[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"        "-oTKIRP-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/KIRP-TP/11541540/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRP-TP/11548605/transformed.cor.cli.txt"

nPatients in clinical file=223, in cluster file=288, common to both=221
[1]  31 221
[1] "AMP PEAK 1(2P23.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          40                          181 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          40                          181 
[1] "AMP PEAK 2(2Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          47                          174 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          47                          174 
[1] "AMP PEAK 3(3Q27.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          77                          144 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          77                          144 
[1] "AMP PEAK 4(5Q35.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          32                          189 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          32                          189 
[1] "AMP PEAK 5(7Q31.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         133                           88 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         133                           88 
[1] "AMP PEAK 6(17Q25.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          158                            63 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          158                            63 
[1] "AMP PEAK 7(19P13.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           23                           198 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           23                           198 
[1] "DEL PEAK  1(1P36.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            42                            179 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            42                            179 
[1] "DEL PEAK  2(2P12) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          4                         217 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          4                         217 
[1] "DEL PEAK  3(2Q22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            7                           214 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            7                           214 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           10                           211 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           10                           211 
[1] "DEL PEAK  5(3P22.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           19                           202 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           19                           202 
[1] "DEL PEAK  6(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           26                           195 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           26                           195 
[1] "DEL PEAK  7(5P15.33) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            10                            211 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            10                            211 
[1] "DEL PEAK  8(5Q35.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           11                           210 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           11                           210 
[1] "DEL PEAK  9(6P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           19                           202 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           19                           202 
[1] "DEL PEAK 10(6Q22.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            21                            200 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            21                            200 
[1] "DEL PEAK 11(6Q25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           23                           198 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           23                           198 
[1] "DEL PEAK 12(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           30                           191 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           30                           191 
[1] "DEL PEAK 13(10Q21.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            15                            206 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            15                            206 
[1] "DEL PEAK 14(11Q22.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            22                            199 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            22                            199 
[1] "DEL PEAK 15(11Q23.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            21                            200 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            21                            200 
[1] "DEL PEAK 16(14Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            44                            177 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            44                            177 
[1] "DEL PEAK 17(14Q24.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            42                            179 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            42                            179 
[1] "DEL PEAK 18(15Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            28                            193 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            28                            193 
[1] "DEL PEAK 19(16Q24.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            10                            211 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            10                            211 
[1] "DEL PEAK 20(19P13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            17                            204 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            17                            204 
[1] "DEL PEAK 21(19Q13.42) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             16                             205 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             16                             205 
[1] "DEL PEAK 22(22Q12.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            53                            168 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            53                            168 
[1] "DEL PEAK 23(XP11.4) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           23                           198 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           23                           198 
[1] "DEL PEAK 24(XQ28) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         19                         202 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         19                         202 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 221 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
         207          554           21          493            3           NA 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
          NA          582           27           NA            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
           2          140          780          729           NA          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
          NA           NA            2          118           87            4 
TCGA-A4-A772 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
          NA           NA         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
         763         1357           26           67          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         659          747          513          108          510           14 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         200         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          452          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
         586          270         1938           NA           NA         1454 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
          NA         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
         403           NA          233           29          364           NA 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
          84         3760           NA         2948         2839           NA 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
        1864         1533         1516          799          612           NA 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
         445           92         1240         2429         2460           NA 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
          10            7           36           13          208         1575 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1479           NA         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
         786          194          197          262           NA         2091 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7128 TCGA-HE-7129 
         546           27          341          140           NA           NA 
TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
          NA         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
         167          511          608           62           NA           NA 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
          NA          677          649          146          376           NA 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
         493          148         3035         2653           NA           NA 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823           NA          578 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
        1175           NA         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=177,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=12,	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=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=25,	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] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 221 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=52, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
146  22  49   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  146    22    51 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
146  22  49   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  146    22    51 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
39 20  4 
[1] "table(vv)"
vv
N0 N1 N2 
39 20  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
39 20  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
39 20  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=19, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK 1(2P23.2) MUTATION ANALYSIS
D1V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 1(2P23.2) MUTATED    32   2
  AMP PEAK 1(2P23.2) WILD-TYPE 155   5
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                          34                          160 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                           2                            5 
$`AMP PEAK 1(2P23.2) MUTATED`
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 
         516            2          118          412           67          223 
TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
         309           14           64          364           84         2948 
TCGA-DW-5561 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-A8LC 
         414           36          208         1575         1194          262 
TCGA-G7-A8LD TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U 
        1967          112          546         2072          360          511 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-P4-A5EB 
          62          364          885          161         1043         2584 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ 
         540          428          876         1266 

$`AMP PEAK 1(2P23.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
         379         1968           87            4         1778         1636 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           26          595          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 
        1029          307          930         1049          379         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         857          803          627           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
         671          585          207            5          452          167 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
          52         2639          586          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         233           29         3760         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         116          353         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 
          97           10            7           13         1479         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
         765          446          786          194          197         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC 
        5925          393          841           32          378           27 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
         341          140          408         1726         2228          167 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608          677          649          146          376            4 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED 
         541          493          148         3035         2653         2816 
TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM 
         391         1457         1443         1005          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
         578         1175          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                           2                            2 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                        2948                         5925 
  AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE 
                       388.0                        583.5 
[1] "2.0 - 2948.0 (388.0)" "2.0 - 5925.0 (583.5)"
[1] "hr=" "1.8"
D1V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 1(2P23.2) MUTATED        24        2         8        5
  AMP PEAK 1(2P23.2) WILD-TYPE     113       14        35        8
D1V3, multiclass
           clus
vv          AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  STAGE I                           24                          113
  STAGE II                           2                           14
  STAGE III                          8                           35
  STAGE IV                           5                            8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 1(2P23.2) MUTATED    24   4    12
  AMP PEAK 1(2P23.2) WILD-TYPE 122  18    39
D1V4, multiclass
       clus
vv      AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  T1                            24                          122
  T2                             4                           18
  T3+T4                         12                           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"
                              vv
clus                           N0 N1 N2
  AMP PEAK 1(2P23.2) MUTATED    4  8  1
  AMP PEAK 1(2P23.2) WILD-TYPE 35 12  3
D1V5, multiclass
    clus
vv   AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  N0                          4                           35
  N1                          8                           12
  N2                          1                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  AMP PEAK 1(2P23.2) MUTATED   11  4 22
  AMP PEAK 1(2P23.2) WILD-TYPE 77  4 90
D1V6, multiclass
    clus
vv   AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  M0                         11                           77
  M1                          4                            4
  MX                         22                           90
[1] 3 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(2P23.2) MUTATED    14  26
  AMP PEAK 1(2P23.2) WILD-TYPE  49 132
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED     14   26
  AMP PEAK 1(2P23.2) WILD-TYPE   49  132
        clus
vv       AMP PEAK 1(2P23.2) MUTATED AMP PEAK 1(2P23.2) WILD-TYPE
  FEMALE                         14                           49
  MALE                           26                          132
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 1(2P23.2) MUTATED                                  0     1
  AMP PEAK 1(2P23.2) WILD-TYPE                                2     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 1(2P23.2) MUTATED                           7    28
  AMP PEAK 1(2P23.2) WILD-TYPE                        45   119
D1V10, multiclass
                                  clus
vv                                 AMP PEAK 1(2P23.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 7
  WHITE                                                    28
                                  clus
vv                                 AMP PEAK 1(2P23.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  45
  WHITE                                                     119
[1] 4 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, binary
                              cls
clus                             0   1
  AMP PEAK 1(2P23.2) MUTATED     2  33
  AMP PEAK 1(2P23.2) WILD-TYPE   7 142
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 1(2P23.2) MUTATED      2   33
  AMP PEAK 1(2P23.2) WILD-TYPE    7  142
                        clus
vv                       AMP PEAK 1(2P23.2) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         33
                        clus
vv                       AMP PEAK 1(2P23.2) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          142
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK 2(2Q32.1) MUTATION ANALYSIS
D2V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 2(2Q32.1) MUTATED    40   1
  AMP PEAK 2(2Q32.1) WILD-TYPE 147   6
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                          41                          153 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                           1                            6 
$`AMP PEAK 2(2Q32.1) MUTATED`
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3471 TCGA-AL-7173 
         516         1968            2          118          412         1357 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B 
          67          223          200          309           14           64 
TCGA-B9-A69E TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
         452         1938          921          364           84         2948 
TCGA-DW-5561 TCGA-DZ-6131 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 
         414         2429           36          208         1575         1194 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NI 
         786          262          112          546         2072          360 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         511           62          364          885          161         1043 
TCGA-P4-A5EB TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ 
        2584          540          428          876         1266 

$`AMP PEAK 2(2Q32.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3472 
         379           87            4         1778         1636          923 
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
         763           26          595          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         108          510           14         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        1049          379         1536          857          803          627 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 
          35          460         1338          671          585          207 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
           5          167           52         2639          586          270 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1454         1242          792          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         233           29         3760         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         116          353         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
         419          114          445           92         1240         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 
          10            7           13         1479         1059          765 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 
         446          194          197         1967         1965         5925 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD 
         393          841           32          378           27          341 
TCGA-GL-A9DE TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40X 
         140          408         1726         2228          167          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z 
         677          649          146          376            4          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 
         493          148         3035         2653         2816          391 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1457         1443         1005          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1175          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                           2                            2 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                        2948                         5925 
  AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE 
                         428                          579 
[1] "2.0 - 2948.0 (428.0)" "2.0 - 5925.0 (579.0)"
[1] "hr=" "1.9"
D2V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 2(2Q32.1) MUTATED        26        2        11        7
  AMP PEAK 2(2Q32.1) WILD-TYPE     111       14        32        6
D2V3, multiclass
           clus
vv          AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  STAGE I                           26                          111
  STAGE II                           2                           14
  STAGE III                         11                           32
  STAGE IV                           7                            6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 2(2Q32.1) MUTATED    26   5    16
  AMP PEAK 2(2Q32.1) WILD-TYPE 120  17    35
D2V4, multiclass
       clus
vv      AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  T1                            26                          120
  T2                             5                           17
  T3+T4                         16                           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"
                              vv
clus                           N0 N1 N2
  AMP PEAK 2(2Q32.1) MUTATED    9  8  2
  AMP PEAK 2(2Q32.1) WILD-TYPE 30 12  2
D2V5, multiclass
    clus
vv   AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  N0                          9                           30
  N1                          8                           12
  N2                          2                            2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  AMP PEAK 2(2Q32.1) MUTATED   15  5 23
  AMP PEAK 2(2Q32.1) WILD-TYPE 73  3 89
D2V6, multiclass
    clus
vv   AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  M0                         15                           73
  M1                          5                            3
  MX                         23                           89
[1] 3 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(2Q32.1) MUTATED    15  32
  AMP PEAK 2(2Q32.1) WILD-TYPE  48 126
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED     15   32
  AMP PEAK 2(2Q32.1) WILD-TYPE   48  126
        clus
vv       AMP PEAK 2(2Q32.1) MUTATED AMP PEAK 2(2Q32.1) WILD-TYPE
  FEMALE                         15                           48
  MALE                           32                          126
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 2(2Q32.1) MUTATED                                  0     1
  AMP PEAK 2(2Q32.1) WILD-TYPE                                2     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 2(2Q32.1) MUTATED                           7    36
  AMP PEAK 2(2Q32.1) WILD-TYPE                        45   111
D2V10, multiclass
                                  clus
vv                                 AMP PEAK 2(2Q32.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                 7
  WHITE                                                    36
                                  clus
vv                                 AMP PEAK 2(2Q32.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  45
  WHITE                                                     111
[1] 4 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, binary
                              cls
clus                             0   1
  AMP PEAK 2(2Q32.1) MUTATED     2  39
  AMP PEAK 2(2Q32.1) WILD-TYPE   7 136
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 2(2Q32.1) MUTATED      2   39
  AMP PEAK 2(2Q32.1) WILD-TYPE    7  136
                        clus
vv                       AMP PEAK 2(2Q32.1) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         39
                        clus
vv                       AMP PEAK 2(2Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          136
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK 3(3Q27.1) MUTATION ANALYSIS
D3V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 3(3Q27.1) MUTATED    64   1
  AMP PEAK 3(3Q27.1) WILD-TYPE 123   6
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                          65                          129 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                           1                            6 
$`AMP PEAK 3(3Q27.1) MUTATED`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8518 
         207           21            2          729          709          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3468 TCGA-AL-3471 
         436          379          516            2         1636          412 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 
          67          223          659          200          930          309 
TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         857           14           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 
          64          167         1454          792          233         2948 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7963 
         214          116         1093         1142          744         1240 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6790 
        2460         1670         1040           10            7         1575 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF 
         197         1967         5925          546          341         2072 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40Y TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         360          167           62          364          885          161 
TCGA-MH-A55W TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71V 
        1043         3035         2653          540          428          876 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-Y8-A895 TCGA-Y8-A8RZ 
         578         1266         1469            2          205 

$`AMP PEAK 3(3Q27.1) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         554          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-A57E 
          49          140          780           23          597         1968 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3472 TCGA-AL-3473 
         118           87            4         1778          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
        1357           26          595          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 
         510           14         1029          307         1049          379 
TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1536          803          627          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         452           52         2639          586          270         1938 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
        1242          792          921          771          403           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364           84         3760         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5560 
        1516          799          612          232          218          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
         414         3950          419          114          445           92 
TCGA-DZ-6131 TCGA-DZ-6134 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY 
        2429         1856          578          757           97           36 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          13          208         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 
         446          786          194          262         1965          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DE 
         112          841           32          378           27          140 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
         408         1726         2228          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-MH-A55Z TCGA-MH-A560 
         649          146          376            4          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71R TCGA-SX-A71S 
         148         2584         2816          391         1457         1443 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SR TCGA-SX-A7SU 
        1005          823         1973         1175          805         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         579          882          224          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          106          104 

  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                           2                            3 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                        5925                         3950 
  AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE 
                         540                          541 
[1] "2.0 - 5925.0 (540.0)" "3.0 - 3950.0 (541.0)"
[1] "hr=" "3.3"
D3V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 3(3Q27.1) MUTATED        53        6        11        3
  AMP PEAK 3(3Q27.1) WILD-TYPE      84       10        32       10
D3V3, multiclass
           clus
vv          AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  STAGE I                           53                           84
  STAGE II                           6                           10
  STAGE III                         11                           32
  STAGE IV                           3                           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T1 T2 T3+T4
  AMP PEAK 3(3Q27.1) MUTATED   55  9    12
  AMP PEAK 3(3Q27.1) WILD-TYPE 91 13    39
D3V4, multiclass
       clus
vv      AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  T1                            55                           91
  T2                             9                           13
  T3+T4                         12                           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"
                              vv
clus                           N0 N1 N2
  AMP PEAK 3(3Q27.1) MUTATED   10  5  1
  AMP PEAK 3(3Q27.1) WILD-TYPE 29 15  3
D3V5, multiclass
    clus
vv   AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  N0                         10                           29
  N1                          5                           15
  N2                          1                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  AMP PEAK 3(3Q27.1) MUTATED   29  0 42
  AMP PEAK 3(3Q27.1) WILD-TYPE 59  8 70
D3V6, multiclass
    clus
vv   AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  M0                         29                           59
  M1                          0                            8
  MX                         42                           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"
D3V7, binary
                              cls
clus                             0   1
  AMP PEAK 3(3Q27.1) MUTATED    19  58
  AMP PEAK 3(3Q27.1) WILD-TYPE  44 100
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.1) MUTATED     19   58
  AMP PEAK 3(3Q27.1) WILD-TYPE   44  100
        clus
vv       AMP PEAK 3(3Q27.1) MUTATED AMP PEAK 3(3Q27.1) WILD-TYPE
  FEMALE                         19                           44
  MALE                           58                          100
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 3(3Q27.1) MUTATED                                  2     1
  AMP PEAK 3(3Q27.1) WILD-TYPE                                0     4
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 3(3Q27.1) MUTATED                          16    50
  AMP PEAK 3(3Q27.1) WILD-TYPE                        36    97
D3V10, multiclass
                                  clus
vv                                 AMP PEAK 3(3Q27.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     1
  BLACK OR AFRICAN AMERICAN                                16
  WHITE                                                    50
                                  clus
vv                                 AMP PEAK 3(3Q27.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       4
  BLACK OR AFRICAN AMERICAN                                  36
  WHITE                                                      97
[1] 4 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, binary
                              cls
clus                             0   1
  AMP PEAK 3(3Q27.1) MUTATED     2  62
  AMP PEAK 3(3Q27.1) WILD-TYPE   7 113
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 3(3Q27.1) MUTATED      2   62
  AMP PEAK 3(3Q27.1) WILD-TYPE    7  113
                        clus
vv                       AMP PEAK 3(3Q27.1) MUTATED
  HISPANIC OR LATINO                              2
  NOT HISPANIC OR LATINO                         62
                        clus
vv                       AMP PEAK 3(3Q27.1) WILD-TYPE
  HISPANIC OR LATINO                                7
  NOT HISPANIC OR LATINO                          113
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK 4(5Q35.2) MUTATION ANALYSIS
D4V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 4(5Q35.2) MUTATED    29   1
  AMP PEAK 4(5Q35.2) WILD-TYPE 158   6
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                          30                          164 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                           1                            6 
$`AMP PEAK 4(5Q35.2) MUTATED`
TCGA-2K-A9WE TCGA-A4-8098 TCGA-A4-8516 TCGA-A4-A48D TCGA-A4-A57E TCGA-AL-3473 
         207          140           23          379         1968          763 
TCGA-B1-5398 TCGA-B1-A656 TCGA-B9-4117 TCGA-B9-A5W9 TCGA-BQ-5878 TCGA-BQ-5887 
         595           14           14            5         1938          771 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-7838 TCGA-EV-5902 TCGA-F9-A7Q0 
         233           29          364          744          578           10 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40X 
          13          208          262           32         2228          608 
TCGA-IA-A40Y TCGA-KV-A6GD TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SQ 
          62          364         3035         2584          428         1266 

$`AMP PEAK 4(5Q35.2) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         554           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          780          729          709 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 
         597          600          436          516            2          118 
TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
          87            4         1778         1636          412          923 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
        1357           26           67          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         513          108          510          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803          627           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
          64          585          207          452          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        2639          586          270         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         921          792          403           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        3950         1093         1142          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 
        1040          757           97            7           36         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1479         1194         1059          765          446          786 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         112          841          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
         140         2072          408          360         1726          167 
TCGA-IA-A40U TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         511          677          649          146          376            4 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2653         2816          391          540         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                           5                            2 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                        3035                         5925 
  AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE 
                         364                          566 
[1] "5.0 - 3035.0 (364.0)" "2.0 - 5925.0 (566.0)"
[1] "hr=" "1.2"
D4V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 4(5Q35.2) MUTATED        15        2        10        3
  AMP PEAK 4(5Q35.2) WILD-TYPE     122       14        33       10
D4V3, multiclass
           clus
vv          AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  STAGE I                           15                          122
  STAGE II                           2                           14
  STAGE III                         10                           33
  STAGE IV                           3                           10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2 T3+T4
  AMP PEAK 4(5Q35.2) MUTATED    17   4    11
  AMP PEAK 4(5Q35.2) WILD-TYPE 129  18    40
D4V4, multiclass
       clus
vv      AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  T1                            17                          129
  T2                             4                           18
  T3+T4                         11                           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"
                              vv
clus                           N0 N1 N2
  AMP PEAK 4(5Q35.2) MUTATED    9  4  1
  AMP PEAK 4(5Q35.2) WILD-TYPE 30 16  3
D4V5, multiclass
    clus
vv   AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  N0                          9                           30
  N1                          4                           16
  N2                          1                            3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           M0 M1 MX
  AMP PEAK 4(5Q35.2) MUTATED   15  2 14
  AMP PEAK 4(5Q35.2) WILD-TYPE 73  6 98
D4V6, multiclass
    clus
vv   AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  M0                         15                           73
  M1                          2                            6
  MX                         14                           98
[1] 3 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(5Q35.2) MUTATED     8  24
  AMP PEAK 4(5Q35.2) WILD-TYPE  55 134
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED      8   24
  AMP PEAK 4(5Q35.2) WILD-TYPE   55  134
        clus
vv       AMP PEAK 4(5Q35.2) MUTATED AMP PEAK 4(5Q35.2) WILD-TYPE
  FEMALE                          8                           55
  MALE                           24                          134
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 4(5Q35.2) MUTATED                                  0     2
  AMP PEAK 4(5Q35.2) WILD-TYPE                                2     3
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 4(5Q35.2) MUTATED                           6    22
  AMP PEAK 4(5Q35.2) WILD-TYPE                        46   125
D4V10, multiclass
                                  clus
vv                                 AMP PEAK 4(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          0
  ASIAN                                                     2
  BLACK OR AFRICAN AMERICAN                                 6
  WHITE                                                    22
                                  clus
vv                                 AMP PEAK 4(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            2
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  46
  WHITE                                                     125
[1] 4 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, binary
                              cls
clus                             0   1
  AMP PEAK 4(5Q35.2) MUTATED     0  27
  AMP PEAK 4(5Q35.2) WILD-TYPE   9 148
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 4(5Q35.2) MUTATED      0   27
  AMP PEAK 4(5Q35.2) WILD-TYPE    9  148
                        clus
vv                       AMP PEAK 4(5Q35.2) MUTATED
  HISPANIC OR LATINO                              0
  NOT HISPANIC OR LATINO                         27
                        clus
vv                       AMP PEAK 4(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                9
  NOT HISPANIC OR LATINO                          148
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK 5(7Q31.2) MUTATION ANALYSIS
D5V1, survival
                              sevent
clus2                            0   1
  AMP PEAK 5(7Q31.2) MUTATED   117   3
  AMP PEAK 5(7Q31.2) WILD-TYPE  70   4
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         120                           74 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                           3                            4 
$`AMP PEAK 5(7Q31.2) MUTATED`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
         207          493          582           27           49            2 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
         780          729          709           23          597          436 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 
         516         1968            2            4         1636          412 
TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N 
         923         1357           26           67          659          747 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 
         108           14          200         1029          930          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH 
          35          460         1338          671          585          167 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
        1454          792          771           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        3760         2948         1533          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
         744          114          445           92         1240         2460 
TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
        1856         1040          757           10            7           36 
TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
         208         1575         1194          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A59R 
         262         1965         5925          112          841          378 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         546          341         2072          408          360         1726 
TCGA-HE-A5NL TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
         167           62          649          146          376          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z 
         885          161         1043          845          616          148 
TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2653          540          428         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
         876         1973          578         1266          805         1469 
TCGA-SX-A7SU TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
        1331            2          186          181          399          106 

$`AMP PEAK 5(7Q31.2) WILD-TYPE`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8518 
         554           21            3            7          140          600 
TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
         379          118           87         1778          763          595 
TCGA-B1-7332 TCGA-B1-A47O TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-A44B 
         223          513          510          307         1049           64 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
         207            5          452           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 
         270         1938         1242          921          792          403 
TCGA-BQ-5890 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
         233         2839         1864         1516          799          612 
TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A97G 
         419         2429         1670          578           97           13 
TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 
        1479         1059          765          446         1967          393 
TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X 
          32           27          140         2228          511          608 
TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 
         677            4          924          841           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         541          493         3035         2584         2816          391 
TCGA-SX-A7SL TCGA-SX-A7SO TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 
         823         1175          579          882          224          219 
TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         205          104 

  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                           2                            3 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                        5925                         3035 
  AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE 
                         543                          527 
[1] "2.0 - 5925.0 (543.0)" "3.0 - 3035.0 (527.0)"
[1] "hr=" "1.9"
D5V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 5(7Q31.2) MUTATED        92        7        15       10
  AMP PEAK 5(7Q31.2) WILD-TYPE      45        9        28        3
D5V3, multiclass
           clus
vv          AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  STAGE I                           92                           45
  STAGE II                           7                            9
  STAGE III                         15                           28
  STAGE IV                          10                            3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           T1 T2 T3+T4
  AMP PEAK 5(7Q31.2) MUTATED   95 14    23
  AMP PEAK 5(7Q31.2) WILD-TYPE 51  8    28
D5V4, multiclass
       clus
vv      AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  T1                            95                           51
  T2                            14                            8
  T3+T4                         23                           28
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                           N0 N1 N2
  AMP PEAK 5(7Q31.2) MUTATED   18  7  3
  AMP PEAK 5(7Q31.2) WILD-TYPE 21 13  1
D5V5, multiclass
    clus
vv   AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  N0                         18                           21
  N1                          7                           13
  N2                          3                            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"
                              vv
clus                           M0 M1 MX
  AMP PEAK 5(7Q31.2) MUTATED   49  5 69
  AMP PEAK 5(7Q31.2) WILD-TYPE 39  3 43
D5V6, multiclass
    clus
vv   AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  M0                         49                           39
  M1                          5                            3
  MX                         69                           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"
D5V7, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED    32 101
  AMP PEAK 5(7Q31.2) WILD-TYPE  31  57
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED     32  101
  AMP PEAK 5(7Q31.2) WILD-TYPE   31   57
        clus
vv       AMP PEAK 5(7Q31.2) MUTATED AMP PEAK 5(7Q31.2) WILD-TYPE
  FEMALE                         32                           31
  MALE                          101                           57
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                              vv
clus                           AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 5(7Q31.2) MUTATED                                  2     3
  AMP PEAK 5(7Q31.2) WILD-TYPE                                0     2
                              vv
clus                           BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 5(7Q31.2) MUTATED                          30    87
  AMP PEAK 5(7Q31.2) WILD-TYPE                        22    60
D5V10, multiclass
                                  clus
vv                                 AMP PEAK 5(7Q31.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                          2
  ASIAN                                                     3
  BLACK OR AFRICAN AMERICAN                                30
  WHITE                                                    87
                                  clus
vv                                 AMP PEAK 5(7Q31.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  22
  WHITE                                                      60
[1] 4 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, binary
                              cls
clus                             0   1
  AMP PEAK 5(7Q31.2) MUTATED     4 110
  AMP PEAK 5(7Q31.2) WILD-TYPE   5  65
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK 5(7Q31.2) MUTATED      4  110
  AMP PEAK 5(7Q31.2) WILD-TYPE    5   65
                        clus
vv                       AMP PEAK 5(7Q31.2) MUTATED
  HISPANIC OR LATINO                              4
  NOT HISPANIC OR LATINO                        110
                        clus
vv                       AMP PEAK 5(7Q31.2) WILD-TYPE
  HISPANIC OR LATINO                                5
  NOT HISPANIC OR LATINO                           65
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK 6(17Q25.2) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 6(17Q25.2) MUTATED   136   5
  AMP PEAK 6(17Q25.2) WILD-TYPE  51   2
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          141                            53 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                            5                             2 
$`AMP PEAK 6(17Q25.2) MUTATED`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          554          493          582           27            7 
TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ 
         597          600          436          516         1968            2 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118           87            4         1636          412          923 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          26           67          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 
         108          510          200         1029          930         1049 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
         379          309         1536          857          803           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5881 TCGA-BQ-5886 
           5          167         2639          270         1454          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7046 
         771          403          233           29          364         2948 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
        1533         1516          214          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 
        1040          757           10            7           36          208 
TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1575         1194         1059          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM 
         262         1967         1965         5925          112           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH 
         378          546           27          341         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 
         360         1726          167          511           62          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146          376            4          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
         148         2653         2584         2816          540          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN 
        1457         1443         1005          876          823          578 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A895 
        1266          805         1469         1331          882            2 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
         181          399          106 

$`AMP PEAK 6(17Q25.2) WILD-TYPE`
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7997 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3473 
          21            3            2          379         1778          763 
TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A656 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A5W8 
        1357          595           14          307          627          207 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 
         452           52          586         1938         1242          792 
TCGA-BQ-5885 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7055 
         921           84         3760         2839         1864          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A4JJ 
         612          232          218         1670          578           97 
TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-GL-7773 TCGA-GL-8500 
          13         1479          765          446          393          841 
TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         140         2228          608           11          369          541 
TCGA-MH-A857 TCGA-P4-A5E6 TCGA-PJ-A5Z8 TCGA-SX-A7SM TCGA-SX-A7SO TCGA-WN-A9G9 
         493         3035          391         1973         1175          579 
TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         224          186          219          205          104 

  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                            2                             2 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                         5925                          3760 
  AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE 
                          540                           541 
[1] "2.0 - 5925.0 (540.0)" "2.0 - 3760.0 (541.0)"
[1] "hr=" "1"  
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 6(17Q25.2) MUTATED       103       11        26        9
  AMP PEAK 6(17Q25.2) WILD-TYPE      34        5        17        4
D6V3, multiclass
           clus
vv          AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  STAGE I                           103                            34
  STAGE II                           11                             5
  STAGE III                          26                            17
  STAGE IV                            9                             4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  AMP PEAK 6(17Q25.2) MUTATED   107  17    33
  AMP PEAK 6(17Q25.2) WILD-TYPE  39   5    18
D6V4, multiclass
       clus
vv      AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  T1                            107                            39
  T2                             17                             5
  T3+T4                          33                            18
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  AMP PEAK 6(17Q25.2) MUTATED   26 12  3
  AMP PEAK 6(17Q25.2) WILD-TYPE 13  8  1
D6V5, multiclass
    clus
vv   AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  N0                          26                            13
  N1                          12                             8
  N2                           3                             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"
                               vv
clus                            M0 M1 MX
  AMP PEAK 6(17Q25.2) MUTATED   53  5 89
  AMP PEAK 6(17Q25.2) WILD-TYPE 35  3 23
D6V6, multiclass
    clus
vv   AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  M0                          53                            35
  M1                           5                             3
  MX                          89                            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"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK 6(17Q25.2) MUTATED    40 118
  AMP PEAK 6(17Q25.2) WILD-TYPE  23  40
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED     40  118
  AMP PEAK 6(17Q25.2) WILD-TYPE   23   40
        clus
vv       AMP PEAK 6(17Q25.2) MUTATED AMP PEAK 6(17Q25.2) WILD-TYPE
  FEMALE                          40                            23
  MALE                           118                            40
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 6(17Q25.2) MUTATED                                  2     4
  AMP PEAK 6(17Q25.2) WILD-TYPE                                0     1
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 6(17Q25.2) MUTATED                          33   109
  AMP PEAK 6(17Q25.2) WILD-TYPE                        19    38
D6V10, multiclass
                                  clus
vv                                 AMP PEAK 6(17Q25.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      4
  BLACK OR AFRICAN AMERICAN                                 33
  WHITE                                                    109
                                  clus
vv                                 AMP PEAK 6(17Q25.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             0
  ASIAN                                                        1
  BLACK OR AFRICAN AMERICAN                                   19
  WHITE                                                       38
[1] 4 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, binary
                               cls
clus                              0   1
  AMP PEAK 6(17Q25.2) MUTATED     6 129
  AMP PEAK 6(17Q25.2) WILD-TYPE   3  46
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 6(17Q25.2) MUTATED      6  129
  AMP PEAK 6(17Q25.2) WILD-TYPE    3   46
                        clus
vv                       AMP PEAK 6(17Q25.2) MUTATED
  HISPANIC OR LATINO                               6
  NOT HISPANIC OR LATINO                         129
                        clus
vv                       AMP PEAK 6(17Q25.2) WILD-TYPE
  HISPANIC OR LATINO                                 3
  NOT HISPANIC OR LATINO                            46
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK 7(19P13.2) MUTATION ANALYSIS
D7V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 7(19P13.2) MUTATED    20   1
  AMP PEAK 7(19P13.2) WILD-TYPE 167   6
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                           21                           173 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                            1                             6 
$`AMP PEAK 7(19P13.2) MUTATED`
TCGA-A4-7732 TCGA-A4-A5XZ TCGA-AL-3472 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 
         582            2          923         1536          627           35 
TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-DW-5561 TCGA-DW-7840 TCGA-EV-5901 
         921           29          364          414          114         1040 
TCGA-F9-A7Q0 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LC TCGA-GL-7966 TCGA-HE-A5NJ 
          10         1194          194          262          112         1726 
TCGA-IZ-8196 TCGA-P4-A5E7 TCGA-SX-A7SU 
         649         2653         1331 

$`AMP PEAK 7(19P13.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7734 
         207          554           21          493            3           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
         516         1968          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
        1636          412          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
        1049          379          309          857          803           14 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          452          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
         270         1938         1454         1242          792          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         771          403          233           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 
         232          214          218          116          353         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7841 TCGA-DW-7842 
        1093         1142          744          419          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5902 
        1240         2429         2460         1856         1670          578 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
         757           97            7           36           13          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 
        1575         1479         1059          765          446          786 
TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         197         1967         1965         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         2228          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608           62          677          146          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
         148         3035         2584         2816          391          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         428         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         579          882          224            2          186          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                            2                             2 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                         2653                          5925 
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                          582                           540 
[1] "2.0 - 2653.0 (582.0)" "2.0 - 5925.0 (540.0)"
[1] "hr=" "1.7"
D7V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 7(19P13.2) MUTATED        14        1         3        0
  AMP PEAK 7(19P13.2) WILD-TYPE     123       15        40       13
D7V3, multiclass
           clus
vv          AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  STAGE I                            14                           123
  STAGE II                            1                            15
  STAGE III                           3                            40
  STAGE IV                            0                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  AMP PEAK 7(19P13.2) MUTATED    15   5     3
  AMP PEAK 7(19P13.2) WILD-TYPE 131  17    48
D7V4, multiclass
       clus
vv      AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  T1                             15                           131
  T2                              5                            17
  T3+T4                           3                            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"
                               vv
clus                            N0 N1 N2
  AMP PEAK 7(19P13.2) MUTATED    5  1  0
  AMP PEAK 7(19P13.2) WILD-TYPE 34 19  4
D7V5, multiclass
    clus
vv   AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  N0                           5                            34
  N1                           1                            19
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  AMP PEAK 7(19P13.2) MUTATED    11   0  10
  AMP PEAK 7(19P13.2) WILD-TYPE  77   8 102
D7V6, multiclass
    clus
vv   AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  M0                          11                            77
  M1                           0                             8
  MX                          10                           102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                               cls
clus                              0   1
  AMP PEAK 7(19P13.2) MUTATED     8  15
  AMP PEAK 7(19P13.2) WILD-TYPE  55 143
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      8   15
  AMP PEAK 7(19P13.2) WILD-TYPE   55  143
        clus
vv       AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE
  FEMALE                           8                            55
  MALE                            15                           143
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK 7(19P13.2) MUTATED"
clus
  AMP PEAK 7(19P13.2) MUTATED AMP PEAK 7(19P13.2) WILD-TYPE 
                            2                            33 
                   TCGA-A4-A48D                    TCGA-A4-A57E 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-A4-A5Y0                    TCGA-B1-A654 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-B9-A44B                    TCGA-B9-A69E 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-F9-A97G                    TCGA-G7-A8LB 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-G7-A8LD                    TCGA-G7-A8LE 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-GL-7773                    TCGA-GL-A59T 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-GL-A9DD                    TCGA-HE-A5NI 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-HE-A5NK                    TCGA-IA-A40U 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-IA-A83S                    TCGA-IZ-A6M8 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-MH-A854                    TCGA-MH-A856 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-P4-A5EB                    TCGA-PJ-A5Z9 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-Q2-A5QZ                    TCGA-SX-A71S 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-SX-A71U                    TCGA-SX-A7SL 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-SX-A7SR 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-SX-A7SS                    TCGA-WN-A9G9 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-Y8-A894                    TCGA-Y8-A896 
"AMP PEAK 7(19P13.2) WILD-TYPE" "AMP PEAK 7(19P13.2) WILD-TYPE" 
                   TCGA-Y8-A8RZ 
"AMP PEAK 7(19P13.2) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  AMP PEAK 7(19P13.2) MUTATED                                  0     1
  AMP PEAK 7(19P13.2) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 7(19P13.2) MUTATED                           8    11
  AMP PEAK 7(19P13.2) WILD-TYPE                        44   136
D7V10, multiclass
                                  clus
vv                                 AMP PEAK 7(19P13.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  8
  WHITE                                                     11
                                  clus
vv                                 AMP PEAK 7(19P13.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   44
  WHITE                                                      136
[1] 4 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, binary
                               cls
clus                              0   1
  AMP PEAK 7(19P13.2) MUTATED     1  19
  AMP PEAK 7(19P13.2) WILD-TYPE   8 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 7(19P13.2) MUTATED      1   19
  AMP PEAK 7(19P13.2) WILD-TYPE    8  156
                        clus
vv                       AMP PEAK 7(19P13.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       AMP PEAK 7(19P13.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           156
[1] 2 2
[1] FALSE

Clustering(8) Variable = DEL PEAK  1(1P36.31) MUTATION ANALYSIS
D8V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.31) MUTATED    33   5
  DEL PEAK  1(1P36.31) WILD-TYPE 154   2
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                            38                            156 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             5                              2 
$`DEL PEAK  1(1P36.31) MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-8098 TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-AL-A5DJ 
         554            3          140            2           87           26 
TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E 
         223          307          627           64          207          452 
TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5894 
        2639          270          921          403          233           84 
TCGA-BQ-7044 TCGA-BQ-7055 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
        3760          799          578           97           10          208 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 
         765          446          786          262         1967          112 
TCGA-GL-8500 TCGA-HE-A5NK TCGA-IA-A40Y TCGA-J7-8537 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
         841         2228           62            4          391          428 
TCGA-WN-A9G9 TCGA-Y8-A8RZ 
         579          205 

$`DEL PEAK  1(1P36.31) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207           21          493          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49            2          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
         597          600          436          379          516         1968 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N 
         763         1357           67          595          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803           14           35          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 
         585            5          167           52          586         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5891 
        1454         1242          792          792          771           29 
TCGA-BQ-5892 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
         364         2948         2839         1864         1533         1516 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
        1856         1670         1040          757            7           36 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM 
          13         1575         1479         1194         1059          194 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-A4EM TCGA-GL-A59R 
         197         1965         5925          393           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
         360         1726          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         649          146          376          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2584         2816          540         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
         805         1469         1331          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         186          219          181          399          106          104 

  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                             2                              2 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                          3760                           5925 
  DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE 
                         288.5                          590.5 
[1] "2.0 - 3760.0 (288.5)" "2.0 - 5925.0 (590.5)"
[1] "hr=" "12" 
D8V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.31) MUTATED        13        3        19        4
  DEL PEAK  1(1P36.31) WILD-TYPE     124       13        24        9
D8V3, multiclass
           clus
vv          DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  STAGE I                             13                            124
  STAGE II                             3                             13
  STAGE III                           19                             24
  STAGE IV                             4                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK  1(1P36.31) MUTATED    16   4    22
  DEL PEAK  1(1P36.31) WILD-TYPE 130  18    29
D8V4, multiclass
       clus
vv      DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  T1                              16                            130
  T2                               4                             18
  T3+T4                           22                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK  1(1P36.31) MUTATED    6 11  1
  DEL PEAK  1(1P36.31) WILD-TYPE 33  9  3
D8V5, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  N0                            6                             33
  N1                           11                              9
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK  1(1P36.31) MUTATED   16  3 19
  DEL PEAK  1(1P36.31) WILD-TYPE 72  5 93
D8V6, multiclass
    clus
vv   DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  M0                           16                             72
  M1                            3                              5
  MX                           19                             93
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED    18  24
  DEL PEAK  1(1P36.31) WILD-TYPE  45 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED     18   24
  DEL PEAK  1(1P36.31) WILD-TYPE   45  134
        clus
vv       DEL PEAK  1(1P36.31) MUTATED DEL PEAK  1(1P36.31) WILD-TYPE
  FEMALE                           18                             45
  MALE                             24                            134
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  1(1P36.31) MUTATED                                  0     2
  DEL PEAK  1(1P36.31) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.31) MUTATED                          10    27
  DEL PEAK  1(1P36.31) WILD-TYPE                        42   120
D8V10, multiclass
                                  clus
vv                                 DEL PEAK  1(1P36.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      27
                                  clus
vv                                 DEL PEAK  1(1P36.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       120
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.31) MUTATED     1  31
  DEL PEAK  1(1P36.31) WILD-TYPE   8 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.31) MUTATED      1   31
  DEL PEAK  1(1P36.31) WILD-TYPE    8  144
                        clus
vv                       DEL PEAK  1(1P36.31) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           31
                        clus
vv                       DEL PEAK  1(1P36.31) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            144
[1] 2 2
[1] FALSE

Clustering(9) Variable = DEL PEAK  2(2P12) MUTATION ANALYSIS
D9V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  2(2P12) MUTATED     4   0
  DEL PEAK  2(2P12) WILD-TYPE 183   7
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          4                         190 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          0                           7 
$`DEL PEAK  2(2P12) MUTATED`
TCGA-A4-A57E TCGA-BQ-5875 TCGA-BQ-5885 TCGA-G7-6792 
        1968         2639          921         1479 

$`DEL PEAK  2(2P12) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         379          516            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
          26           67          595          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         307          930         1049          379          309         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         452          167           52          586          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1454         1242          792          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6795 
           7           36           13          208         1575         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1059          765          446          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         262         1967         1965         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
        1175         1266          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                        921                           2 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                       2639                        5925 
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                     1723.5                       514.5 
[1] "921.0 - 2639.0 (1723.5)" "2.0 - 5925.0 (514.5)"   
[1] "hr="     "2.7e+07"
D9V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(2P12) MUTATED         1        0         2        1
  DEL PEAK  2(2P12) WILD-TYPE     136       16        41       12
D9V3, multiclass
           clus
vv          DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  STAGE I                           1                         136
  STAGE II                          0                          16
  STAGE III                         2                          41
  STAGE IV                          1                          12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2 T3+T4
  DEL PEAK  2(2P12) MUTATED     1   1     2
  DEL PEAK  2(2P12) WILD-TYPE 145  21    49
D9V4, multiclass
       clus
vv      DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  T1                            1                         145
  T2                            1                          21
  T3+T4                         2                          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"
                             vv
clus                          N0 N1 N2
  DEL PEAK  2(2P12) MUTATED    2  0  0
  DEL PEAK  2(2P12) WILD-TYPE 37 20  4
D9V5, multiclass
[1] "Remove cluster labels:"    "DEL PEAK  2(2P12) MUTATED"
clus
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          2                          61 
                 TCGA-A4-7583                  TCGA-A4-7585 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-7915                  TCGA-A4-A5Y1 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-AL-3466                  TCGA-AL-3472 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-AL-3473                  TCGA-AL-7173 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B1-5398                  TCGA-B1-A47O 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B1-A655                  TCGA-B1-A656 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B1-A657                  TCGA-B9-7268 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-5877                  TCGA-BQ-5878 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-5879                  TCGA-BQ-5880 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-5882                  TCGA-BQ-5887 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-5888                  TCGA-BQ-5889 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-5890                  TCGA-BQ-5891 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-5892                  TCGA-BQ-5893 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-5894                  TCGA-BQ-7045 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-7048                  TCGA-BQ-7050 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-7051                  TCGA-BQ-7056 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-BQ-7058                  TCGA-DW-7963 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DZ-6131                  TCGA-F9-A8NY 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-F9-A97G                  TCGA-G7-6789 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-6793                  TCGA-G7-6795 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-7501                  TCGA-G7-A8LD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-GL-6846                  TCGA-GL-7966 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-GL-A59R                  TCGA-GL-A9DC 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-IA-A40U                  TCGA-IA-A40Y 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-IA-A83W                  TCGA-J7-6720 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-J7-8537                  TCGA-KV-A74V 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-P4-A5E6                  TCGA-P4-A5E8 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-P4-A5EA                  TCGA-SX-A71R 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SM                  TCGA-SX-A7SP 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SS                  TCGA-Y8-A897 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Y8-A8RZ 
"DEL PEAK  2(2P12) WILD-TYPE" 
                             vv
clus                           M0  M1  MX
  DEL PEAK  2(2P12) MUTATED     2   1   1
  DEL PEAK  2(2P12) WILD-TYPE  86   7 111
D9V6, multiclass
    clus
vv   DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  M0                         2                          86
  M1                         1                           7
  MX                         1                         111
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                             cls
clus                            0   1
  DEL PEAK  2(2P12) MUTATED     1   3
  DEL PEAK  2(2P12) WILD-TYPE  62 155
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(2P12) MUTATED      1    3
  DEL PEAK  2(2P12) WILD-TYPE   62  155
        clus
vv       DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  FEMALE                         1                          62
  MALE                           3                         155
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:"    "DEL PEAK  2(2P12) MUTATED"
clus
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          1                          55 
                 TCGA-A4-7286                  TCGA-A4-7828 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-8310                  TCGA-A4-8311 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-8312                  TCGA-A4-8518 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-8630                  TCGA-A4-A4ZT 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-A5DU                  TCGA-A4-A5XZ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-A4-A6HP                  TCGA-AL-3466 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-5560                  TCGA-DW-5561 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7834                  TCGA-DW-7836 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7837                  TCGA-DW-7838 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7839                  TCGA-DW-7840 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7841                  TCGA-DW-7842 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-DW-7963                  TCGA-EV-5901 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-EV-5902                  TCGA-EV-5903 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-6790                  TCGA-G7-6793 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-6796                  TCGA-G7-6797 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-7501                  TCGA-G7-7502 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A4TM                  TCGA-G7-A8LB 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LC                  TCGA-G7-A8LD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LE                  TCGA-IA-A40U 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-IA-A40X                  TCGA-IA-A40Y 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-J7-8537                  TCGA-Q2-A5QZ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A71R                  TCGA-SX-A71S 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A71U                  TCGA-SX-A71V 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SL                  TCGA-SX-A7SM 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SN                  TCGA-SX-A7SO 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SP                  TCGA-SX-A7SQ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SR                  TCGA-SX-A7SS 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SU 
"DEL PEAK  2(2P12) WILD-TYPE" 
D9V9, continuous
[1] "Remove cluster labels:"    "DEL PEAK  2(2P12) MUTATED"
clus
  DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE 
                          1                          34 
                 TCGA-A4-A48D                  TCGA-A4-A5Y0 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B1-A654                  TCGA-B9-A44B 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-B9-A69E                  TCGA-F9-A97G 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LB                  TCGA-G7-A8LD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-G7-A8LE                  TCGA-GL-7773 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-GL-A59T                  TCGA-GL-A9DD 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-HE-A5NI                  TCGA-HE-A5NJ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-HE-A5NK                  TCGA-IA-A40U 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-IA-A83S                  TCGA-IZ-A6M8 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-MH-A854                  TCGA-MH-A856 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-P4-A5E7                  TCGA-P4-A5EB 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-PJ-A5Z9                  TCGA-Q2-A5QZ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A71S                  TCGA-SX-A71U 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SL                  TCGA-SX-A7SM 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-SX-A7SR                  TCGA-SX-A7SS 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-WN-A9G9                  TCGA-Y8-A894 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                 TCGA-Y8-A896                  TCGA-Y8-A8RZ 
"DEL PEAK  2(2P12) WILD-TYPE" "DEL PEAK  2(2P12) WILD-TYPE" 
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  2(2P12) MUTATED                                  0     0
  DEL PEAK  2(2P12) WILD-TYPE                                2     5
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(2P12) MUTATED                           1     3
  DEL PEAK  2(2P12) WILD-TYPE                        51   144
D9V10, multiclass
                                  clus
vv                                 DEL PEAK  2(2P12) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    0
  BLACK OR AFRICAN AMERICAN                                1
  WHITE                                                    3
                                  clus
vv                                 DEL PEAK  2(2P12) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      5
  BLACK OR AFRICAN AMERICAN                                 51
  WHITE                                                    144
[1] 4 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, binary
                             cls
clus                            0   1
  DEL PEAK  2(2P12) MUTATED     0   3
  DEL PEAK  2(2P12) WILD-TYPE   9 172
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  2(2P12) MUTATED      0    3
  DEL PEAK  2(2P12) WILD-TYPE    9  172
                        clus
vv                       DEL PEAK  2(2P12) MUTATED DEL PEAK  2(2P12) WILD-TYPE
  HISPANIC OR LATINO                             0                           9
  NOT HISPANIC OR LATINO                         3                         172
[1] 2 2
[1] FALSE

Clustering(10) Variable = DEL PEAK  3(2Q22.1) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  3(2Q22.1) MUTATED     4   1
  DEL PEAK  3(2Q22.1) WILD-TYPE 183   6
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            5                           189 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            1                             6 
$`DEL PEAK  3(2Q22.1) MUTATED`
TCGA-A4-A5Y1 TCGA-B9-A69E TCGA-BQ-5878 TCGA-BQ-5888 TCGA-Q2-A5QZ 
          87          452         1938          403          428 

$`DEL PEAK  3(2Q22.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
          26           67          595          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         307          930         1049          379          309         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 
         167           52         2639          586          270         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 
        1242          792          921          792          771          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
          29          364           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1040          578          757           97           10            7 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          36           13          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1059          765          446          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         262         1967         1965         5925          393          112 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
        2584         2816          391          540         1457         1443 
TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1005          876          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                           87                             2 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                         1938                          5925 
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                          428                           546 
[1] "87.0 - 1938.0 (428.0)" "2.0 - 5925.0 (546.0)" 
[1] "hr=" "8.1"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(2Q22.1) MUTATED         1        0         5        1
  DEL PEAK  3(2Q22.1) WILD-TYPE     136       16        38       12
D10V3, multiclass
           clus
vv          DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  STAGE I                             1                           136
  STAGE II                            0                            16
  STAGE III                           5                            38
  STAGE IV                            1                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK  3(2Q22.1) MUTATED     2   0     5
  DEL PEAK  3(2Q22.1) WILD-TYPE 144  22    46
D10V4, multiclass
       clus
vv      DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  T1                              2                           144
  T2                              0                            22
  T3+T4                           5                            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"
                               vv
clus                            N0 N1 N2
  DEL PEAK  3(2Q22.1) MUTATED    1  3  0
  DEL PEAK  3(2Q22.1) WILD-TYPE 38 17  4
D10V5, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  N0                           1                            38
  N1                           3                            17
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  3(2Q22.1) MUTATED     3   1   2
  DEL PEAK  3(2Q22.1) WILD-TYPE  85   7 110
D10V6, multiclass
    clus
vv   DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  M0                           3                            85
  M1                           1                             7
  MX                           2                           110
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     4   3
  DEL PEAK  3(2Q22.1) WILD-TYPE  59 155
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      4    3
  DEL PEAK  3(2Q22.1) WILD-TYPE   59  155
        clus
vv       DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE
  FEMALE                           4                            59
  MALE                             3                           155
[1] 2 2
[1] FALSE
D10V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  3(2Q22.1) MUTATED"
clus
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            2                            54 
                   TCGA-A4-7286                    TCGA-A4-7828 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-A4-8310                    TCGA-A4-8311 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-A4-8312                    TCGA-A4-8518 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-A4-8630                    TCGA-A4-A4ZT 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-A4-A57E                    TCGA-A4-A5DU 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-A4-A5XZ                    TCGA-A4-A6HP 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-DW-5560                    TCGA-DW-5561 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-DW-7834                    TCGA-DW-7836 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-DW-7837                    TCGA-DW-7838 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-DW-7839                    TCGA-DW-7840 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-DW-7841                    TCGA-DW-7842 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-DW-7963                    TCGA-EV-5901 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-EV-5902                    TCGA-EV-5903 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-G7-6790                    TCGA-G7-6793 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-G7-6796                    TCGA-G7-6797 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-G7-7501                    TCGA-G7-7502 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-G7-A4TM                    TCGA-G7-A8LB 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-G7-A8LC                    TCGA-G7-A8LD 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-G7-A8LE                    TCGA-IA-A40U 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-IA-A40X                    TCGA-IA-A40Y 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-J7-8537                    TCGA-SX-A71R 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A71S                    TCGA-SX-A71U 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A71V                    TCGA-SX-A7SL 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-SX-A7SN 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A7SO                    TCGA-SX-A7SP 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A7SQ                    TCGA-SX-A7SR 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A7SS                    TCGA-SX-A7SU 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
D10V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK  3(2Q22.1) MUTATED"
clus
  DEL PEAK  3(2Q22.1) MUTATED DEL PEAK  3(2Q22.1) WILD-TYPE 
                            2                            33 
                   TCGA-A4-A48D                    TCGA-A4-A57E 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-A4-A5Y0                    TCGA-B1-A654 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-B9-A44B                    TCGA-F9-A97G 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-G7-A8LB                    TCGA-G7-A8LD 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-G7-A8LE                    TCGA-GL-7773 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-GL-A59T                    TCGA-GL-A9DD 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-HE-A5NI                    TCGA-HE-A5NJ 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-HE-A5NK                    TCGA-IA-A40U 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-IA-A83S                    TCGA-IZ-A6M8 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-MH-A854                    TCGA-MH-A856 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-P4-A5E7                    TCGA-P4-A5EB 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-PJ-A5Z9                    TCGA-SX-A71S 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A71U                    TCGA-SX-A7SL 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A7SM                    TCGA-SX-A7SR 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-SX-A7SS                    TCGA-WN-A9G9 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-Y8-A894                    TCGA-Y8-A896 
"DEL PEAK  3(2Q22.1) WILD-TYPE" "DEL PEAK  3(2Q22.1) WILD-TYPE" 
                   TCGA-Y8-A8RZ 
"DEL PEAK  3(2Q22.1) WILD-TYPE" 
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  3(2Q22.1) MUTATED                                  0     0
  DEL PEAK  3(2Q22.1) WILD-TYPE                                2     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(2Q22.1) MUTATED                           1     5
  DEL PEAK  3(2Q22.1) WILD-TYPE                        51   142
D10V10, multiclass
                                  clus
vv                                 DEL PEAK  3(2Q22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      5
                                  clus
vv                                 DEL PEAK  3(2Q22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   51
  WHITE                                                      142
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK  3(2Q22.1) MUTATED     0   4
  DEL PEAK  3(2Q22.1) WILD-TYPE   9 171
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  3(2Q22.1) MUTATED      0    4
  DEL PEAK  3(2Q22.1) WILD-TYPE    9  171
                        clus
vv                       DEL PEAK  3(2Q22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           4
                        clus
vv                       DEL PEAK  3(2Q22.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           171
[1] 2 2
[1] FALSE

Clustering(11) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED     8   0
  DEL PEAK  4(2Q37.3) WILD-TYPE 179   7
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            8                           186 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            0                             7 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-A4-A5Y0 TCGA-B3-4104 TCGA-B9-4117 TCGA-B9-A69E TCGA-BQ-5878 TCGA-MH-A855 
         118         1049           14          452         1938          369 
TCGA-Q2-A5QZ TCGA-Y8-A8RZ 
         428          205 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y1 TCGA-A4-A6HP 
         379          516         1968            2           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
          26           67          595          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         307          930          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         803          627           35          460         1338          671 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI 
          64          585          207            5          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
        2639          586          270         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 
         921          792          771          403          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1240         2429         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          13          208         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
         765          446          786          194          197          262 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
        1967         1965         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         845          924          841          616           11          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         493          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         186          219          181          399          106          104 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           14                             2 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         1938                          5925 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                        398.5                         550.0 
[1] "14.0 - 1938.0 (398.5)" "2.0 - 5925.0 (550.0)" 
[1] "hr="     "2.6e+07"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED         2        2         5        0
  DEL PEAK  4(2Q37.3) WILD-TYPE     135       14        38       13
D11V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                             2                           135
  STAGE II                            2                            14
  STAGE III                           5                            38
  STAGE IV                            0                            13
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK  4(2Q37.3) MUTATED     2   3     5
  DEL PEAK  4(2Q37.3) WILD-TYPE 144  19    46
D11V4, multiclass
       clus
vv      DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                              2                           144
  T2                              3                            19
  T3+T4                           5                            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"
                               vv
clus                            N0 N1 N2
  DEL PEAK  4(2Q37.3) MUTATED    2  1  0
  DEL PEAK  4(2Q37.3) WILD-TYPE 37 19  4
D11V5, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  N0                           2                            37
  N1                           1                            19
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  4(2Q37.3) MUTATED     4   0   4
  DEL PEAK  4(2Q37.3) WILD-TYPE  84   8 108
D11V6, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  M0                           4                            84
  M1                           0                             8
  MX                           4                           108
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     6   4
  DEL PEAK  4(2Q37.3) WILD-TYPE  57 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      6    4
  DEL PEAK  4(2Q37.3) WILD-TYPE   57  154
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                           6                            57
  MALE                             4                           154
[1] 2 2
[1] FALSE
D11V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  4(2Q37.3) MUTATED"
clus
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            1                            55 
                   TCGA-A4-7286                    TCGA-A4-7828 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8310                    TCGA-A4-8311 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8312                    TCGA-A4-8518 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-8630                    TCGA-A4-A4ZT 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A57E                    TCGA-A4-A5DU 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-A4-A5XZ                    TCGA-A4-A6HP 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-AL-3466                    TCGA-DW-5560 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-5561                    TCGA-DW-7834 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7836                    TCGA-DW-7837 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7838                    TCGA-DW-7839 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7840                    TCGA-DW-7841 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DW-7842                    TCGA-DW-7963 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-EV-5901                    TCGA-EV-5902 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-EV-5903                    TCGA-G7-6790 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6793                    TCGA-G7-6796 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-6797                    TCGA-G7-7501 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-7502                    TCGA-G7-A4TM 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-A8LB                    TCGA-G7-A8LC 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-G7-A8LD                    TCGA-G7-A8LE 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-IA-A40U                    TCGA-IA-A40X 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-IA-A40Y                    TCGA-J7-8537 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A71R                    TCGA-SX-A71S 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A71U                    TCGA-SX-A71V 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SL                    TCGA-SX-A7SM 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SN                    TCGA-SX-A7SO 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SP                    TCGA-SX-A7SQ 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SR                    TCGA-SX-A7SS 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-SX-A7SU 
"DEL PEAK  4(2Q37.3) WILD-TYPE" 
D11V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  4(2Q37.3) MUTATED                                  0     0
  DEL PEAK  4(2Q37.3) WILD-TYPE                                2     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED                           3     6
  DEL PEAK  4(2Q37.3) WILD-TYPE                        49   141
D11V10, multiclass
                                  clus
vv                                 DEL PEAK  4(2Q37.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                      6
                                  clus
vv                                 DEL PEAK  4(2Q37.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   49
  WHITE                                                      141
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED     0   8
  DEL PEAK  4(2Q37.3) WILD-TYPE   9 167
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      0    8
  DEL PEAK  4(2Q37.3) WILD-TYPE    9  167
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           8
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           167
[1] 2 2
[1] FALSE

Clustering(12) Variable = DEL PEAK  5(3P22.1) MUTATION ANALYSIS
D12V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P22.1) MUTATED    14   4
  DEL PEAK  5(3P22.1) WILD-TYPE 173   3
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                           18                           176 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                            4                             3 
$`DEL PEAK  5(3P22.1) MUTATED`
TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5877 
        1968           87          763           64          452          270 
TCGA-BQ-5892 TCGA-DZ-6131 TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD 
         364         2429          208          446          262         1967 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-WN-A9G9 TCGA-Y8-A8RZ 
         112           62            4          428          579          205 

$`DEL PEAK  5(3P22.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
         379          516            2          118            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
        1636          412          923         1357           26           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         585          207            5          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
         586         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5894 
         792          771          403          233           29           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 
         419          114          445           92         1240         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
          10            7           36           13         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1194         1059          765          786          194          197 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965         5925          393          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146          376          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
        2653         2584         2816          391          540         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C 
        1175         1266          805         1469         1331          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         224            2          186          219          181          399 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                            4                             2 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                         2429                          5925 
  DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE 
                          317                           578 
[1] "4.0 - 2429.0 (317.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "13" 
D12V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(3P22.1) MUTATED         4        1        11        3
  DEL PEAK  5(3P22.1) WILD-TYPE     133       15        32       10
D12V3, multiclass
           clus
vv          DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  STAGE I                             4                           133
  STAGE II                            1                            15
  STAGE III                          11                            32
  STAGE IV                            3                            10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK  5(3P22.1) MUTATED     5   2    12
  DEL PEAK  5(3P22.1) WILD-TYPE 141  20    39
D12V4, multiclass
       clus
vv      DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  T1                              5                           141
  T2                              2                            20
  T3+T4                          12                            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"
                               vv
clus                            N0 N1 N2
  DEL PEAK  5(3P22.1) MUTATED    6  7  1
  DEL PEAK  5(3P22.1) WILD-TYPE 33 13  3
D12V5, multiclass
    clus
vv   DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  N0                           6                            33
  N1                           7                            13
  N2                           1                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  5(3P22.1) MUTATED     4   2  11
  DEL PEAK  5(3P22.1) WILD-TYPE  84   6 101
D12V6, multiclass
    clus
vv   DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  M0                           4                            84
  M1                           2                             6
  MX                          11                           101
[1] 3 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
  DEL PEAK  5(3P22.1) MUTATED     6  13
  DEL PEAK  5(3P22.1) WILD-TYPE  57 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      6   13
  DEL PEAK  5(3P22.1) WILD-TYPE   57  145
        clus
vv       DEL PEAK  5(3P22.1) MUTATED DEL PEAK  5(3P22.1) WILD-TYPE
  FEMALE                           6                            57
  MALE                            13                           145
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  5(3P22.1) MUTATED                                  0     1
  DEL PEAK  5(3P22.1) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P22.1) MUTATED                           4    13
  DEL PEAK  5(3P22.1) WILD-TYPE                        48   134
D12V10, multiclass
                                  clus
vv                                 DEL PEAK  5(3P22.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  4
  WHITE                                                     13
                                  clus
vv                                 DEL PEAK  5(3P22.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   48
  WHITE                                                      134
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P22.1) MUTATED     0  16
  DEL PEAK  5(3P22.1) WILD-TYPE   9 159
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P22.1) MUTATED      0   16
  DEL PEAK  5(3P22.1) WILD-TYPE    9  159
                        clus
vv                       DEL PEAK  5(3P22.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          16
                        clus
vv                       DEL PEAK  5(3P22.1) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           159
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  6(4Q34.3) MUTATION ANALYSIS
D13V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(4Q34.3) MUTATED    20   2
  DEL PEAK  6(4Q34.3) WILD-TYPE 167   5
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                           22                           172 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                            2                             5 
$`DEL PEAK  6(4Q34.3) MUTATED`
TCGA-A4-7287 TCGA-A4-8098 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 
          21          140         1968           87           26          223 
TCGA-B3-3926 TCGA-B3-4104 TCGA-BQ-5876 TCGA-BQ-5890 TCGA-BQ-5894 TCGA-DZ-6131 
         307         1049          586          233           84         2429 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-7501 TCGA-GL-7966 TCGA-HE-A5NK 
          97           10           13          446          112         2228 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ TCGA-SX-A7SS 
          62            4          428         1469 

$`DEL PEAK  6(4Q34.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
           2          118            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         923          763         1357           67          595          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
        1029          930          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          452 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
          29          364         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        1240         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
         757            7           36          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1194         1059          765          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 
         262         1967         1965         5925          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
         608          677          649          146          376          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          540 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SU TCGA-WN-A9G9 
         578         1175         1266          805         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                            4                             2 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                         2429                          5925 
  DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE 
                        181.5                         578.5 
[1] "4.0 - 2429.0 (181.5)" "2.0 - 5925.0 (578.5)"
[1] "hr=" "3.4"
D13V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(4Q34.3) MUTATED         6        2        15        2
  DEL PEAK  6(4Q34.3) WILD-TYPE     131       14        28       11
D13V3, multiclass
           clus
vv          DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  STAGE I                             6                           131
  STAGE II                            2                            14
  STAGE III                          15                            28
  STAGE IV                            2                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK  6(4Q34.3) MUTATED     8   4    14
  DEL PEAK  6(4Q34.3) WILD-TYPE 138  18    37
D13V4, multiclass
       clus
vv      DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  T1                              8                           138
  T2                              4                            18
  T3+T4                          14                            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"
                               vv
clus                            N0 N1 N2
  DEL PEAK  6(4Q34.3) MUTATED    6  8  0
  DEL PEAK  6(4Q34.3) WILD-TYPE 33 12  4
D13V5, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  N0                           6                            33
  N1                           8                            12
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  6(4Q34.3) MUTATED    12   2  12
  DEL PEAK  6(4Q34.3) WILD-TYPE  76   6 100
D13V6, multiclass
    clus
vv   DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  M0                          12                            76
  M1                           2                             6
  MX                          12                           100
[1] 3 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
  DEL PEAK  6(4Q34.3) MUTATED    13  13
  DEL PEAK  6(4Q34.3) WILD-TYPE  50 145
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED     13   13
  DEL PEAK  6(4Q34.3) WILD-TYPE   50  145
        clus
vv       DEL PEAK  6(4Q34.3) MUTATED DEL PEAK  6(4Q34.3) WILD-TYPE
  FEMALE                          13                            50
  MALE                            13                           145
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  6(4Q34.3) MUTATED                                  0     3
  DEL PEAK  6(4Q34.3) WILD-TYPE                                2     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(4Q34.3) MUTATED                           5    14
  DEL PEAK  6(4Q34.3) WILD-TYPE                        47   133
D13V10, multiclass
                                  clus
vv                                 DEL PEAK  6(4Q34.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  5
  WHITE                                                     14
                                  clus
vv                                 DEL PEAK  6(4Q34.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   47
  WHITE                                                      133
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK  6(4Q34.3) MUTATED     1  19
  DEL PEAK  6(4Q34.3) WILD-TYPE   8 156
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(4Q34.3) MUTATED      1   19
  DEL PEAK  6(4Q34.3) WILD-TYPE    8  156
                        clus
vv                       DEL PEAK  6(4Q34.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       DEL PEAK  6(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           156
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  7(5P15.33) MUTATION ANALYSIS
D14V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  7(5P15.33) MUTATED     5   1
  DEL PEAK  7(5P15.33) WILD-TYPE 182   6
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                             6                            188 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                             1                              6 
$`DEL PEAK  7(5P15.33) MUTATED`
TCGA-A4-7286 TCGA-BQ-5878 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-GL-7773 TCGA-P4-A5E6 
         554         1938           84           97          393         3035 

$`DEL PEAK  7(5P15.33) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
          26           67          595          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 
         307          930         1049          379          309         1536 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
         857          803          627           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
         452          167           52         2639          586          270 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 
         403          233           29          364         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1670         1040          578          757           10            7 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          36           13          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1059          765          446          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
         262         1967         1965         5925          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         376            4          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          493          148         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          540          428         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                            84                              2 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                          3035                           5925 
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                         473.5                          540.5 
[1] "84.0 - 3035.0 (473.5)" "2.0 - 5925.0 (540.5)" 
[1] "hr=" "3.5"
D14V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(5P15.33) MUTATED         2        0         5        2
  DEL PEAK  7(5P15.33) WILD-TYPE     135       16        38       11
D14V3, multiclass
           clus
vv          DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  STAGE I                              2                            135
  STAGE II                             0                             16
  STAGE III                            5                             38
  STAGE IV                             2                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK  7(5P15.33) MUTATED     2   1     7
  DEL PEAK  7(5P15.33) WILD-TYPE 144  21    44
D14V4, multiclass
       clus
vv      DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  T1                               2                            144
  T2                               1                             21
  T3+T4                            7                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK  7(5P15.33) MUTATED    0  5  1
  DEL PEAK  7(5P15.33) WILD-TYPE 39 15  3
D14V5, multiclass
    clus
vv   DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  N0                            0                             39
  N1                            5                             15
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK  7(5P15.33) MUTATED     3   1   5
  DEL PEAK  7(5P15.33) WILD-TYPE  85   7 107
D14V6, multiclass
    clus
vv   DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  M0                            3                             85
  M1                            1                              7
  MX                            5                            107
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                                cls
clus                               0   1
  DEL PEAK  7(5P15.33) MUTATED     5   5
  DEL PEAK  7(5P15.33) WILD-TYPE  58 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.33) MUTATED      5    5
  DEL PEAK  7(5P15.33) WILD-TYPE   58  153
        clus
vv       DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE
  FEMALE                            5                             58
  MALE                              5                            153
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:"       "DEL PEAK  7(5P15.33) MUTATED"
clus
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                             2                             54 
                    TCGA-A4-7828                     TCGA-A4-8310 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8311                     TCGA-A4-8312 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-8518                     TCGA-A4-8630 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A4ZT                     TCGA-A4-A57E 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A5DU                     TCGA-A4-A5XZ 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A6HP                     TCGA-AL-3466 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-5560                     TCGA-DW-5561 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7834                     TCGA-DW-7836 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7837                     TCGA-DW-7838 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7839                     TCGA-DW-7840 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7841                     TCGA-DW-7842 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-DW-7963                     TCGA-EV-5901 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-EV-5902                     TCGA-EV-5903 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-6790                     TCGA-G7-6796 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-6797                     TCGA-G7-7501 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-7502                     TCGA-G7-A4TM 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-A8LB                     TCGA-G7-A8LC 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-A8LD                     TCGA-G7-A8LE 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-IA-A40U                     TCGA-IA-A40X 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-IA-A40Y                     TCGA-J7-8537 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-Q2-A5QZ                     TCGA-SX-A71R 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A71S                     TCGA-SX-A71U 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A71V                     TCGA-SX-A7SL 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SM                     TCGA-SX-A7SN 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SO                     TCGA-SX-A7SP 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SQ                     TCGA-SX-A7SR 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SS                     TCGA-SX-A7SU 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
D14V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK  7(5P15.33) MUTATED"
clus
  DEL PEAK  7(5P15.33) MUTATED DEL PEAK  7(5P15.33) WILD-TYPE 
                             1                             34 
                    TCGA-A4-A48D                     TCGA-A4-A57E 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-A4-A5Y0                     TCGA-B1-A654 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-B9-A44B                     TCGA-B9-A69E 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-F9-A97G                     TCGA-G7-A8LB 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-G7-A8LD                     TCGA-G7-A8LE 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-GL-A59T                     TCGA-GL-A9DD 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-HE-A5NI                     TCGA-HE-A5NJ 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-HE-A5NK                     TCGA-IA-A40U 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-IA-A83S                     TCGA-IZ-A6M8 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-MH-A854                     TCGA-MH-A856 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-P4-A5E7                     TCGA-P4-A5EB 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-PJ-A5Z9                     TCGA-Q2-A5QZ 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A71S                     TCGA-SX-A71U 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SL                     TCGA-SX-A7SM 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-SX-A7SR                     TCGA-SX-A7SS 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-WN-A9G9                     TCGA-Y8-A894 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                    TCGA-Y8-A896                     TCGA-Y8-A8RZ 
"DEL PEAK  7(5P15.33) WILD-TYPE" "DEL PEAK  7(5P15.33) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  7(5P15.33) MUTATED                                  0     0
  DEL PEAK  7(5P15.33) WILD-TYPE                                2     5
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(5P15.33) MUTATED                           2     6
  DEL PEAK  7(5P15.33) WILD-TYPE                        50   141
D14V10, multiclass
                                  clus
vv                                 DEL PEAK  7(5P15.33) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       0
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                       6
                                  clus
vv                                 DEL PEAK  7(5P15.33) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         5
  BLACK OR AFRICAN AMERICAN                                    50
  WHITE                                                       141
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK  7(5P15.33) MUTATED     1   5
  DEL PEAK  7(5P15.33) WILD-TYPE   8 170
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  7(5P15.33) MUTATED      1    5
  DEL PEAK  7(5P15.33) WILD-TYPE    8  170
                        clus
vv                       DEL PEAK  7(5P15.33) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                            5
                        clus
vv                       DEL PEAK  7(5P15.33) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            170
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  8(5Q35.2) MUTATION ANALYSIS
D15V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(5Q35.2) MUTATED     7   1
  DEL PEAK  8(5Q35.2) WILD-TYPE 180   6
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            8                           186 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            1                             6 
$`DEL PEAK  8(5Q35.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-AL-A5DJ TCGA-B3-4104 TCGA-BQ-5894 TCGA-DZ-6131 
         554           21           26         1049           84         2429 
TCGA-F9-A4JJ TCGA-GL-7966 
          97          112 

$`DEL PEAK  8(5Q35.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-AL-3467 
        1968            2          118           87            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU 
        1636          412          923          763         1357           67 
TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
         595          223          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379          309         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B 
          14           35          460         1338          671           64 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          452          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
          29          364         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        1533         1516          799          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         218          116          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 
        1142          744          419          114          445           92 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
        1240         2460         1856         1670         1040          578 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
         757           10            7           36           13          208 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1575         1479         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
         786          194          197          262         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
        1726         2228          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD 
         677          649          146          376            4          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        3035         2653         2584         2816          391          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         428         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                           21                             2 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                         2429                          5925 
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                        104.5                         543.5 
[1] "21.0 - 2429.0 (104.5)" "2.0 - 5925.0 (543.5)" 
[1] "hr=" "4.3"
D15V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(5Q35.2) MUTATED         1        1         7        1
  DEL PEAK  8(5Q35.2) WILD-TYPE     136       15        36       12
D15V3, multiclass
           clus
vv          DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  STAGE I                             1                           136
  STAGE II                            1                            15
  STAGE III                           7                            36
  STAGE IV                            1                            12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK  8(5Q35.2) MUTATED     1   1     9
  DEL PEAK  8(5Q35.2) WILD-TYPE 145  21    42
D15V4, multiclass
       clus
vv      DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  T1                              1                           145
  T2                              1                            21
  T3+T4                           9                            42
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK  8(5Q35.2) MUTATED    1  4  0
  DEL PEAK  8(5Q35.2) WILD-TYPE 38 16  4
D15V5, multiclass
    clus
vv   DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  N0                           1                            38
  N1                           4                            16
  N2                           0                             4
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  8(5Q35.2) MUTATED     3   1   6
  DEL PEAK  8(5Q35.2) WILD-TYPE  85   7 106
D15V6, multiclass
    clus
vv   DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  M0                           3                            85
  M1                           1                             7
  MX                           6                           106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(5Q35.2) MUTATED     7   4
  DEL PEAK  8(5Q35.2) WILD-TYPE  56 154
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      7    4
  DEL PEAK  8(5Q35.2) WILD-TYPE   56  154
        clus
vv       DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE
  FEMALE                           7                            56
  MALE                             4                           154
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:"      "DEL PEAK  8(5Q35.2) MUTATED"
clus
  DEL PEAK  8(5Q35.2) MUTATED DEL PEAK  8(5Q35.2) WILD-TYPE 
                            1                            55 
                   TCGA-A4-7828                    TCGA-A4-8310 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8311                    TCGA-A4-8312 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-8518                    TCGA-A4-8630 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A4ZT                    TCGA-A4-A57E 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A5DU                    TCGA-A4-A5XZ 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-A4-A6HP                    TCGA-AL-3466 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-5560                    TCGA-DW-5561 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7834                    TCGA-DW-7836 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7837                    TCGA-DW-7838 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7839                    TCGA-DW-7840 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7841                    TCGA-DW-7842 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-DW-7963                    TCGA-EV-5901 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-EV-5902                    TCGA-EV-5903 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6790                    TCGA-G7-6793 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-6796                    TCGA-G7-6797 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-7501                    TCGA-G7-7502 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A4TM                    TCGA-G7-A8LB 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A8LC                    TCGA-G7-A8LD 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-G7-A8LE                    TCGA-IA-A40U 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-IA-A40X                    TCGA-IA-A40Y 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-J7-8537                    TCGA-Q2-A5QZ 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A71R                    TCGA-SX-A71S 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A71U                    TCGA-SX-A71V 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SL                    TCGA-SX-A7SM 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SN                    TCGA-SX-A7SO 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SP                    TCGA-SX-A7SQ 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SR                    TCGA-SX-A7SS 
"DEL PEAK  8(5Q35.2) WILD-TYPE" "DEL PEAK  8(5Q35.2) WILD-TYPE" 
                   TCGA-SX-A7SU 
"DEL PEAK  8(5Q35.2) WILD-TYPE" 
D15V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  8(5Q35.2) MUTATED                                  0     0
  DEL PEAK  8(5Q35.2) WILD-TYPE                                2     5
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(5Q35.2) MUTATED                           1     8
  DEL PEAK  8(5Q35.2) WILD-TYPE                        51   139
D15V10, multiclass
                                  clus
vv                                 DEL PEAK  8(5Q35.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      0
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                      8
                                  clus
vv                                 DEL PEAK  8(5Q35.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        5
  BLACK OR AFRICAN AMERICAN                                   51
  WHITE                                                      139
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK  8(5Q35.2) MUTATED     1   6
  DEL PEAK  8(5Q35.2) WILD-TYPE   8 169
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(5Q35.2) MUTATED      1    6
  DEL PEAK  8(5Q35.2) WILD-TYPE    8  169
                        clus
vv                       DEL PEAK  8(5Q35.2) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                           6
                        clus
vv                       DEL PEAK  8(5Q35.2) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           169
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  9(6P12.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(6P12.3) MUTATED    14   1
  DEL PEAK  9(6P12.3) WILD-TYPE 173   6
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           15                           179 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                            1                             6 
$`DEL PEAK  9(6P12.3) MUTATED`
TCGA-A4-7286 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5890 TCGA-BQ-7048 
         554           26          307           64          233         2839 
TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7502 
         612          578           10          208          765          786 
TCGA-G7-A8LC TCGA-SX-A7SL TCGA-Y8-A896 
         262          823          186 

$`DEL PEAK  9(6P12.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
         108          510           14          200         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          452          167           52 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
        2639          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 
         792          921          792          771          403           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 
         364           84         3760         2948         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
        1516          799          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
        2460         1856         1670         1040          757           97 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36           13         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
        1059          446          194          197         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
          62          677          649          146          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         540          428         1457         1443         1005          876 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
        1331          579          882          224            2          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         181          399          205          106          104 

  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                           10                             2 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                         2839                          5925 
  DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE 
                          307                           541 
[1] "10.0 - 2839.0 (307.0)" "2.0 - 5925.0 (541.0)" 
[1] "hr=" "2.4"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(6P12.3) MUTATED         6        0        10        2
  DEL PEAK  9(6P12.3) WILD-TYPE     131       16        33       11
D16V3, multiclass
           clus
vv          DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  STAGE I                             6                           131
  STAGE II                            0                            16
  STAGE III                          10                            33
  STAGE IV                            2                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK  9(6P12.3) MUTATED     7   1    11
  DEL PEAK  9(6P12.3) WILD-TYPE 139  21    40
D16V4, multiclass
       clus
vv      DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  T1                              7                           139
  T2                              1                            21
  T3+T4                          11                            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"
                               vv
clus                            N0 N1 N2
  DEL PEAK  9(6P12.3) MUTATED    4  1  2
  DEL PEAK  9(6P12.3) WILD-TYPE 35 19  2
D16V5, multiclass
    clus
vv   DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  N0                           4                            35
  N1                           1                            19
  N2                           2                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK  9(6P12.3) MUTATED    10   0   7
  DEL PEAK  9(6P12.3) WILD-TYPE  78   8 105
D16V6, multiclass
    clus
vv   DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  M0                          10                            78
  M1                           0                             8
  MX                           7                           105
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(6P12.3) MUTATED     7  12
  DEL PEAK  9(6P12.3) WILD-TYPE  56 146
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED      7   12
  DEL PEAK  9(6P12.3) WILD-TYPE   56  146
        clus
vv       DEL PEAK  9(6P12.3) MUTATED DEL PEAK  9(6P12.3) WILD-TYPE
  FEMALE                           7                            56
  MALE                            12                           146
[1] 2 2
[1] FALSE
D16V8, continuous
D16V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK  9(6P12.3) MUTATED                                  0     1
  DEL PEAK  9(6P12.3) WILD-TYPE                                2     4
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(6P12.3) MUTATED                           1    14
  DEL PEAK  9(6P12.3) WILD-TYPE                        51   133
D16V10, multiclass
                                  clus
vv                                 DEL PEAK  9(6P12.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      1
  BLACK OR AFRICAN AMERICAN                                  1
  WHITE                                                     14
                                  clus
vv                                 DEL PEAK  9(6P12.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        4
  BLACK OR AFRICAN AMERICAN                                   51
  WHITE                                                      133
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK  9(6P12.3) MUTATED     0  15
  DEL PEAK  9(6P12.3) WILD-TYPE   9 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(6P12.3) MUTATED      0   15
  DEL PEAK  9(6P12.3) WILD-TYPE    9  160
                        clus
vv                       DEL PEAK  9(6P12.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK  9(6P12.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           160
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK 10(6Q22.31) MUTATION ANALYSIS
D17V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 10(6Q22.31) MUTATED    16   1
  DEL PEAK 10(6Q22.31) WILD-TYPE 171   6
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                            17                            177 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                             1                              6 
$`DEL PEAK 10(6Q22.31) MUTATED`
TCGA-A4-7286 TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5888 TCGA-BQ-7056 
         554          307           64         2639          403          612 
TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 
         578           10          208          786          262          112 
TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SL TCGA-Y8-A896 
           4         2584          428          823          186 

$`DEL PEAK 10(6Q22.31) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N 
          26           67          595          223          659          747 
TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 
         513          108          510           14          200         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
         671          585          207            5          452          167 
TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52          586          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
         792          921          792          771          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
         364           84         3760         2948         2839         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          799          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 
        2429         2460         1856         1670         1040          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
          97            7           36           13         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB 
        1194         1059          765          446          194          197 
TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM 
        1967         1965         5925          393          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146          376 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
         148         3035         2653         2816          391          540 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN 
        1457         1443         1005          876         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
        1175         1266          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         882          224            2          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         205          106          104 

  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                             4                              2 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                          2639                           5925 
  DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE 
                           403                            546 
[1] "4.0 - 2639.0 (403.0)" "2.0 - 5925.0 (546.0)"
[1] "hr=" "1.6"
D17V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(6Q22.31) MUTATED         8        0         9        3
  DEL PEAK 10(6Q22.31) WILD-TYPE     129       16        34       10
D17V3, multiclass
           clus
vv          DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  STAGE I                              8                            129
  STAGE II                             0                             16
  STAGE III                            9                             34
  STAGE IV                             3                             10
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 10(6Q22.31) MUTATED     8   0    13
  DEL PEAK 10(6Q22.31) WILD-TYPE 138  22    38
D17V4, multiclass
       clus
vv      DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  T1                               8                            138
  T2                               0                             22
  T3+T4                           13                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 10(6Q22.31) MUTATED    3  3  2
  DEL PEAK 10(6Q22.31) WILD-TYPE 36 17  2
D17V5, multiclass
    clus
vv   DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  N0                            3                             36
  N1                            3                             17
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 10(6Q22.31) MUTATED    10   1   8
  DEL PEAK 10(6Q22.31) WILD-TYPE  78   7 104
D17V6, multiclass
    clus
vv   DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  M0                           10                             78
  M1                            1                              7
  MX                            8                            104
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V7, binary
                                cls
clus                               0   1
  DEL PEAK 10(6Q22.31) MUTATED    11  10
  DEL PEAK 10(6Q22.31) WILD-TYPE  52 148
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED     11   10
  DEL PEAK 10(6Q22.31) WILD-TYPE   52  148
        clus
vv       DEL PEAK 10(6Q22.31) MUTATED DEL PEAK 10(6Q22.31) WILD-TYPE
  FEMALE                           11                             52
  MALE                             10                            148
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 10(6Q22.31) MUTATED                                  0     2
  DEL PEAK 10(6Q22.31) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q22.31) MUTATED                           2    14
  DEL PEAK 10(6Q22.31) WILD-TYPE                        50   133
D17V10, multiclass
                                  clus
vv                                 DEL PEAK 10(6Q22.31) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                      14
                                  clus
vv                                 DEL PEAK 10(6Q22.31) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    50
  WHITE                                                       133
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 10(6Q22.31) MUTATED     0  15
  DEL PEAK 10(6Q22.31) WILD-TYPE   9 160
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 10(6Q22.31) MUTATED      0   15
  DEL PEAK 10(6Q22.31) WILD-TYPE    9  160
                        clus
vv                       DEL PEAK 10(6Q22.31) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           15
                        clus
vv                       DEL PEAK 10(6Q22.31) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            160
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK 11(6Q25.3) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 11(6Q25.3) MUTATED    19   1
  DEL PEAK 11(6Q25.3) WILD-TYPE 168   6
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                           20                           174 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                            1                             6 
$`DEL PEAK 11(6Q25.3) MUTATED`
TCGA-A4-7286 TCGA-AL-A5DJ TCGA-B3-3926 TCGA-B9-A44B TCGA-BQ-5875 TCGA-BQ-5888 
         554           26          307           64         2639          403 
TCGA-BQ-5890 TCGA-BQ-7056 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-7502 
         233          612          578           10          208          786 
TCGA-G7-A8LC TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-P4-A5EB TCGA-Q2-A5QZ 
         262          112           62            4         2584          428 
TCGA-SX-A7SL TCGA-Y8-A896 
         823          186 

$`DEL PEAK 11(6Q25.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
         516         1968            2          118           87            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 
         108          510           14          200         1029          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
        1049          379          309         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          452          167           52 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 
         586          270         1938         1454         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         921          792          771           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         799          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7VF 
        1856         1670         1040          757           97            7 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          36           13         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE 
         765          446          194          197         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
        1726         2228          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         649          146          376          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          540         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         876         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                            4                             2 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                         2639                          5925 
  DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE 
                        284.5                         578.5 
[1] "4.0 - 2639.0 (284.5)" "2.0 - 5925.0 (578.5)"
[1] "hr=" "1.6"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q25.3) MUTATED         8        0        12        2
  DEL PEAK 11(6Q25.3) WILD-TYPE     129       16        31       11
D18V3, multiclass
           clus
vv          DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  STAGE I                             8                           129
  STAGE II                            0                            16
  STAGE III                          12                            31
  STAGE IV                            2                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK 11(6Q25.3) MUTATED     8   0    15
  DEL PEAK 11(6Q25.3) WILD-TYPE 138  22    36
D18V4, multiclass
       clus
vv      DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  T1                              8                           138
  T2                              0                            22
  T3+T4                          15                            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"
                               vv
clus                            N0 N1 N2
  DEL PEAK 11(6Q25.3) MUTATED    4  3  2
  DEL PEAK 11(6Q25.3) WILD-TYPE 35 17  2
D18V5, multiclass
    clus
vv   DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  N0                           4                            35
  N1                           3                            17
  N2                           2                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 11(6Q25.3) MUTATED    11   0  10
  DEL PEAK 11(6Q25.3) WILD-TYPE  77   8 102
D18V6, multiclass
    clus
vv   DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  M0                          11                            77
  M1                           0                             8
  MX                          10                           102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V7, binary
                               cls
clus                              0   1
  DEL PEAK 11(6Q25.3) MUTATED    13  10
  DEL PEAK 11(6Q25.3) WILD-TYPE  50 148
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q25.3) MUTATED     13   10
  DEL PEAK 11(6Q25.3) WILD-TYPE   50  148
        clus
vv       DEL PEAK 11(6Q25.3) MUTATED DEL PEAK 11(6Q25.3) WILD-TYPE
  FEMALE                          13                            50
  MALE                            10                           148
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 11(6Q25.3) MUTATED                                  0     2
  DEL PEAK 11(6Q25.3) WILD-TYPE                                2     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q25.3) MUTATED                           2    16
  DEL PEAK 11(6Q25.3) WILD-TYPE                        50   131
D18V10, multiclass
                                  clus
vv                                 DEL PEAK 11(6Q25.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  2
  WHITE                                                     16
                                  clus
vv                                 DEL PEAK 11(6Q25.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   50
  WHITE                                                      131
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK 11(6Q25.3) MUTATED     0  17
  DEL PEAK 11(6Q25.3) WILD-TYPE   9 158
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 11(6Q25.3) MUTATED      0   17
  DEL PEAK 11(6Q25.3) WILD-TYPE    9  158
                        clus
vv                       DEL PEAK 11(6Q25.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          17
                        clus
vv                       DEL PEAK 11(6Q25.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           158
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK 12(9P21.3) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(9P21.3) MUTATED    20   4
  DEL PEAK 12(9P21.3) WILD-TYPE 167   3
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                           24                           170 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                            4                             3 
$`DEL PEAK 12(9P21.3) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B3-3926 
         554           21         1968           87           26          307 
TCGA-B9-4116 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5888 TCGA-BQ-7048 TCGA-BQ-7056 
         627          452          270          403         2839          612 
TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LC 
        2429           10          208         1059          446          262 
TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-SX-A71V TCGA-Y8-A896 
        1967          112           62            4          876          186 

$`DEL PEAK 12(9P21.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
           2          118            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
         923          763         1357           67          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         659          747          513          108          510           14 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
         200         1029          930         1049          379          309 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
        1338          671           64          585          207            5 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          586         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 
        1242          792          921          792          771          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 
          29          364           84         3760         2948         1864 
TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1533         1516          799          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A4JJ TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
          97            7           36           13         1575         1479 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
        1194          765          786          194          197         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
        5925          393          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
        1726         2228          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         649          146          376          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
        1043          845          924          841          616           11 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R 
        2584         2816          391          540          428         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
        1443         1005          823         1973          578         1175 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C 
        1266          805         1469         1331          579          882 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
         224            2          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                            4                             2 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                         2839                          5925 
  DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE 
                          355                           578 
[1] "4.0 - 2839.0 (355.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "8.7"
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(9P21.3) MUTATED         7        0        15        6
  DEL PEAK 12(9P21.3) WILD-TYPE     130       16        28        7
D19V3, multiclass
           clus
vv          DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  STAGE I                             7                           130
  STAGE II                            0                            16
  STAGE III                          15                            28
  STAGE IV                            6                             7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK 12(9P21.3) MUTATED     8   2    20
  DEL PEAK 12(9P21.3) WILD-TYPE 138  20    31
D19V4, multiclass
       clus
vv      DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  T1                              8                           138
  T2                              2                            20
  T3+T4                          20                            31
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            N0 N1 N2
  DEL PEAK 12(9P21.3) MUTATED    5 11  2
  DEL PEAK 12(9P21.3) WILD-TYPE 34  9  2
D19V5, multiclass
    clus
vv   DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  N0                           5                            34
  N1                          11                             9
  N2                           2                             2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                            M0 M1 MX
  DEL PEAK 12(9P21.3) MUTATED    9  4 14
  DEL PEAK 12(9P21.3) WILD-TYPE 79  4 98
D19V6, multiclass
    clus
vv   DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  M0                           9                            79
  M1                           4                             4
  MX                          14                            98
[1] 3 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 12(9P21.3) MUTATED    16  14
  DEL PEAK 12(9P21.3) WILD-TYPE  47 144
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED     16   14
  DEL PEAK 12(9P21.3) WILD-TYPE   47  144
        clus
vv       DEL PEAK 12(9P21.3) MUTATED DEL PEAK 12(9P21.3) WILD-TYPE
  FEMALE                          16                            47
  MALE                            14                           144
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 12(9P21.3) MUTATED                                  0     2
  DEL PEAK 12(9P21.3) WILD-TYPE                                2     3
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(9P21.3) MUTATED                           3    24
  DEL PEAK 12(9P21.3) WILD-TYPE                        49   123
D19V10, multiclass
                                  clus
vv                                 DEL PEAK 12(9P21.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      2
  BLACK OR AFRICAN AMERICAN                                  3
  WHITE                                                     24
                                  clus
vv                                 DEL PEAK 12(9P21.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        3
  BLACK OR AFRICAN AMERICAN                                   49
  WHITE                                                      123
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK 12(9P21.3) MUTATED     0  25
  DEL PEAK 12(9P21.3) WILD-TYPE   9 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(9P21.3) MUTATED      0   25
  DEL PEAK 12(9P21.3) WILD-TYPE    9  150
                        clus
vv                       DEL PEAK 12(9P21.3) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          25
                        clus
vv                       DEL PEAK 12(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           150
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK 13(10Q21.1) MUTATION ANALYSIS
D20V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 13(10Q21.1) MUTATED    11   2
  DEL PEAK 13(10Q21.1) WILD-TYPE 176   5
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                            13                            181 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                             2                              5 
$`DEL PEAK 13(10Q21.1) MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-BQ-5876 TCGA-DZ-6131 TCGA-G7-6789 
          87           26           64          586         2429          208 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-GL-7966 TCGA-J7-8537 TCGA-P4-A5E6 
         446          786          262          112            4         3035 
TCGA-Q2-A5QZ 
         428 

$`DEL PEAK 13(10Q21.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH 
         671          585          207            5          452          167 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 
          52         2639          270         1938         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 
         792          921          792          771          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
          29          364           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          13         1575         1479         1194         1059          765 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 
         194          197         1967         1965         5925          393 
TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD 
         841           32          378          546           27          341 
TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
         140         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 
         167          511          608           62          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         146          376          364          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 
         845          924          841          616           11          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         541          493          148         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                             4                              2 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                          3035                           5925 
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                           262                            554 
[1] "4.0 - 3035.0 (262.0)" "2.0 - 5925.0 (554.0)"
[1] "hr=" "4.9"
D20V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(10Q21.1) MUTATED         3        0        11        1
  DEL PEAK 13(10Q21.1) WILD-TYPE     134       16        32       12
D20V3, multiclass
           clus
vv          DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  STAGE I                              3                            134
  STAGE II                             0                             16
  STAGE III                           11                             32
  STAGE IV                             1                             12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 13(10Q21.1) MUTATED     5   0    10
  DEL PEAK 13(10Q21.1) WILD-TYPE 141  22    41
D20V4, multiclass
       clus
vv      DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  T1                               5                            141
  T2                               0                             22
  T3+T4                           10                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 13(10Q21.1) MUTATED    2  5  1
  DEL PEAK 13(10Q21.1) WILD-TYPE 37 15  3
D20V5, multiclass
    clus
vv   DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  N0                            2                             37
  N1                            5                             15
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 13(10Q21.1) MUTATED     4   0  10
  DEL PEAK 13(10Q21.1) WILD-TYPE  84   8 102
D20V6, multiclass
    clus
vv   DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  M0                            4                             84
  M1                            0                              8
  MX                           10                            102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V7, binary
                                cls
clus                               0   1
  DEL PEAK 13(10Q21.1) MUTATED     7   8
  DEL PEAK 13(10Q21.1) WILD-TYPE  56 150
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q21.1) MUTATED      7    8
  DEL PEAK 13(10Q21.1) WILD-TYPE   56  150
        clus
vv       DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE
  FEMALE                            7                             56
  MALE                              8                            150
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 13(10Q21.1) MUTATED"
clus
  DEL PEAK 13(10Q21.1) MUTATED DEL PEAK 13(10Q21.1) WILD-TYPE 
                             2                             33 
                    TCGA-A4-A48D                     TCGA-A4-A57E 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-A4-A5Y0                     TCGA-B1-A654 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-B9-A69E                     TCGA-F9-A97G 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-G7-A8LB                     TCGA-G7-A8LD 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-G7-A8LE                     TCGA-GL-7773 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-GL-A59T                     TCGA-GL-A9DD 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-HE-A5NI                     TCGA-HE-A5NJ 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-HE-A5NK                     TCGA-IA-A40U 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-IA-A83S                     TCGA-IZ-A6M8 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-MH-A854                     TCGA-MH-A856 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-P4-A5E7                     TCGA-P4-A5EB 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-PJ-A5Z9                     TCGA-SX-A71S 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-SX-A71U                     TCGA-SX-A7SL 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-SX-A7SM                     TCGA-SX-A7SR 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-SX-A7SS                     TCGA-WN-A9G9 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-Y8-A894                     TCGA-Y8-A896 
"DEL PEAK 13(10Q21.1) WILD-TYPE" "DEL PEAK 13(10Q21.1) WILD-TYPE" 
                    TCGA-Y8-A8RZ 
"DEL PEAK 13(10Q21.1) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 13(10Q21.1) MUTATED                                  0     1
  DEL PEAK 13(10Q21.1) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(10Q21.1) MUTATED                           4     8
  DEL PEAK 13(10Q21.1) WILD-TYPE                        48   139
D20V10, multiclass
                                  clus
vv                                 DEL PEAK 13(10Q21.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                       8
                                  clus
vv                                 DEL PEAK 13(10Q21.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       139
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 13(10Q21.1) MUTATED     0  11
  DEL PEAK 13(10Q21.1) WILD-TYPE   9 164
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 13(10Q21.1) MUTATED      0   11
  DEL PEAK 13(10Q21.1) WILD-TYPE    9  164
                        clus
vv                       DEL PEAK 13(10Q21.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           11
                        clus
vv                       DEL PEAK 13(10Q21.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            164
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK 14(11Q22.3) MUTATION ANALYSIS
D21V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 14(11Q22.3) MUTATED    14   4
  DEL PEAK 14(11Q22.3) WILD-TYPE 173   3
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                            18                            176 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                             4                              3 
$`DEL PEAK 14(11Q22.3) MUTATED`
TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 
          87          223         1049           64          586          270 
TCGA-BQ-5890 TCGA-BQ-7044 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
         233         3760           13          208          786         1967 
TCGA-IA-A40Y TCGA-J7-8537 TCGA-PJ-A5Z8 TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8S1 
          62            4          391          224          186          104 

$`DEL PEAK 14(11Q22.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          26           67          595          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 
         930          379          309         1536          857          803 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         627           14           35          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI 
         585          207            5          452          167           52 
TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 
        2639         1938         1454         1242          792          921 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         792          771          403           29          364           84 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
          10            7           36         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
        1059          765          446          194          197          262 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1965         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD 
         608          677          649          146          376          364 
TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 
         885          161         1043          845          924          841 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z 
         616           11          369          541          493          148 
TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        3035         2653         2584         2816          540          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
         579          882            2          219          181          399 
TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         205          106 

  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                             4                              2 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                          3760                           5925 
  DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE 
                         223.5                          578.0 
[1] "4.0 - 3760.0 (223.5)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "16" 
D21V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(11Q22.3) MUTATED         5        2        11        4
  DEL PEAK 14(11Q22.3) WILD-TYPE     132       14        32        9
D21V3, multiclass
           clus
vv          DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  STAGE I                              5                            132
  STAGE II                             2                             14
  STAGE III                           11                             32
  STAGE IV                             4                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 14(11Q22.3) MUTATED     6   2    14
  DEL PEAK 14(11Q22.3) WILD-TYPE 140  20    37
D21V4, multiclass
       clus
vv      DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  T1                               6                            140
  T2                               2                             20
  T3+T4                           14                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 14(11Q22.3) MUTATED    3  6  2
  DEL PEAK 14(11Q22.3) WILD-TYPE 36 14  2
D21V5, multiclass
    clus
vv   DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  N0                            3                             36
  N1                            6                             14
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 14(11Q22.3) MUTATED     9   2  10
  DEL PEAK 14(11Q22.3) WILD-TYPE  79   6 102
D21V6, multiclass
    clus
vv   DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  M0                            9                             79
  M1                            2                              6
  MX                           10                            102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                                cls
clus                               0   1
  DEL PEAK 14(11Q22.3) MUTATED     8  14
  DEL PEAK 14(11Q22.3) WILD-TYPE  55 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED      8   14
  DEL PEAK 14(11Q22.3) WILD-TYPE   55  144
        clus
vv       DEL PEAK 14(11Q22.3) MUTATED DEL PEAK 14(11Q22.3) WILD-TYPE
  FEMALE                            8                             55
  MALE                             14                            144
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 14(11Q22.3) MUTATED                                  0     2
  DEL PEAK 14(11Q22.3) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(11Q22.3) MUTATED                           3    15
  DEL PEAK 14(11Q22.3) WILD-TYPE                        49   132
D21V10, multiclass
                                  clus
vv                                 DEL PEAK 14(11Q22.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      15
                                  clus
vv                                 DEL PEAK 14(11Q22.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    49
  WHITE                                                       132
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 14(11Q22.3) MUTATED     0  17
  DEL PEAK 14(11Q22.3) WILD-TYPE   9 158
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 14(11Q22.3) MUTATED      0   17
  DEL PEAK 14(11Q22.3) WILD-TYPE    9  158
                        clus
vv                       DEL PEAK 14(11Q22.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           17
                        clus
vv                       DEL PEAK 14(11Q22.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            158
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK 15(11Q23.3) MUTATION ANALYSIS
D22V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 15(11Q23.3) MUTATED    13   4
  DEL PEAK 15(11Q23.3) WILD-TYPE 174   3
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                            17                            177 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                             4                              3 
$`DEL PEAK 15(11Q23.3) MUTATED`
TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-4104 TCGA-B9-A44B TCGA-BQ-5876 
          87           26          223         1049           64          586 
TCGA-BQ-5877 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-7502 
         270          233         3760           13          208          786 
TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-Y8-A896 TCGA-Y8-A8S1 
        1967           62            4          186          104 

$`DEL PEAK 15(11Q23.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 
         207          554           21          493            3          582 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
          27            7           49            2          140          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 
         729          709           23          597          600          436 
TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP 
         379          516         1968            2          118            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 
        1778         1636          412          923          763         1357 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
          67          595          659          747          513          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 
         510           14          200         1029          307          930 
TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         379          309         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 
          14           35          460         1338          671          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          452          167           52         2639 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7046 
         771          403           29          364           84         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
           7           36         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
         765          446          194          197          262         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146          376          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ 
        2653         2584         2816          391          540          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM 
        1457         1443         1005          876          823         1973 
TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         578         1175         1266          805         1469         1331 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
         579          882          224            2          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         399          205          106 

  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                             4                              2 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                          3760                           5925 
  DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE 
                           208                            578 
[1] "4.0 - 3760.0 (208.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "18" 
D22V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(11Q23.3) MUTATED         3        2        12        4
  DEL PEAK 15(11Q23.3) WILD-TYPE     134       14        31        9
D22V3, multiclass
           clus
vv          DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  STAGE I                              3                            134
  STAGE II                             2                             14
  STAGE III                           12                             31
  STAGE IV                             4                              9
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 15(11Q23.3) MUTATED     4   2    15
  DEL PEAK 15(11Q23.3) WILD-TYPE 142  20    36
D22V4, multiclass
       clus
vv      DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  T1                               4                            142
  T2                               2                             20
  T3+T4                           15                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 15(11Q23.3) MUTATED    3  6  2
  DEL PEAK 15(11Q23.3) WILD-TYPE 36 14  2
D22V5, multiclass
    clus
vv   DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  N0                            3                             36
  N1                            6                             14
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 15(11Q23.3) MUTATED     8   2  10
  DEL PEAK 15(11Q23.3) WILD-TYPE  80   6 102
D22V6, multiclass
    clus
vv   DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  M0                            8                             80
  M1                            2                              6
  MX                           10                            102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                                cls
clus                               0   1
  DEL PEAK 15(11Q23.3) MUTATED     7  14
  DEL PEAK 15(11Q23.3) WILD-TYPE  56 144
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      7   14
  DEL PEAK 15(11Q23.3) WILD-TYPE   56  144
        clus
vv       DEL PEAK 15(11Q23.3) MUTATED DEL PEAK 15(11Q23.3) WILD-TYPE
  FEMALE                            7                             56
  MALE                             14                            144
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 15(11Q23.3) MUTATED                                  0     2
  DEL PEAK 15(11Q23.3) WILD-TYPE                                2     3
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(11Q23.3) MUTATED                           3    14
  DEL PEAK 15(11Q23.3) WILD-TYPE                        49   133
D22V10, multiclass
                                  clus
vv                                 DEL PEAK 15(11Q23.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       2
  BLACK OR AFRICAN AMERICAN                                   3
  WHITE                                                      14
                                  clus
vv                                 DEL PEAK 15(11Q23.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         3
  BLACK OR AFRICAN AMERICAN                                    49
  WHITE                                                       133
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 15(11Q23.3) MUTATED     0  16
  DEL PEAK 15(11Q23.3) WILD-TYPE   9 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 15(11Q23.3) MUTATED      0   16
  DEL PEAK 15(11Q23.3) WILD-TYPE    9  159
                        clus
vv                       DEL PEAK 15(11Q23.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       DEL PEAK 15(11Q23.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            159
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 16(14Q11.2) MUTATION ANALYSIS
D23V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(14Q11.2) MUTATED    34   4
  DEL PEAK 16(14Q11.2) WILD-TYPE 153   3
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                            38                            156 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                             4                              3 
$`DEL PEAK 16(14Q11.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-A5Y1 TCGA-AL-3473 
         554            3            2          140           87          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 TCGA-B3-4103 
        1357           26          223          510          307          930 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5894 
         627          207          586          921          403           84 
TCGA-DW-5560 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 
         353         2429         2460           97           10          208 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 
        1059          446          786          262         1967          841 
TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y TCGA-MH-A854 TCGA-PJ-A5Z8 
         140         2228          511           62           11          391 
TCGA-SX-A71V TCGA-WN-A9G9 
         876          579 

$`DEL PEAK 16(14Q11.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207           21          493          582           27            7 
TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 
          49          780          729          709           23          597 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ 
         600          436          379          516         1968            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 
          67          595          659          747          513          108 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
          14          200         1029         1049          379          309 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671           64          585            5          452 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
        1242          792          792          771          233           29 
TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         116          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6134 
         419          114          445           92         1240         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY 
        1670         1040          578          757            7           36 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A4TM 
          13         1575         1479         1194          765          194 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM 
         197         1965         5925          393          112           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NH 
         378          546           27          341         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 
         360         1726          167          608          677          649 
TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V 
         146          376            4          364          885          161 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A855 
        1043          845          924          841          616          369 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB 
         541          493          148         3035         2653         2584 
TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          540          428         1457         1443         1005 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1469         1331          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                             2                              2 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                          2460                           5925 
  DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE 
                         424.5                          578.0 
[1] "2.0 - 2460.0 (424.5)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "5.8"
D23V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(14Q11.2) MUTATED        20        3        12        6
  DEL PEAK 16(14Q11.2) WILD-TYPE     117       13        31        7
D23V3, multiclass
           clus
vv          DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  STAGE I                             20                            117
  STAGE II                             3                             13
  STAGE III                           12                             31
  STAGE IV                             6                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 16(14Q11.2) MUTATED    22   4    18
  DEL PEAK 16(14Q11.2) WILD-TYPE 124  18    33
D23V4, multiclass
       clus
vv      DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  T1                              22                            124
  T2                               4                             18
  T3+T4                           18                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 16(14Q11.2) MUTATED    8  8  3
  DEL PEAK 16(14Q11.2) WILD-TYPE 31 12  1
D23V5, multiclass
    clus
vv   DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  N0                            8                             31
  N1                            8                             12
  N2                            3                              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"
                                vv
clus                             M0 M1 MX
  DEL PEAK 16(14Q11.2) MUTATED   18  3 21
  DEL PEAK 16(14Q11.2) WILD-TYPE 70  5 91
D23V6, multiclass
    clus
vv   DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  M0                           18                             70
  M1                            3                              5
  MX                           21                             91
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(14Q11.2) MUTATED    18  26
  DEL PEAK 16(14Q11.2) WILD-TYPE  45 132
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED     18   26
  DEL PEAK 16(14Q11.2) WILD-TYPE   45  132
        clus
vv       DEL PEAK 16(14Q11.2) MUTATED DEL PEAK 16(14Q11.2) WILD-TYPE
  FEMALE                           18                             45
  MALE                             26                            132
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 16(14Q11.2) MUTATED                                  0     1
  DEL PEAK 16(14Q11.2) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(14Q11.2) MUTATED                           9    30
  DEL PEAK 16(14Q11.2) WILD-TYPE                        43   117
D23V10, multiclass
                                  clus
vv                                 DEL PEAK 16(14Q11.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   9
  WHITE                                                      30
                                  clus
vv                                 DEL PEAK 16(14Q11.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    43
  WHITE                                                       117
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 16(14Q11.2) MUTATED     1  36
  DEL PEAK 16(14Q11.2) WILD-TYPE   8 139
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(14Q11.2) MUTATED      1   36
  DEL PEAK 16(14Q11.2) WILD-TYPE    8  139
                        clus
vv                       DEL PEAK 16(14Q11.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           36
                        clus
vv                       DEL PEAK 16(14Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            139
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 17(14Q24.2) MUTATION ANALYSIS
D24V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(14Q24.2) MUTATED    33   4
  DEL PEAK 17(14Q24.2) WILD-TYPE 154   3
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                            37                            157 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                             4                              3 
$`DEL PEAK 17(14Q24.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-A5Y1 
         554           21            3            2          140           87 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3926 
         763         1357           26          223          510          307 
TCGA-B9-4116 TCGA-B9-A5W8 TCGA-BQ-5876 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5894 
         627          207          586          921          403           84 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 
        2429         2460           97           10          208         1059 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-8500 TCGA-GL-A9DE 
         446          786          262         1967          841          140 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y TCGA-MH-A854 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
        2228          511           62           11          391          428 
TCGA-WN-A9G9 
         579 

$`DEL PEAK 17(14Q24.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         207          493          582           27            7           49 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 
         780          729          709           23          597          600 
TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 
         436          379          516         1968            2          118 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU 
           4         1778         1636          412          923           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A656 
         595          659          747          513          108           14 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
         200         1029          930         1049          379          309 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 
        1536          857          803           14           35          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E 
        1338          671           64          585            5          452 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
        1242          792          792          771          233           29 
TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364         3760         2948         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
        1516          799          612          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
        1856         1670         1040          578          757            7 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
          36           13         1575         1479         1194          765 
TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         194          197         1965         5925          393          112 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NF 
          32          378          546           27          341         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-8195 
         408          360         1726          167          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146          376            4          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
         369          541          493          148         3035         2653 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2584         2816          540         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
         805         1469         1331          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                             2                              2 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                          2460                           5925 
  DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE 
                           403                            582 
[1] "2.0 - 2460.0 (403.0)" "2.0 - 5925.0 (582.0)"
[1] "hr=" "6.1"
D24V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(14Q24.2) MUTATED        18        3        12        6
  DEL PEAK 17(14Q24.2) WILD-TYPE     119       13        31        7
D24V3, multiclass
           clus
vv          DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  STAGE I                             18                            119
  STAGE II                             3                             13
  STAGE III                           12                             31
  STAGE IV                             6                              7
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 17(14Q24.2) MUTATED    20   4    18
  DEL PEAK 17(14Q24.2) WILD-TYPE 126  18    33
D24V4, multiclass
       clus
vv      DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  T1                              20                            126
  T2                               4                             18
  T3+T4                           18                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 17(14Q24.2) MUTATED    7  9  3
  DEL PEAK 17(14Q24.2) WILD-TYPE 32 11  1
D24V5, multiclass
    clus
vv   DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  N0                            7                             32
  N1                            9                             11
  N2                            3                              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"
                                vv
clus                             M0 M1 MX
  DEL PEAK 17(14Q24.2) MUTATED   14  3 23
  DEL PEAK 17(14Q24.2) WILD-TYPE 74  5 89
D24V6, multiclass
    clus
vv   DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  M0                           14                             74
  M1                            3                              5
  MX                           23                             89
[1] 3 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 17(14Q24.2) MUTATED    18  24
  DEL PEAK 17(14Q24.2) WILD-TYPE  45 134
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q24.2) MUTATED     18   24
  DEL PEAK 17(14Q24.2) WILD-TYPE   45  134
        clus
vv       DEL PEAK 17(14Q24.2) MUTATED DEL PEAK 17(14Q24.2) WILD-TYPE
  FEMALE                           18                             45
  MALE                             24                            134
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 17(14Q24.2) MUTATED                                  0     1
  DEL PEAK 17(14Q24.2) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(14Q24.2) MUTATED                          10    28
  DEL PEAK 17(14Q24.2) WILD-TYPE                        42   119
D24V10, multiclass
                                  clus
vv                                 DEL PEAK 17(14Q24.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      28
                                  clus
vv                                 DEL PEAK 17(14Q24.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       119
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 17(14Q24.2) MUTATED     1  34
  DEL PEAK 17(14Q24.2) WILD-TYPE   8 141
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q24.2) MUTATED      1   34
  DEL PEAK 17(14Q24.2) WILD-TYPE    8  141
                        clus
vv                       DEL PEAK 17(14Q24.2) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           34
                        clus
vv                       DEL PEAK 17(14Q24.2) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            141
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 18(15Q13.3) MUTATION ANALYSIS
D25V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 18(15Q13.3) MUTATED    18   4
  DEL PEAK 18(15Q13.3) WILD-TYPE 169   3
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                            22                            172 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                             4                              3 
$`DEL PEAK 18(15Q13.3) MUTATED`
TCGA-A4-7286 TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-B1-5398 TCGA-B3-3926 TCGA-B9-A5W8 
         554            3           87          595          307          207 
TCGA-B9-A8YI TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6796 
          52           84           97           10          208         1059 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-HE-A5NK 
         786          262         1967         5925          112         2228 
TCGA-IA-A40Y TCGA-PJ-A5Z8 TCGA-Y8-A896 TCGA-Y8-A8S1 
          62          391          186          104 

$`DEL PEAK 18(15Q13.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207           21          493          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        1968            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
         223          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14          200         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
           5          452          167         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 
         771          403          233           29          364         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 
        2948         2839         1864         1533         1516          799 
TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 
         612          232          214          218          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 
         114          445           92         1240         2429         2460 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF 
        1856         1670         1040          578          757            7 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
          36           13         1575         1479         1194          765 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 
         446          194          197         1965          393          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        2072          408          360         1726          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 
         608          677          649          146          376            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z9 
         148         3035         2653         2584         2816          540 
TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         428         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 
        1331          579          882          224            2          219 
TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         181          399          205          106 

  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                             3                              2 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                          5925                           3950 
  DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE 
                         207.5                          578.5 
[1] "3.0 - 5925.0 (207.5)" "2.0 - 3950.0 (578.5)"
[1] "hr=" "11" 
D25V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 18(15Q13.3) MUTATED         9        1        11        5
  DEL PEAK 18(15Q13.3) WILD-TYPE     128       15        32        8
D25V3, multiclass
           clus
vv          DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  STAGE I                              9                            128
  STAGE II                             1                             15
  STAGE III                           11                             32
  STAGE IV                             5                              8
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 18(15Q13.3) MUTATED    11   1    16
  DEL PEAK 18(15Q13.3) WILD-TYPE 135  21    35
D25V4, multiclass
       clus
vv      DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  T1                              11                            135
  T2                               1                             21
  T3+T4                           16                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 18(15Q13.3) MUTATED    3 10  1
  DEL PEAK 18(15Q13.3) WILD-TYPE 36 10  3
D25V5, multiclass
    clus
vv   DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  N0                            3                             36
  N1                           10                             10
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 18(15Q13.3) MUTATED   10  3 14
  DEL PEAK 18(15Q13.3) WILD-TYPE 78  5 98
D25V6, multiclass
    clus
vv   DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  M0                           10                             78
  M1                            3                              5
  MX                           14                             98
[1] 3 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 18(15Q13.3) MUTATED    10  18
  DEL PEAK 18(15Q13.3) WILD-TYPE  53 140
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q13.3) MUTATED     10   18
  DEL PEAK 18(15Q13.3) WILD-TYPE   53  140
        clus
vv       DEL PEAK 18(15Q13.3) MUTATED DEL PEAK 18(15Q13.3) WILD-TYPE
  FEMALE                           10                             53
  MALE                             18                            140
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 18(15Q13.3) MUTATED                                  0     1
  DEL PEAK 18(15Q13.3) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 18(15Q13.3) MUTATED                           4    19
  DEL PEAK 18(15Q13.3) WILD-TYPE                        48   128
D25V10, multiclass
                                  clus
vv                                 DEL PEAK 18(15Q13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      19
                                  clus
vv                                 DEL PEAK 18(15Q13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       128
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 18(15Q13.3) MUTATED     1  22
  DEL PEAK 18(15Q13.3) WILD-TYPE   8 153
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 18(15Q13.3) MUTATED      1   22
  DEL PEAK 18(15Q13.3) WILD-TYPE    8  153
                        clus
vv                       DEL PEAK 18(15Q13.3) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           22
                        clus
vv                       DEL PEAK 18(15Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                  8
  NOT HISPANIC OR LATINO                            153
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 19(16Q24.1) MUTATION ANALYSIS
D26V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 19(16Q24.1) MUTATED     4   2
  DEL PEAK 19(16Q24.1) WILD-TYPE 183   5
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                             6                            188 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                             2                              5 
$`DEL PEAK 19(16Q24.1) MUTATED`
TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B9-A8YI TCGA-F9-A97G TCGA-G7-A8LD TCGA-IA-A40X 
          21           87           52           13         1967          608 

$`DEL PEAK 19(16Q24.1) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207          554          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 
           7           49            2          140          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D 
         709           23          597          600          436          379 
TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 
         516         1968            2          118            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
        1636          412          923          763         1357           26 
TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O 
          67          595          223          659          747          513 
TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 
         108          510           14          200         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379          309         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          452 
TCGA-B9-A8YH TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 
         167         2639          586          270         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 
        1242          792          921          792          771          403 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
         233           29          364           84         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2839         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
         445           92         1240         2429         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        1670         1040          578          757           97           10 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 
           7           36          208         1575         1479         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1059          765          446          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         262         1965         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          167 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         511           62          677          649          146          376 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         493          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         391          540          428         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ 
         876          823         1973          578         1175         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 
         805         1469         1331          579          882          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ 
           2          186          219          181          399          205 
TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         106          104 

  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                            13                              2 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                          1967                           5925 
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                          69.5                          543.5 
[1] "13.0 - 1967.0 (69.5)" "2.0 - 5925.0 (543.5)"
[1] "hr=" "21" 
D26V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 19(16Q24.1) MUTATED         3        0         5        2
  DEL PEAK 19(16Q24.1) WILD-TYPE     134       16        38       11
D26V3, multiclass
           clus
vv          DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  STAGE I                              3                            134
  STAGE II                             0                             16
  STAGE III                            5                             38
  STAGE IV                             2                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 19(16Q24.1) MUTATED     4   0     6
  DEL PEAK 19(16Q24.1) WILD-TYPE 142  22    45
D26V4, multiclass
       clus
vv      DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  T1                               4                            142
  T2                               0                             22
  T3+T4                            6                             45
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 19(16Q24.1) MUTATED    2  3  1
  DEL PEAK 19(16Q24.1) WILD-TYPE 37 17  3
D26V5, multiclass
    clus
vv   DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  N0                            2                             37
  N1                            3                             17
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 19(16Q24.1) MUTATED     3   1   6
  DEL PEAK 19(16Q24.1) WILD-TYPE  85   7 106
D26V6, multiclass
    clus
vv   DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  M0                            3                             85
  M1                            1                              7
  MX                            6                            106
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                                cls
clus                               0   1
  DEL PEAK 19(16Q24.1) MUTATED     4   6
  DEL PEAK 19(16Q24.1) WILD-TYPE  59 152
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16Q24.1) MUTATED      4    6
  DEL PEAK 19(16Q24.1) WILD-TYPE   59  152
        clus
vv       DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE
  FEMALE                            4                             59
  MALE                              6                            152
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK 19(16Q24.1) MUTATED"
clus
  DEL PEAK 19(16Q24.1) MUTATED DEL PEAK 19(16Q24.1) WILD-TYPE 
                             2                             33 
                    TCGA-A4-A48D                     TCGA-A4-A57E 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-A4-A5Y0                     TCGA-B1-A654 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-B9-A44B                     TCGA-B9-A69E 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-G7-A8LB                     TCGA-G7-A8LE 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-GL-7773                     TCGA-GL-A59T 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-GL-A9DD                     TCGA-HE-A5NI 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-HE-A5NJ                     TCGA-HE-A5NK 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-IA-A40U                     TCGA-IA-A83S 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-IZ-A6M8                     TCGA-MH-A854 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-MH-A856                     TCGA-P4-A5E7 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-P4-A5EB                     TCGA-PJ-A5Z9 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-Q2-A5QZ                     TCGA-SX-A71S 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-SX-A71U                     TCGA-SX-A7SL 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-SX-A7SM                     TCGA-SX-A7SR 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-SX-A7SS                     TCGA-WN-A9G9 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-Y8-A894                     TCGA-Y8-A896 
"DEL PEAK 19(16Q24.1) WILD-TYPE" "DEL PEAK 19(16Q24.1) WILD-TYPE" 
                    TCGA-Y8-A8RZ 
"DEL PEAK 19(16Q24.1) WILD-TYPE" 
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 19(16Q24.1) MUTATED                                  0     1
  DEL PEAK 19(16Q24.1) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 19(16Q24.1) MUTATED                           2     5
  DEL PEAK 19(16Q24.1) WILD-TYPE                        50   142
D26V10, multiclass
                                  clus
vv                                 DEL PEAK 19(16Q24.1) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   2
  WHITE                                                       5
                                  clus
vv                                 DEL PEAK 19(16Q24.1) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    50
  WHITE                                                       142
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 19(16Q24.1) MUTATED     0   8
  DEL PEAK 19(16Q24.1) WILD-TYPE   9 167
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 19(16Q24.1) MUTATED      0    8
  DEL PEAK 19(16Q24.1) WILD-TYPE    9  167
                        clus
vv                       DEL PEAK 19(16Q24.1) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                            8
                        clus
vv                       DEL PEAK 19(16Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            167
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 20(19P13.3) MUTATION ANALYSIS
D27V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 20(19P13.3) MUTATED    13   3
  DEL PEAK 20(19P13.3) WILD-TYPE 174   4
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                            16                            178 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                             3                              4 
$`DEL PEAK 20(19P13.3) MUTATED`
TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B9-A44B 
         554          780          597           87          223           64 
TCGA-B9-A5W7 TCGA-BQ-5876 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-G7-6789 TCGA-G7-7502 
         585          586          233           29          208          786 
TCGA-G7-A8LD TCGA-IA-A40Y TCGA-J7-8537 TCGA-Q2-A5QZ 
        1967           62            4          428 

$`DEL PEAK 20(19P13.3) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8311 TCGA-A4-8515 
           7           49            2          140          729          709 
TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
          23          600          436          379          516         1968 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
           2          118            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         659          747          513          108          510           14 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         200         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W8 TCGA-B9-A5W9 
          35          460         1338          671          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5878 
         452          167           52         2639          270         1938 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
        1454         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
         403          364           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF 
        1040          578          757           97           10            7 
TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 
          36           13         1575         1479         1194         1059 
TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
         765          446          194          197          262         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146          376          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
        2653         2584         2816          391          540         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
        1175         1266          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                             4                              2 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                          1967                           5925 
  DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE 
                         330.5                          543.5 
[1] "4.0 - 1967.0 (330.5)" "2.0 - 5925.0 (543.5)"
[1] "hr=" "15" 
D27V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 20(19P13.3) MUTATED         4        1         9        2
  DEL PEAK 20(19P13.3) WILD-TYPE     133       15        34       11
D27V3, multiclass
           clus
vv          DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  STAGE I                              4                            133
  STAGE II                             1                             15
  STAGE III                            9                             34
  STAGE IV                             2                             11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 20(19P13.3) MUTATED     5   1    11
  DEL PEAK 20(19P13.3) WILD-TYPE 141  21    40
D27V4, multiclass
       clus
vv      DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  T1                               5                            141
  T2                               1                             21
  T3+T4                           11                             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"
                                vv
clus                             N0 N1 N2
  DEL PEAK 20(19P13.3) MUTATED    2  5  1
  DEL PEAK 20(19P13.3) WILD-TYPE 37 15  3
D27V5, multiclass
    clus
vv   DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  N0                            2                             37
  N1                            5                             15
  N2                            1                              3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              M0  M1  MX
  DEL PEAK 20(19P13.3) MUTATED     4   1   9
  DEL PEAK 20(19P13.3) WILD-TYPE  84   7 103
D27V6, multiclass
    clus
vv   DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  M0                            4                             84
  M1                            1                              7
  MX                            9                            103
[1] 3 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 20(19P13.3) MUTATED     6  11
  DEL PEAK 20(19P13.3) WILD-TYPE  57 147
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      6   11
  DEL PEAK 20(19P13.3) WILD-TYPE   57  147
        clus
vv       DEL PEAK 20(19P13.3) MUTATED DEL PEAK 20(19P13.3) WILD-TYPE
  FEMALE                            6                             57
  MALE                             11                            147
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 20(19P13.3) MUTATED                                  0     1
  DEL PEAK 20(19P13.3) WILD-TYPE                                2     4
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 20(19P13.3) MUTATED                           4    12
  DEL PEAK 20(19P13.3) WILD-TYPE                        48   135
D27V10, multiclass
                                  clus
vv                                 DEL PEAK 20(19P13.3) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       1
  BLACK OR AFRICAN AMERICAN                                   4
  WHITE                                                      12
                                  clus
vv                                 DEL PEAK 20(19P13.3) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         4
  BLACK OR AFRICAN AMERICAN                                    48
  WHITE                                                       135
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 20(19P13.3) MUTATED     0  16
  DEL PEAK 20(19P13.3) WILD-TYPE   9 159
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 20(19P13.3) MUTATED      0   16
  DEL PEAK 20(19P13.3) WILD-TYPE    9  159
                        clus
vv                       DEL PEAK 20(19P13.3) MUTATED
  HISPANIC OR LATINO                                0
  NOT HISPANIC OR LATINO                           16
                        clus
vv                       DEL PEAK 20(19P13.3) WILD-TYPE
  HISPANIC OR LATINO                                  9
  NOT HISPANIC OR LATINO                            159
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 21(19Q13.42) MUTATION ANALYSIS
D28V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 21(19Q13.42) MUTATED    12   4
  DEL PEAK 21(19Q13.42) WILD-TYPE 175   3
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             16                             178 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                              4                               3 
$`DEL PEAK 21(19Q13.42) MUTATED`
TCGA-A4-7286 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8517 TCGA-A4-A5Y1 TCGA-B1-7332 
         554          140          780          597           87          223 
TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-7048 TCGA-BQ-7060 TCGA-F9-A4JJ TCGA-G7-6789 
         921           29         2839          214           97          208 
TCGA-G7-7502 TCGA-G7-A8LD TCGA-IA-A40Y TCGA-Q2-A5QZ 
         786         1967           62          428 

$`DEL PEAK 21(19Q13.42) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 
         207           21          493            3          582           27 
TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           7           49            2          729          709           23 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ 
         600          436          379          516         1968            2 
TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         118            4         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M 
         763         1357           26           67          595          659 
TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 
         747          513          108          510           14          200 
TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
        1029          307          930         1049          379          309 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
           5          452          167           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 
         270         1938         1454         1242          792          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         771          403          233          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 
        2948         1864         1533         1516          799          612 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         232          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 
          92         1240         2429         2460         1856         1670 
TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
        1040          578          757           10            7           36 
TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          13         1575         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 
         446          194          197          262         1965         5925 
TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T 
         393          112          841           32          378          546 
TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI 
          27          341          140         2072          408          360 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-8195 
        1726         2228          167          511          608          677 
TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE 
         649          146          376            4          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 
          11          369          541          493          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R 
        2653         2584         2816          391          540         1457 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN 
        1443         1005          876          823         1973          578 
TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 
        1175         1266          805         1469         1331          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 
         882          224            2          186          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          205          106          104 

  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                             29                               2 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                           2839                            5925 
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                          325.5                           543.5 
[1] "29.0 - 2839.0 (325.5)" "2.0 - 5925.0 (543.5)" 
[1] "hr=" "16" 
D28V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 21(19Q13.42) MUTATED         4        1         9        1
  DEL PEAK 21(19Q13.42) WILD-TYPE     133       15        34       12
D28V3, multiclass
           clus
vv          DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  STAGE I                               4                             133
  STAGE II                              1                              15
  STAGE III                             9                              34
  STAGE IV                              1                              12
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               T1  T2 T3+T4
  DEL PEAK 21(19Q13.42) MUTATED     5   1    10
  DEL PEAK 21(19Q13.42) WILD-TYPE 141  21    41
D28V4, multiclass
       clus
vv      DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  T1                                5                             141
  T2                                1                              21
  T3+T4                            10                              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"
                                 vv
clus                              N0 N1 N2
  DEL PEAK 21(19Q13.42) MUTATED    3  3  1
  DEL PEAK 21(19Q13.42) WILD-TYPE 36 17  3
D28V5, multiclass
    clus
vv   DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  N0                             3                              36
  N1                             3                              17
  N2                             1                               3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                 vv
clus                               M0  M1  MX
  DEL PEAK 21(19Q13.42) MUTATED     4   0  11
  DEL PEAK 21(19Q13.42) WILD-TYPE  84   8 101
D28V6, multiclass
    clus
vv   DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  M0                             4                              84
  M1                             0                               8
  MX                            11                             101
[1] 3 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 21(19Q13.42) MUTATED     6  10
  DEL PEAK 21(19Q13.42) WILD-TYPE  57 148
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(19Q13.42) MUTATED      6   10
  DEL PEAK 21(19Q13.42) WILD-TYPE   57  148
        clus
vv       DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE
  FEMALE                             6                              57
  MALE                              10                             148
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
[1] "Remove cluster labels:"        "DEL PEAK 21(19Q13.42) MUTATED"
clus
  DEL PEAK 21(19Q13.42) MUTATED DEL PEAK 21(19Q13.42) WILD-TYPE 
                              2                              33 
                     TCGA-A4-A48D                      TCGA-A4-A57E 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-A4-A5Y0                      TCGA-B1-A654 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-B9-A44B                      TCGA-B9-A69E 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-F9-A97G                      TCGA-G7-A8LB 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-G7-A8LE                      TCGA-GL-7773 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-GL-A59T                      TCGA-GL-A9DD 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-HE-A5NI                      TCGA-HE-A5NJ 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-HE-A5NK                      TCGA-IA-A40U 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-IA-A83S                      TCGA-IZ-A6M8 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-MH-A854                      TCGA-MH-A856 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-P4-A5E7                      TCGA-P4-A5EB 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-PJ-A5Z9                      TCGA-SX-A71S 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-SX-A71U                      TCGA-SX-A7SL 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-SX-A7SM                      TCGA-SX-A7SR 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-SX-A7SS                      TCGA-WN-A9G9 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-Y8-A894                      TCGA-Y8-A896 
"DEL PEAK 21(19Q13.42) WILD-TYPE" "DEL PEAK 21(19Q13.42) WILD-TYPE" 
                     TCGA-Y8-A8RZ 
"DEL PEAK 21(19Q13.42) WILD-TYPE" 
                                 vv
clus                              AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 21(19Q13.42) MUTATED                                  1     0
  DEL PEAK 21(19Q13.42) WILD-TYPE                                1     5
                                 vv
clus                              BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 21(19Q13.42) MUTATED                           4    11
  DEL PEAK 21(19Q13.42) WILD-TYPE                        48   136
D28V10, multiclass
                                  clus
vv                                 DEL PEAK 21(19Q13.42) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                             1
  ASIAN                                                        0
  BLACK OR AFRICAN AMERICAN                                    4
  WHITE                                                       11
                                  clus
vv                                 DEL PEAK 21(19Q13.42) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                               1
  ASIAN                                                          5
  BLACK OR AFRICAN AMERICAN                                     48
  WHITE                                                        136
[1] 4 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, binary
                                 cls
clus                                0   1
  DEL PEAK 21(19Q13.42) MUTATED     0  15
  DEL PEAK 21(19Q13.42) WILD-TYPE   9 160
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 21(19Q13.42) MUTATED      0   15
  DEL PEAK 21(19Q13.42) WILD-TYPE    9  160
                        clus
vv                       DEL PEAK 21(19Q13.42) MUTATED
  HISPANIC OR LATINO                                 0
  NOT HISPANIC OR LATINO                            15
                        clus
vv                       DEL PEAK 21(19Q13.42) WILD-TYPE
  HISPANIC OR LATINO                                   9
  NOT HISPANIC OR LATINO                             160
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 22(22Q12.2) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 22(22Q12.2) MUTATED    42   5
  DEL PEAK 22(22Q12.2) WILD-TYPE 145   2
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                            47                            147 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                             5                              2 
$`DEL PEAK 22(22Q12.2) MUTATED`
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         554          493          140          597          118           87 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B1-A47O TCGA-B3-3925 TCGA-B3-3926 TCGA-B9-A44B 
          26          223          513         1029          307           64 
TCGA-B9-A5W8 TCGA-BQ-5875 TCGA-BQ-5877 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5890 
         207         2639          270          792          921          233 
TCGA-BQ-5891 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7055 
          29           84         3760         1864         1533          799 
TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-EV-5902 TCGA-F9-A4JJ TCGA-F9-A7Q0 
         612          218         2429          578           97           10 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC 
          36          208          765          446          786          262 
TCGA-GL-7966 TCGA-IA-A40Y TCGA-J7-8537 TCGA-MH-A856 TCGA-P4-A5EB TCGA-Q2-A5QZ 
         112           62            4          541         2584          428 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8RZ 
         823         1973          882          186          205 

$`DEL PEAK 22(22Q12.2) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207           21            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
          49            2          780          729          709           23 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E TCGA-A4-A5XZ 
         600          436          379          516         1968            2 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
           4         1778         1636          412          923          763 
TCGA-AL-7173 TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
        1357           67          595          659          747          108 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         510           14          200          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W9 
          35          460         1338          671          585            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 
         452          167           52          586         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7046 
        1242          792          771          403          364         2948 
TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 
        2839         1516          232          214          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         414         3950         1093         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 
         114          445           92         1240         2460         1856 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A97G TCGA-G7-6790 
        1670         1040          757            7           13         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LD 
        1479         1194         1059          194          197         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        1965         5925          393          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NH 
         546           27          341          140         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
         360         1726         2228          167          511          608 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE 
         677          649          146          376          364          885 
TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 
         161         1043          845          924          841          616 
TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 
          11          369          493          148         3035         2653 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
        2816          391          540         1457         1443         1005 
TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
         876          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 
        1331          579          224            2          219          181 
TCGA-Y8-A8RY TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         399          106          104 

  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                             4                              2 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                          3760                           5925 
  DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE 
                           428                            582 
[1] "4.0 - 3760.0 (428.0)" "2.0 - 5925.0 (582.0)"
[1] "hr=" "7.7"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 22(22Q12.2) MUTATED        19        3        22        7
  DEL PEAK 22(22Q12.2) WILD-TYPE     118       13        21        6
D29V3, multiclass
           clus
vv          DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  STAGE I                             19                            118
  STAGE II                             3                             13
  STAGE III                           22                             21
  STAGE IV                             7                              6
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2 T3+T4
  DEL PEAK 22(22Q12.2) MUTATED    21   5    27
  DEL PEAK 22(22Q12.2) WILD-TYPE 125  17    24
D29V4, multiclass
       clus
vv      DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  T1                              21                            125
  T2                               5                             17
  T3+T4                           27                             24
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             N0 N1 N2
  DEL PEAK 22(22Q12.2) MUTATED    9 13  2
  DEL PEAK 22(22Q12.2) WILD-TYPE 30  7  2
D29V5, multiclass
    clus
vv   DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  N0                            9                             30
  N1                           13                              7
  N2                            2                              2
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                             M0 M1 MX
  DEL PEAK 22(22Q12.2) MUTATED   22  5 24
  DEL PEAK 22(22Q12.2) WILD-TYPE 66  3 88
D29V6, multiclass
    clus
vv   DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  M0                           22                             66
  M1                            5                              3
  MX                           24                             88
[1] 3 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 22(22Q12.2) MUTATED    25  28
  DEL PEAK 22(22Q12.2) WILD-TYPE  38 130
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(22Q12.2) MUTATED     25   28
  DEL PEAK 22(22Q12.2) WILD-TYPE   38  130
        clus
vv       DEL PEAK 22(22Q12.2) MUTATED DEL PEAK 22(22Q12.2) WILD-TYPE
  FEMALE                           25                             38
  MALE                             28                            130
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
                                vv
clus                             AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 22(22Q12.2) MUTATED                                  0     3
  DEL PEAK 22(22Q12.2) WILD-TYPE                                2     2
                                vv
clus                             BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 22(22Q12.2) MUTATED                          10    37
  DEL PEAK 22(22Q12.2) WILD-TYPE                        42   110
D29V10, multiclass
                                  clus
vv                                 DEL PEAK 22(22Q12.2) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                            0
  ASIAN                                                       3
  BLACK OR AFRICAN AMERICAN                                  10
  WHITE                                                      37
                                  clus
vv                                 DEL PEAK 22(22Q12.2) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                              2
  ASIAN                                                         2
  BLACK OR AFRICAN AMERICAN                                    42
  WHITE                                                       110
[1] 4 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, binary
                                cls
clus                               0   1
  DEL PEAK 22(22Q12.2) MUTATED     3  37
  DEL PEAK 22(22Q12.2) WILD-TYPE   6 138
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 22(22Q12.2) MUTATED      3   37
  DEL PEAK 22(22Q12.2) WILD-TYPE    6  138
                        clus
vv                       DEL PEAK 22(22Q12.2) MUTATED
  HISPANIC OR LATINO                                3
  NOT HISPANIC OR LATINO                           37
                        clus
vv                       DEL PEAK 22(22Q12.2) WILD-TYPE
  HISPANIC OR LATINO                                  6
  NOT HISPANIC OR LATINO                            138
[1] 2 2
[1] FALSE

Clustering(30) Variable = DEL PEAK 23(XP11.4) MUTATION ANALYSIS
D30V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 23(XP11.4) MUTATED    15   4
  DEL PEAK 23(XP11.4) WILD-TYPE 172   3
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                           19                           175 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                            4                             3 
$`DEL PEAK 23(XP11.4) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 
         554           21           87          223          307          627 
TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5887 TCGA-DZ-6131 TCGA-F9-A4JJ 
          64          586          270          771         2429           97 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD TCGA-J7-8537 
          10           13          765          446         1967            4 
TCGA-Q2-A5QZ 
         428 

$`DEL PEAK 23(XP11.4) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 
         207          493            3          582           27            7 
TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 
          49            2          140          780          729          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
        1968            2          118            4         1778         1636 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU 
         412          923          763         1357           26           67 
TCGA-B1-5398 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 
         595          659          747          513          108          510 
TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
          14          200         1029          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
         309         1536          857          803           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 
         460         1338          671          585          207            5 
TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 
         452          167           52         2639         1938         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5888 TCGA-BQ-5890 
        1242          792          921          792          403          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
          29          364           84         3760         2948         2839 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        1864         1533         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
         214          218          116          353          414         3950 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 
        1093         1142          744          419          114          445 
TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
          92         1240         2460         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6790 
         578          757            7           36          208         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1479         1194         1059          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 
         262         1965         5925          393          112          841 
TCGA-GL-A4EM TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE 
          32          378          546           27          341          140 
TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL 
        2072          408          360         1726         2228          167 
TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         511          608           62          677          649          146 
TCGA-IZ-A6M9 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
         376          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED 
         493          148         3035         2653         2584         2816 
TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
         391          540         1457         1443         1005          876 
TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR 
         823         1973          578         1175         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 

  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                            4                             2 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                         2429                          5925 
  DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE 
                          307                           578 
[1] "4.0 - 2429.0 (307.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "15" 
D30V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 23(XP11.4) MUTATED         4        1        14        2
  DEL PEAK 23(XP11.4) WILD-TYPE     133       15        29       11
D30V3, multiclass
           clus
vv          DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  STAGE I                             4                           133
  STAGE II                            1                            15
  STAGE III                          14                            29
  STAGE IV                            2                            11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2 T3+T4
  DEL PEAK 23(XP11.4) MUTATED     6   2    15
  DEL PEAK 23(XP11.4) WILD-TYPE 140  20    36
D30V4, multiclass
       clus
vv      DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  T1                              6                           140
  T2                              2                            20
  T3+T4                          15                            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"
                               vv
clus                            N0 N1 N2
  DEL PEAK 23(XP11.4) MUTATED    4  6  1
  DEL PEAK 23(XP11.4) WILD-TYPE 35 14  3
D30V5, multiclass
    clus
vv   DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  N0                           4                            35
  N1                           6                            14
  N2                           1                             3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             M0  M1  MX
  DEL PEAK 23(XP11.4) MUTATED     9   1  10
  DEL PEAK 23(XP11.4) WILD-TYPE  79   7 102
D30V6, multiclass
    clus
vv   DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  M0                           9                            79
  M1                           1                             7
  MX                          10                           102
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D30V7, binary
                               cls
clus                              0   1
  DEL PEAK 23(XP11.4) MUTATED    12  11
  DEL PEAK 23(XP11.4) WILD-TYPE  51 147
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP11.4) MUTATED     12   11
  DEL PEAK 23(XP11.4) WILD-TYPE   51  147
        clus
vv       DEL PEAK 23(XP11.4) MUTATED DEL PEAK 23(XP11.4) WILD-TYPE
  FEMALE                          12                            51
  MALE                            11                           147
[1] 2 2
[1] FALSE
D30V8, continuous
D30V9, continuous
                               vv
clus                            AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 23(XP11.4) MUTATED                                  0     3
  DEL PEAK 23(XP11.4) WILD-TYPE                                2     2
                               vv
clus                            BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 23(XP11.4) MUTATED                           7    11
  DEL PEAK 23(XP11.4) WILD-TYPE                        45   136
D30V10, multiclass
                                  clus
vv                                 DEL PEAK 23(XP11.4) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                           0
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                  7
  WHITE                                                     11
                                  clus
vv                                 DEL PEAK 23(XP11.4) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                             2
  ASIAN                                                        2
  BLACK OR AFRICAN AMERICAN                                   45
  WHITE                                                      136
[1] 4 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, binary
                               cls
clus                              0   1
  DEL PEAK 23(XP11.4) MUTATED     0  15
  DEL PEAK 23(XP11.4) WILD-TYPE   9 160
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 23(XP11.4) MUTATED      0   15
  DEL PEAK 23(XP11.4) WILD-TYPE    9  160
                        clus
vv                       DEL PEAK 23(XP11.4) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       DEL PEAK 23(XP11.4) WILD-TYPE
  HISPANIC OR LATINO                                 9
  NOT HISPANIC OR LATINO                           160
[1] 2 2
[1] FALSE

Clustering(31) Variable = DEL PEAK 24(XQ28) MUTATION ANALYSIS
D31V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 24(XQ28) MUTATED    11   3
  DEL PEAK 24(XQ28) WILD-TYPE 176   4
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                         14                         180 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                          3                           4 
$`DEL PEAK 24(XQ28) MUTATED`
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-A5Y1 TCGA-B1-7332 TCGA-B3-3926 
         554           21            3           87          223          307 
TCGA-BQ-5876 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-A8LD 
         586           97           10          765          446         1967 
TCGA-J7-8537 TCGA-Q2-A5QZ 
           4          428 

$`DEL PEAK 24(XQ28) WILD-TYPE`
TCGA-2K-A9WE TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
         207          493          582           27            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           2          140          780          729          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
         597          600          436          379          516         1968 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 
           2          118            4         1778         1636          412 
TCGA-AL-3472 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 
         923          763         1357           26           67          595 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         659          747          513          108          510           14 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 
         200         1029          930         1049          379          309 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 
        1536          857          803          627           14           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
         460         1338          671           64          585          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5877 
           5          452          167           52         2639          270 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
        1938         1454         1242          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 
         771          403          233           29          364           84 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        3760         2948         2839         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
         799          612          232          214          218          116 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 
         353          414         3950         1093         1142          744 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 
         419          114          445           92         1240         2429 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
        2460         1856         1670         1040          578          757 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 
           7           36           13          208         1575         1479 
TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
        1194         1059          786          194          197          262 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
        1965         5925          393          112          841           32 
TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
         378          546           27          341          140         2072 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U 
         408          360         1726         2228          167          511 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
         608           62          677          649          146          376 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         364          885          161         1043          845          924 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 
         841          616           11          369          541          493 
TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
         148         3035         2653         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
         540         1457         1443         1005          876          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
        1973          578         1175         1266          805         1469 
TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
        1331          579          882          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 TCGA-Y8-A8S1 
         219          181          399          205          106          104 

  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                          3                           2 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                       1967                        5925 
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                        265                         578 
[1] "3.0 - 1967.0 (265.0)" "2.0 - 5925.0 (578.0)"
[1] "hr=" "18" 
D31V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 24(XQ28) MUTATED         5        1        10        2
  DEL PEAK 24(XQ28) WILD-TYPE     132       15        33       11
D31V3, multiclass
           clus
vv          DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  STAGE I                           5                         132
  STAGE II                          1                          15
  STAGE III                        10                          33
  STAGE IV                          2                          11
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2 T3+T4
  DEL PEAK 24(XQ28) MUTATED     7   1    11
  DEL PEAK 24(XQ28) WILD-TYPE 139  21    40
D31V4, multiclass
       clus
vv      DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  T1                            7                         139
  T2                            1                          21
  T3+T4                        11                          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"
                             vv
clus                          N0 N1 N2
  DEL PEAK 24(XQ28) MUTATED    2  6  1
  DEL PEAK 24(XQ28) WILD-TYPE 37 14  3
D31V5, multiclass
    clus
vv   DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  N0                         2                          37
  N1                         6                          14
  N2                         1                           3
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           M0  M1  MX
  DEL PEAK 24(XQ28) MUTATED     8   1   9
  DEL PEAK 24(XQ28) WILD-TYPE  80   7 103
D31V6, multiclass
    clus
vv   DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  M0                         8                          80
  M1                         1                           7
  MX                         9                         103
[1] 3 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 24(XQ28) MUTATED    11   8
  DEL PEAK 24(XQ28) WILD-TYPE  52 150
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(XQ28) MUTATED     11    8
  DEL PEAK 24(XQ28) WILD-TYPE   52  150
        clus
vv       DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  FEMALE                        11                          52
  MALE                           8                         150
[1] 2 2
[1] FALSE
D31V8, continuous
D31V9, continuous
[1] "Remove cluster labels:"    "DEL PEAK 24(XQ28) MUTATED"
clus
  DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE 
                          2                          33 
                 TCGA-A4-A48D                  TCGA-A4-A57E 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-A4-A5Y0                  TCGA-B1-A654 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-B9-A44B                  TCGA-B9-A69E 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-F9-A97G                  TCGA-G7-A8LB 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-G7-A8LE                  TCGA-GL-7773 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-GL-A59T                  TCGA-GL-A9DD 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-HE-A5NI                  TCGA-HE-A5NJ 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-HE-A5NK                  TCGA-IA-A40U 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-IA-A83S                  TCGA-IZ-A6M8 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-MH-A854                  TCGA-MH-A856 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-P4-A5E7                  TCGA-P4-A5EB 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-PJ-A5Z9                  TCGA-SX-A71S 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-SX-A71U                  TCGA-SX-A7SL 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-SX-A7SM                  TCGA-SX-A7SR 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-SX-A7SS                  TCGA-WN-A9G9 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-Y8-A894                  TCGA-Y8-A896 
"DEL PEAK 24(XQ28) WILD-TYPE" "DEL PEAK 24(XQ28) WILD-TYPE" 
                 TCGA-Y8-A8RZ 
"DEL PEAK 24(XQ28) WILD-TYPE" 
                             vv
clus                          AMERICAN INDIAN OR ALASKA NATIVE ASIAN
  DEL PEAK 24(XQ28) MUTATED                                  0     2
  DEL PEAK 24(XQ28) WILD-TYPE                                2     3
                             vv
clus                          BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 24(XQ28) MUTATED                           5    10
  DEL PEAK 24(XQ28) WILD-TYPE                        47   137
D31V10, multiclass
                                  clus
vv                                 DEL PEAK 24(XQ28) MUTATED
  AMERICAN INDIAN OR ALASKA NATIVE                         0
  ASIAN                                                    2
  BLACK OR AFRICAN AMERICAN                                5
  WHITE                                                   10
                                  clus
vv                                 DEL PEAK 24(XQ28) WILD-TYPE
  AMERICAN INDIAN OR ALASKA NATIVE                           2
  ASIAN                                                      3
  BLACK OR AFRICAN AMERICAN                                 47
  WHITE                                                    137
[1] 4 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, binary
                             cls
clus                            0   1
  DEL PEAK 24(XQ28) MUTATED     0  14
  DEL PEAK 24(XQ28) WILD-TYPE   9 161
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 24(XQ28) MUTATED      0   14
  DEL PEAK 24(XQ28) WILD-TYPE    9  161
                        clus
vv                       DEL PEAK 24(XQ28) MUTATED DEL PEAK 24(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                           9
  NOT HISPANIC OR LATINO                        14                         161
[1] 2 2
[1] FALSE
