-TYPE     0                         5    66
D45V12, multiclass
                           clus
vv                          DEL PEAK 27(19Q13.41) MUTATED
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                 8
                           clus
vv                          DEL PEAK 27(19Q13.41) WILD-TYPE
  ASIAN                                                   0
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  66
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(46) Variable = DEL PEAK 28(21Q21.1) MUTATION ANALYSIS
D46V1, survival
                                sevent
clus2                             0  1
  DEL PEAK 28(21Q21.1) MUTATED   19  6
  DEL PEAK 28(21Q21.1) WILD-TYPE 31  5
  DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE 
                            25                             36 
  DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE 
                             6                              5 
$`DEL PEAK 28(21Q21.1) MUTATED`
TCGA-FB-A545 TCGA-FB-A78T TCGA-H6-8124 TCGA-H8-A6C1 TCGA-HZ-7918 TCGA-HZ-7919 
         385            1          392          396           28           20 
TCGA-HZ-7922 TCGA-HZ-8636 TCGA-HZ-A4BH TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q 
           4            5          194           46           11           33 
TCGA-IB-7644 TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7885 TCGA-IB-7886 TCGA-IB-A5SP 
         347         1951         1989          851         1975          300 
TCGA-IB-A5SS TCGA-IB-A6UG TCGA-LB-A7SX TCGA-M8-A5N4 TCGA-OE-A75W TCGA-YB-A89D 
        1991         1968          127          584          110          160 
TCGA-YY-A8LH 
        1834 

$`DEL PEAK 28(21Q21.1) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-F2-A44H TCGA-FB-A4P5 TCGA-FB-A5VM 
         295          360          153          586            4          449 
TCGA-FB-A7DR TCGA-H6-A45N TCGA-HZ-7289 TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 
         166          233          240            8          369          361 
TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 
           8           19           24           21           28           16 
TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G TCGA-HZ-A49H TCGA-HZ-A77P TCGA-IB-7652 
           3           91           23           29           13          476 
TCGA-IB-7891 TCGA-IB-8126 TCGA-IB-8127 TCGA-IB-A5SO TCGA-IB-A5ST TCGA-IB-A7M4 
         488           17          522          329            8          181 
TCGA-L1-A7W4 TCGA-LB-A8F3 TCGA-PZ-A5RE TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         164           35          247          416         1955          844 

  DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE 
                             1                              3 
  DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE 
                          1991                           1955 
  DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE 
                           300                            165 
[1] "1.0 - 1991.0 (300.0)" "3.0 - 1955.0 (165.0)"
[1] "hr=" "3.8"
D46V2, continuous
                                vv
clus                             STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 28(21Q21.1) MUTATED          0        0         4        26
  DEL PEAK 28(21Q21.1) WILD-TYPE        2        4        10        35
                                vv
clus                             STAGE III STAGE IV
  DEL PEAK 28(21Q21.1) MUTATED           0        2
  DEL PEAK 28(21Q21.1) WILD-TYPE         2        1
D46V3, multiclass
           clus
vv          DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE
  STAGE IA                             0                              2
  STAGE IB                             0                              4
  STAGE IIA                            4                             10
  STAGE IIB                           26                             35
  STAGE III                            0                              2
  STAGE IV                             2                              1
[1] 6 2
[1] 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(21Q21.1) MUTATED       1    31
  DEL PEAK 28(21Q21.1) WILD-TYPE     7    47
D46V4, multiclass
       clus
vv      DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE
  T1+T2                            1                              7
  T3+T4                           31                             47
[1] 2 2
[1] FALSE
D46V5, binary
                                cls
clus                              0  1
  DEL PEAK 28(21Q21.1) MUTATED    5 27
  DEL PEAK 28(21Q21.1) WILD-TYPE 16 37
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(21Q21.1) MUTATED      5   27
  DEL PEAK 28(21Q21.1) WILD-TYPE   16   37
   clus
vv  DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE
  0                            5                             16
  1                           27                             37
[1] 2 2
[1] FALSE
                                vv
clus                             M0 M1 MX
  DEL PEAK 28(21Q21.1) MUTATED   17  2 13
  DEL PEAK 28(21Q21.1) WILD-TYPE 24  1 29
D46V6, multiclass
    clus
vv   DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE
  M0                           17                             24
  M1                            2                              1
  MX                           13                             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"
D46V7, binary
                                cls
clus                              0  1
  DEL PEAK 28(21Q21.1) MUTATED   18 14
  DEL PEAK 28(21Q21.1) WILD-TYPE 26 28
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 28(21Q21.1) MUTATED     18   14
  DEL PEAK 28(21Q21.1) WILD-TYPE   26   28
        clus
vv       DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE
  FEMALE                           18                             26
  MALE                             14                             28
[1] 2 2
[1] FALSE
                                vv
clus                             PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 28(21Q21.1) MUTATED                                    29
  DEL PEAK 28(21Q21.1) WILD-TYPE                                  45
                                vv
clus                             PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 28(21Q21.1) MUTATED                                       3
  DEL PEAK 28(21Q21.1) WILD-TYPE                                     5
                                vv
clus                             PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 28(21Q21.1) MUTATED                                                  0
  DEL PEAK 28(21Q21.1) WILD-TYPE                                                3
D46V8, multiclass
                                                  clus
vv                                                 DEL PEAK 28(21Q21.1) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                        29
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                       3
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                            0
                                                  clus
vv                                                 DEL PEAK 28(21Q21.1) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                          45
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                         5
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                              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"
D46V9, continuous
                                vv
clus                             R0 R1 R2 RX
  DEL PEAK 28(21Q21.1) MUTATED   17 14  0  0
  DEL PEAK 28(21Q21.1) WILD-TYPE 38 11  1  2
D46V10, multiclass
    clus
vv   DEL PEAK 28(21Q21.1) MUTATED DEL PEAK 28(21Q21.1) WILD-TYPE
  R0                           17                             38
  R1                           14                             11
  R2                            0                              1
  RX                            0                              2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D46V11, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 28(21Q21.1) MUTATED       0                         2    28
  DEL PEAK 28(21Q21.1) WILD-TYPE     2                         4    46
D46V12, multiclass
                           clus
vv                          DEL PEAK 28(21Q21.1) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               28
                           clus
vv                          DEL PEAK 28(21Q21.1) WILD-TYPE
  ASIAN                                                  2
  BLACK OR AFRICAN AMERICAN                              4
  WHITE                                                 46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(47) Variable = DEL PEAK 29(22Q13.31) MUTATION ANALYSIS
D47V1, survival
                                 sevent
clus2                              0  1
  DEL PEAK 29(22Q13.31) MUTATED   18  3
  DEL PEAK 29(22Q13.31) WILD-TYPE 32  8
  DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE 
                             21                              40 
  DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE 
                              3                               8 
$`DEL PEAK 29(22Q13.31) MUTATED`
TCGA-F2-A44H TCGA-FB-A78T TCGA-FB-A7DR TCGA-HZ-7919 TCGA-HZ-8636 TCGA-HZ-A4BH 
         586            1          166           20            5          194 
TCGA-HZ-A4BK TCGA-HZ-A77O TCGA-HZ-A77Q TCGA-IB-7644 TCGA-IB-7886 TCGA-IB-7891 
          46           11           33          347         1975          488 
TCGA-IB-8127 TCGA-IB-A5SP TCGA-IB-A6UG TCGA-IB-A7M4 TCGA-L1-A7W4 TCGA-OE-A75W 
         522          300         1968          181          164          110 
TCGA-PZ-A5RE TCGA-YB-A89D TCGA-YY-A8LH 
         247          160         1834 

$`DEL PEAK 29(22Q13.31) WILD-TYPE`
TCGA-F2-6880 TCGA-F2-7273 TCGA-F2-A44G TCGA-FB-A4P5 TCGA-FB-A545 TCGA-FB-A5VM 
         295          360          153            4          385          449 
TCGA-H6-8124 TCGA-H6-A45N TCGA-H8-A6C1 TCGA-HZ-7289 TCGA-HZ-7918 TCGA-HZ-7922 
         392          233          396          240           28            4 
TCGA-HZ-7923 TCGA-HZ-7924 TCGA-HZ-7925 TCGA-HZ-7926 TCGA-HZ-8001 TCGA-HZ-8002 
           8          369          361            8           19           24 
TCGA-HZ-8003 TCGA-HZ-8315 TCGA-HZ-8317 TCGA-HZ-8519 TCGA-HZ-8638 TCGA-HZ-A49G 
          21           28           16            3           91           23 
TCGA-HZ-A49H TCGA-HZ-A77P TCGA-IB-7649 TCGA-IB-7651 TCGA-IB-7652 TCGA-IB-7885 
          29           13         1951         1989          476          851 
TCGA-IB-8126 TCGA-IB-A5SO TCGA-IB-A5SS TCGA-IB-A5ST TCGA-LB-A7SX TCGA-LB-A8F3 
          17          329         1991            8          127           35 
TCGA-M8-A5N4 TCGA-Q3-A5QY TCGA-US-A774 TCGA-US-A776 
         584          416         1955          844 

  DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE 
                              1                               3 
  DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE 
                           1975                            1991 
  DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE 
                            181                             193 
[1] "1.0 - 1975.0 (181.0)" "3.0 - 1991.0 (193.0)"
[1] "hr=" "1.1"
D47V2, continuous
                                 vv
clus                              STAGE IA STAGE IB STAGE IIA STAGE IIB
  DEL PEAK 29(22Q13.31) MUTATED          0        0         4        22
  DEL PEAK 29(22Q13.31) WILD-TYPE        2        4        10        39
                                 vv
clus                              STAGE III STAGE IV
  DEL PEAK 29(22Q13.31) MUTATED           0        2
  DEL PEAK 29(22Q13.31) WILD-TYPE         2        1
D47V3, multiclass
           clus
vv          DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE
  STAGE IA                              0                               2
  STAGE IB                              0                               4
  STAGE IIA                             4                              10
  STAGE IIB                            22                              39
  STAGE III                             0                               2
  STAGE IV                              2                               1
[1] 6 2
[1] 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(22Q13.31) MUTATED       1    27
  DEL PEAK 29(22Q13.31) WILD-TYPE     7    51
D47V4, multiclass
       clus
vv      DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE
  T1+T2                             1                               7
  T3+T4                            27                              51
[1] 2 2
[1] FALSE
D47V5, binary
                                 cls
clus                               0  1
  DEL PEAK 29(22Q13.31) MUTATED    4 23
  DEL PEAK 29(22Q13.31) WILD-TYPE 17 41
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(22Q13.31) MUTATED      4   23
  DEL PEAK 29(22Q13.31) WILD-TYPE   17   41
   clus
vv  DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE
  0                             4                              17
  1                            23                              41
[1] 2 2
[1] FALSE
                                 vv
clus                              M0 M1 MX
  DEL PEAK 29(22Q13.31) MUTATED   14  2 12
  DEL PEAK 29(22Q13.31) WILD-TYPE 27  1 30
D47V6, multiclass
    clus
vv   DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE
  M0                            14                              27
  M1                             2                               1
  MX                            12                              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"
D47V7, binary
                                 cls
clus                               0  1
  DEL PEAK 29(22Q13.31) MUTATED   11 17
  DEL PEAK 29(22Q13.31) WILD-TYPE 33 25
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 29(22Q13.31) MUTATED     11   17
  DEL PEAK 29(22Q13.31) WILD-TYPE   33   25
        clus
vv       DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE
  FEMALE                            11                              33
  MALE                              17                              25
[1] 2 2
[1] FALSE
                                 vv
clus                              PANCREAS-ADENOCARCINOMA DUCTAL TYPE
  DEL PEAK 29(22Q13.31) MUTATED                                    24
  DEL PEAK 29(22Q13.31) WILD-TYPE                                  50
                                 vv
clus                              PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE
  DEL PEAK 29(22Q13.31) MUTATED                                       2
  DEL PEAK 29(22Q13.31) WILD-TYPE                                     6
                                 vv
clus                              PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA
  DEL PEAK 29(22Q13.31) MUTATED                                                  1
  DEL PEAK 29(22Q13.31) WILD-TYPE                                                2
D47V8, multiclass
                                                  clus
vv                                                 DEL PEAK 29(22Q13.31) MUTATED
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                         24
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                        2
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                             1
                                                  clus
vv                                                 DEL PEAK 29(22Q13.31) WILD-TYPE
  PANCREAS-ADENOCARCINOMA DUCTAL TYPE                                           50
  PANCREAS-ADENOCARCINOMA-OTHER SUBTYPE                                          6
  PANCREAS-COLLOID (MUCINOUS NON-CYSTIC) CARCINOMA                               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"
D47V9, continuous
                                 vv
clus                              R0 R1 R2 RX
  DEL PEAK 29(22Q13.31) MUTATED   15 11  1  0
  DEL PEAK 29(22Q13.31) WILD-TYPE 40 14  0  2
D47V10, multiclass
    clus
vv   DEL PEAK 29(22Q13.31) MUTATED DEL PEAK 29(22Q13.31) WILD-TYPE
  R0                            15                              40
  R1                            11                              14
  R2                             1                               0
  RX                             0                               2
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D47V11, continuous
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 29(22Q13.31) MUTATED       1                         1    26
  DEL PEAK 29(22Q13.31) WILD-TYPE     1                         5    48
D47V12, multiclass
                           clus
vv                          DEL PEAK 29(22Q13.31) MUTATED
  ASIAN                                                 1
  BLACK OR AFRICAN AMERICAN                             1
  WHITE                                                26
                           clus
vv                          DEL PEAK 29(22Q13.31) WILD-TYPE
  ASIAN                                                   1
  BLACK OR AFRICAN AMERICAN                               5
  WHITE                                                  48
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
