[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"        "-oTKIRC-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/KIRC-TP/10005959/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/10013764/transformed.cor.cli.txt"

nPatients in clinical file=515, in cluster file=527, common to both=505
[1]  29 505
[1] "AMP PEAK  1(1Q24.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                           61                           444 
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                           61                           444 
[1] "AMP PEAK  2(1Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           61                           444 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           61                           444 
[1] "AMP PEAK  3(3Q26.32) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            86                            419 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            86                            419 
[1] "AMP PEAK  4(4Q32.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                           16                           489 
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                           16                           489 
[1] "AMP PEAK  5(5Q35.1) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                          321                           184 
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                          321                           184 
[1] "AMP PEAK  6(7Q36.3) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                          170                           335 
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                          170                           335 
[1] "AMP PEAK  7(8Q24.22) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                            77                            428 
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                            77                            428 
[1] "AMP PEAK  8(10P14) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                          20                          485 
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                          20                          485 
[1] "AMP PEAK  9(XP22.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                           30                           475 
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                           30                           475 
[1] "AMP PEAK 10(XP11.4) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                           32                           473 
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                           32                           473 
[1] "AMP PEAK 11(XQ11.2) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                           28                           477 
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                           28                           477 
[1] "AMP PEAK 12(XQ28) MUTATION ANALYSIS"
[1] 3
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         35                         470 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         35                         470 
[1] "DEL PEAK  1(1P36.23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                           101                            404 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                           101                            404 
[1] "DEL PEAK  2(1P31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           75                           430 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           75                           430 
[1] "DEL PEAK  3(1Q43) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         40                         465 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         40                         465 
[1] "DEL PEAK  4(2Q37.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           50                           455 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           50                           455 
[1] "DEL PEAK  5(3P25.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE 
                          445                            60 
  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE 
                          445                            60 
[1] "DEL PEAK  6(3P12.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE 
                          321                           184 
  DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE 
                          321                           184 
[1] "DEL PEAK  7(3P11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE 
                          237                           268 
  DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE 
                          237                           268 
[1] "DEL PEAK  8(3Q11.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE 
                          156                           349 
  DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE 
                          156                           349 
[1] "DEL PEAK  9(4Q34.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                           78                           427 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                           78                           427 
[1] "DEL PEAK 10(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                        147                         358 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                        147                         358 
[1] "DEL PEAK 11(6Q26) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        147                         358 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        147                         358 
[1] "DEL PEAK 12(8P23.2) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                          151                           354 
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                          151                           354 
[1] "DEL PEAK 13(9P23) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                        146                         359 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                        146                         359 
[1] "DEL PEAK 14(9P21.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          154                           351 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                          154                           351 
[1] "DEL PEAK 15(10Q23.31) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             94                             411 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             94                             411 
[1] "DEL PEAK 16(13Q13.3) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE 
                            79                            426 
  DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE 
                            79                            426 
[1] "DEL PEAK 17(14Q31.1) MUTATION ANALYSIS"
[1] 3
  DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE 
                           221                            284 
  DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE 
                           221                            284 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 505 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
        1120         1436           16           NA          735         1493 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
        1491         1130         1508         1478         1106         1186 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
         751         1137         1485          665         1043          945 
TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 
          NA         1610         1385          910           NA         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
        2274          735         1621         1314         1070          630 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         567          574          861         1993          617            3 
TCGA-A3-A8OX TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
          NA         3343           NA         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1397          874           NA         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 
         853          369         1238           43           NA           NA 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
         110           NA           NA           NA           26           NA 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
          96           NA           NA           NA          616           NA 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
          NA           18           NA           NA           NA           NA 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
          NA          183           NA           NA           NA           NA 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 TCGA-B0-4836 TCGA-B0-4837 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5084 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
         665           NA           NA           NA           NA           NA 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
          NA           NA          911           NA         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        3076           NA         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         358          315          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
          11            7           NA          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
          66          110         3377           NA         2881         2746 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        3074         2839           NA         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
         701           NA         1893         1879         1955         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
        2964         1625           NA          845         1888           NA 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
        1133          645          461           NA         2859           NA 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4346 TCGA-BP-4347 
          NA           NA           NA         1666           NA         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
         372          970           NA           NA           NA           NA 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
         374         2208         2372         2361          182           NA 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
          NA         2184         1462          400         1876           NA 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
          NA         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
         354         1854           NA         1489           NA          620 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1107           NA           NA         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
        1487         1502         1384           NA         1433         1632 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
         454           NA         1014         1413           NA          785 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
        1124           NA          118         1413          501          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        1308         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
        1126          840         1140         1071           NA           NA 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
          NA          193         2412           NA         2257          932 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
          NA          293           NA         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        1416         1924           NA           NA         2308         1998 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
          NA         1628         1793           NA          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
        1952           NA           NA         1946         2085           NA 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
        1521          750          841           NA         1808         1528 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
          NA         1450         1520         1560         1792         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
        1499         1531         1657           NA         1373           NA 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
          NA           NA         1943           NA         2430         2575 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
          NA           NA           NA           NA          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
        1889         2231         2038           NA         1855           NA 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
          NA         1906         2548           NA           NA         2799 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2489           NA         2609         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6097 
        2271           NA         3222         2552         3146           NA 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
         774         1404           18           NA         1943         1787 
TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 
          NA           NA         1843         1928         2830           NA 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
        1868         1929         1789           25           NA           NA 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
        1712         1683         1732         1683         1430          330 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
          NA          662         1740         1446          685           NA 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
          59          946          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130          723         1729 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC 
          NA          551          119          206          127           NA 
TCGA-GK-A6C7 
          61 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=157,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=335,	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=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=14,	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 505 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=59, 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 
250  67 177  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
250  67 177  11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
250  67 177  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
250  67 177  11 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=6, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = AMP PEAK  1(1Q24.1) MUTATION ANALYSIS
D1V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  1(1Q24.1) MUTATED    33   5
  AMP PEAK  1(1Q24.1) WILD-TYPE 305  21
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                           38                           326 
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                            5                            21 
$`AMP PEAK  1(1Q24.1) MUTATED`
TCGA-A3-3316 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3430 
        1493         1043          945          735          574          480 
TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4819 TCGA-B0-5115 TCGA-B0-5706 TCGA-B4-5843 
        1779          874          183          797         2414           11 
TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4756 
          15         2746         1879         1955          845          374 
TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4986 TCGA-BP-5175 TCGA-CJ-4635 
        2184          400         2080          785          932         1416 
TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4916 TCGA-CJ-5675 
        1998         2259         1955         2014         1373         2430 
TCGA-CJ-6027 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 
        1855         2226         2378         2552         1404         1943 
TCGA-CZ-4859 TCGA-CZ-5452 
        1787         1789 

$`AMP PEAK  1(1Q24.1) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1485          665         1610         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2274         1621         1314         1070          630          567 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 
         861         1993          617            3         3343         2566 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
        2223         2017         1853         2192         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
        1745         1423         1471         1280         1217         1481 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
        1397         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1238           43          110           26           96          616 
TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5116 
          18          665          911         1092          359          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        1203         3668         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
         507          291          175            7           38           16 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141          166            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 
         522          505          194          434         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
         110         3377         2881         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 
          13         2718          701         1893         1670         2964 
TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
        1625         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          970         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2361          182         1462         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
         411         1731          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 
        1384         1433         1632          454         1014         1413 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 
        1063          951           29         1820         1924         2308 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        1628         1793          646         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
        1435         2283         2353         2186         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         841         1808         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-5671 
        1792         1496         1499         1531         1657         1943 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        1906         2548         2799         2489         2609         2017 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4862 
        2271         3222         3146          774           18         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5456 
        1928         2830         1868         1929           25         1712 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1683         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
        1740         1446          685           59          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                           11                             3 
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                         2746                          3668 
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                       1636.0                        1227.5 
[1] "11.0 - 2746.0 (1636.0)" "3.0 - 3668.0 (1227.5)" 
[1] "hr=" "1.9"
D1V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  1(1Q24.1) MUTATED        23        9        17       12
  AMP PEAK  1(1Q24.1) WILD-TYPE     221       47       109       67
D1V3, multiclass
           clus
vv          AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  STAGE I                            23                           221
  STAGE II                            9                            47
  STAGE III                          17                           109
  STAGE IV                           12                            67
[1] 4 2
[1] 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(1Q24.1) MUTATED    25  12  24   0
  AMP PEAK  1(1Q24.1) WILD-TYPE 225  55 153  11
D1V4, multiclass
    clus
vv   AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  T1                          25                           225
  T2                          12                            55
  T3                          24                           153
  T4                           0                            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"
D1V5, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q24.1) MUTATED    29   5
  AMP PEAK  1(1Q24.1) WILD-TYPE 201  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.1) MUTATED     29    5
  AMP PEAK  1(1Q24.1) WILD-TYPE  201   13
   clus
vv  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  0                          29                           201
  1                           5                            13
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  1(1Q24.1) MUTATED    48  13   0
  AMP PEAK  1(1Q24.1) WILD-TYPE 369  65   9
D1V6, multiclass
    clus
vv   AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  M0                          48                           369
  M1                          13                            65
  MX                           0                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
                               cls
clus                              0   1
  AMP PEAK  1(1Q24.1) MUTATED    20  41
  AMP PEAK  1(1Q24.1) WILD-TYPE 158 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.1) MUTATED     20   41
  AMP PEAK  1(1Q24.1) WILD-TYPE  158  286
        clus
vv       AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE
  FEMALE                          20                           158
  MALE                            41                           286
[1] 2 2
[1] FALSE
D1V8, continuous
D1V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK  1(1Q24.1) MUTATED"
clus
  AMP PEAK  1(1Q24.1) MUTATED AMP PEAK  1(1Q24.1) WILD-TYPE 
                            1                             7 
                   TCGA-A3-A8CQ                    TCGA-B2-A4SR 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-B8-4621                    TCGA-B8-5158 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-B8-5164                    TCGA-B8-A54F 
"AMP PEAK  1(1Q24.1) WILD-TYPE" "AMP PEAK  1(1Q24.1) WILD-TYPE" 
                   TCGA-B8-A54G 
"AMP PEAK  1(1Q24.1) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  1(1Q24.1) MUTATED       1                         3    57
  AMP PEAK  1(1Q24.1) WILD-TYPE     7                        30   400
D1V10, multiclass
                           clus
vv                          AMP PEAK  1(1Q24.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              57
                           clus
vv                          AMP PEAK  1(1Q24.1) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            30
  WHITE                                               400
[1] 3 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(1Q24.1) MUTATED     4  38
  AMP PEAK  1(1Q24.1) WILD-TYPE  20 292
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  1(1Q24.1) MUTATED      4   38
  AMP PEAK  1(1Q24.1) WILD-TYPE   20  292
                        clus
vv                       AMP PEAK  1(1Q24.1) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          38
                        clus
vv                       AMP PEAK  1(1Q24.1) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           292
[1] 2 2
[1] FALSE

Clustering(2) Variable = AMP PEAK  2(1Q32.1) MUTATION ANALYSIS
D2V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  2(1Q32.1) MUTATED    34   5
  AMP PEAK  2(1Q32.1) WILD-TYPE 304  21
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           39                           325 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                            5                            21 
$`AMP PEAK  2(1Q32.1) MUTATED`
TCGA-A3-3316 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3430 
        1493         1043          945          735          574          480 
TCGA-AK-3450 TCGA-B0-4819 TCGA-B0-5115 TCGA-B0-5701 TCGA-B4-5843 TCGA-B8-5551 
        1779          183          797         1732           11           15 
TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4756 TCGA-BP-4768 
        2746         1879         1955          845          374          400 
TCGA-BP-4781 TCGA-BP-4963 TCGA-BP-4971 TCGA-BP-4975 TCGA-BP-4986 TCGA-BP-5175 
        2080         1834         1487         1433          785          932 
TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4916 
        1416         1998         2259         1955         2014         1373 
TCGA-CJ-5675 TCGA-CJ-6027 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-6090 TCGA-CZ-4854 
        2430         1855         2548         2226         2552         1404 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-5452 
        1943         1787         1789 

$`AMP PEAK  2(1Q32.1) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1485          665         1610         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2274         1621         1314         1070          630          567 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 
         861         1993          617            3         3343         2566 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 
        2223         2017         1853         2192         2087         2044 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 
        1745         1423         1471         1280         1217         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
         616           18          665          911         1092          359 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 
        1420         1727         1835         2583         2741         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          16          141          166            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
         737          522          505          194          434         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 
          66          110         3377         2881         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 
        3037           13         2718          701         1893         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        2964         1625         1888         1133          645          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4758 
        2859         1666         1367          372          970         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2372         2361          182         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
        1885         1843          411         1731          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 
         211         2660         2172         1935         1785         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 
        1871          205         1746         1794          433         1502 
TCGA-BP-4973 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
        1384         1632          454         1014         1413         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
         118         1413          501          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
        1140         1071          193         2412         2257          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2263         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4642 
         951           29         1820         1924         2308         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2283         2353         2186         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1808         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 
        1496         1499         1531         1657         1943         2575 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 
         552         1883         1889         2231         2038         1906 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        2799         2489         2609         2017         2378         2271 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 
        3222         3146          774           18         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 
        2830         1868         1929           25         1712         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
        1446          685           59          946          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                           11                             3 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         2746                          3668 
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                         1493                          1203 
[1] "11.0 - 2746.0 (1493.0)" "3.0 - 3668.0 (1203.0)" 
[1] "hr=" "1.8"
D2V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  2(1Q32.1) MUTATED        22        9        19       11
  AMP PEAK  2(1Q32.1) WILD-TYPE     222       47       107       68
D2V3, multiclass
           clus
vv          AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  STAGE I                            22                           222
  STAGE II                            9                            47
  STAGE III                          19                           107
  STAGE IV                           11                            68
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  2(1Q32.1) MUTATED    24  11  26   0
  AMP PEAK  2(1Q32.1) WILD-TYPE 226  56 151  11
D2V4, multiclass
    clus
vv   AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  T1                          24                           226
  T2                          11                            56
  T3                          26                           151
  T4                           0                            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"
D2V5, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    29   3
  AMP PEAK  2(1Q32.1) WILD-TYPE 201  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     29    3
  AMP PEAK  2(1Q32.1) WILD-TYPE  201   15
   clus
vv  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  0                          29                           201
  1                           3                            15
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  2(1Q32.1) MUTATED    49  12   0
  AMP PEAK  2(1Q32.1) WILD-TYPE 368  66   9
D2V6, multiclass
    clus
vv   AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  M0                          49                           368
  M1                          12                            66
  MX                           0                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
                               cls
clus                              0   1
  AMP PEAK  2(1Q32.1) MUTATED    20  41
  AMP PEAK  2(1Q32.1) WILD-TYPE 158 286
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED     20   41
  AMP PEAK  2(1Q32.1) WILD-TYPE  158  286
        clus
vv       AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE
  FEMALE                          20                           158
  MALE                            41                           286
[1] 2 2
[1] FALSE
D2V8, continuous
D2V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK  2(1Q32.1) MUTATED"
clus
  AMP PEAK  2(1Q32.1) MUTATED AMP PEAK  2(1Q32.1) WILD-TYPE 
                            1                             7 
                   TCGA-A3-A8CQ                    TCGA-B2-A4SR 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-B8-4621                    TCGA-B8-5158 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-B8-5164                    TCGA-B8-A54F 
"AMP PEAK  2(1Q32.1) WILD-TYPE" "AMP PEAK  2(1Q32.1) WILD-TYPE" 
                   TCGA-B8-A54G 
"AMP PEAK  2(1Q32.1) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  2(1Q32.1) MUTATED       1                         3    57
  AMP PEAK  2(1Q32.1) WILD-TYPE     7                        30   400
D2V10, multiclass
                           clus
vv                          AMP PEAK  2(1Q32.1) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           3
  WHITE                                              57
                           clus
vv                          AMP PEAK  2(1Q32.1) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            30
  WHITE                                               400
[1] 3 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(1Q32.1) MUTATED     5  37
  AMP PEAK  2(1Q32.1) WILD-TYPE  19 293
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  2(1Q32.1) MUTATED      5   37
  AMP PEAK  2(1Q32.1) WILD-TYPE   19  293
                        clus
vv                       AMP PEAK  2(1Q32.1) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          37
                        clus
vv                       AMP PEAK  2(1Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           293
[1] 2 2
[1] FALSE

Clustering(3) Variable = AMP PEAK  3(3Q26.32) MUTATION ANALYSIS
D3V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  3(3Q26.32) MUTATED    52   7
  AMP PEAK  3(3Q26.32) WILD-TYPE 286  19
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            59                            305 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                             7                             19 
$`AMP PEAK  3(3Q26.32) MUTATED`
TCGA-A3-3325 TCGA-A3-3374 TCGA-A3-3387 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         751         1314          617         2087         2044         1745 
TCGA-AK-3453 TCGA-B0-4699 TCGA-B0-5097 TCGA-B0-5116 TCGA-B0-5690 TCGA-B0-5696 
        1397          110          665          657         2408         1727 
TCGA-B0-5710 TCGA-B0-5712 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4621 
        1459         2722           16          166          777          788 
TCGA-B8-5163 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 
         822          194           15           53          150         2839 
TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4768 
        2718          845         2859          970          182          400 
TCGA-BP-4781 TCGA-BP-4960 TCGA-BP-4964 TCGA-BP-4969 TCGA-BP-4994 TCGA-BP-5169 
        2080         2172         1862         1794         1308          193 
TCGA-BP-5175 TCGA-BP-5198 TCGA-CJ-4640 TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4873 
         932          603         1998          646         2423         2259 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CW-5588 
        2186         2014         1808         1450         1499         2017 
TCGA-CW-5591 TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 
        2271         1943         1712         1430          330         1740 
TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
        1446           59          946         2067          119 

$`AMP PEAK  3(3Q26.32) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
         873         2270         2274          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ 
         630          567          574          861         1993            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
        3343         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        2192         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1481          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
         369         1238           43           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
          18          183          911         1092          359          797 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5697 
         449         3431         1487         3076         1420         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        2414         3117         2931         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
           7           38          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4622 
         826          838          762          750          523          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         636          722           36           26          737          522 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         505          434         1046          435          830          519 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         256           66          110         3377         2881         2746 
TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3074         3037           13          701         1893         1879 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 
        1955         1670         2964         1625         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 
         645          461         1666         1367          372          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2208         2372         2361         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
        1885         1843          411         1731          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 
         211         2660         1935         1785         1834         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
         205         1746          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
        1124          118         1413          501          177         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 
        1140         1071         2412         2257          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
         749         1018         1355         1063          951           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 
        1820         1416         1924         2308         1628         1793 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2554         1498         1435         2283         2353         1955 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 
        1521          750          841         1528         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1792         1496         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2430         2575          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2609         2226         2378         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
         774         1404           18         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 
        2830         1868         1929         1789           25         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 
        1732         1683          662          685          386         2439 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          206          127           61 

  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                            15                              3 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                          2859                           3668 
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                          1430                           1238 
[1] "15.0 - 2859.0 (1430.0)" "3.0 - 3668.0 (1238.0)" 
[1] "hr=" "1.9"
D3V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  3(3Q26.32) MUTATED        28        6        27       25
  AMP PEAK  3(3Q26.32) WILD-TYPE     216       50        99       54
D3V3, multiclass
           clus
vv          AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  STAGE I                             28                            216
  STAGE II                             6                             50
  STAGE III                           27                             99
  STAGE IV                            25                             54
[1] 4 2
[1] 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(3Q26.32) MUTATED    29   8  45   4
  AMP PEAK  3(3Q26.32) WILD-TYPE 221  59 132   7
D3V4, multiclass
    clus
vv   AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  T1                           29                            221
  T2                            8                             59
  T3                           45                            132
  T4                            4                              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"
D3V5, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.32) MUTATED    42   7
  AMP PEAK  3(3Q26.32) WILD-TYPE 188  11
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED     42    7
  AMP PEAK  3(3Q26.32) WILD-TYPE  188   11
   clus
vv  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  0                           42                            188
  1                            7                             11
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK  3(3Q26.32) MUTATED    59  25   2
  AMP PEAK  3(3Q26.32) WILD-TYPE 358  53   7
D3V6, multiclass
    clus
vv   AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  M0                           59                            358
  M1                           25                             53
  MX                            2                              7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
                                cls
clus                               0   1
  AMP PEAK  3(3Q26.32) MUTATED    32  54
  AMP PEAK  3(3Q26.32) WILD-TYPE 146 273
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED     32   54
  AMP PEAK  3(3Q26.32) WILD-TYPE  146  273
        clus
vv       AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE
  FEMALE                           32                            146
  MALE                             54                            273
[1] 2 2
[1] FALSE
D3V8, continuous
D3V9, continuous
[1] "Remove cluster labels:"       "AMP PEAK  3(3Q26.32) MUTATED"
clus
  AMP PEAK  3(3Q26.32) MUTATED AMP PEAK  3(3Q26.32) WILD-TYPE 
                             2                              6 
                    TCGA-A3-A8CQ                     TCGA-B2-A4SR 
"AMP PEAK  3(3Q26.32) WILD-TYPE" "AMP PEAK  3(3Q26.32) WILD-TYPE" 
                    TCGA-B8-5158                     TCGA-B8-5164 
"AMP PEAK  3(3Q26.32) WILD-TYPE" "AMP PEAK  3(3Q26.32) WILD-TYPE" 
                    TCGA-B8-A54F                     TCGA-G6-A5PC 
"AMP PEAK  3(3Q26.32) WILD-TYPE" "AMP PEAK  3(3Q26.32) WILD-TYPE" 
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  3(3Q26.32) MUTATED       0                         7    78
  AMP PEAK  3(3Q26.32) WILD-TYPE     8                        26   379
D3V10, multiclass
                           clus
vv                          AMP PEAK  3(3Q26.32) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            7
  WHITE                                               78
                           clus
vv                          AMP PEAK  3(3Q26.32) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             26
  WHITE                                                379
[1] 3 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(3Q26.32) MUTATED     4  56
  AMP PEAK  3(3Q26.32) WILD-TYPE  20 274
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  3(3Q26.32) MUTATED      4   56
  AMP PEAK  3(3Q26.32) WILD-TYPE   20  274
                        clus
vv                       AMP PEAK  3(3Q26.32) MUTATED
  HISPANIC OR LATINO                                4
  NOT HISPANIC OR LATINO                           56
                        clus
vv                       AMP PEAK  3(3Q26.32) WILD-TYPE
  HISPANIC OR LATINO                                 20
  NOT HISPANIC OR LATINO                            274
[1] 2 2
[1] FALSE

Clustering(4) Variable = AMP PEAK  4(4Q32.1) MUTATION ANALYSIS
D4V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  4(4Q32.1) MUTATED    10   2
  AMP PEAK  4(4Q32.1) WILD-TYPE 328  24
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                           12                           352 
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                            2                            24 
$`AMP PEAK  4(4Q32.1) MUTATED`
TCGA-A3-3374 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3440 TCGA-BP-4166 TCGA-BP-4782 
        1314          480         2192         1745           13          354 
TCGA-BP-4977 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5177 TCGA-CZ-4856 TCGA-CZ-5469 
         454          118         1308          293           18          946 

$`AMP PEAK  4(4Q32.1) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        1853         2087         2044         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 
        1217         1779         1481         1397          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         110           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          16          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 
        2746         3074         2839         3037         2718          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2372         2361          182         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 
        1014         1413          785         1124         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
         177         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        2257          932         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         967          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
        1355         1063          951           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1924         2308         1998         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
        2554         1498         2423         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2353         1955         2186         2014         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         841         1808         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1792         1496         1499         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1943         2430         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        2489         2609         2226         2017         2378         2271 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4858 
        3222         2552         3146          774         1404         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1789           25         1712         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1430          330          662         1740         1446          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                           13                             3 
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                         2192                          3668 
  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE 
                          467                          1342 
[1] "13.0 - 2192.0 (467.0)" "3.0 - 3668.0 (1342.0)"
[1] "hr=" "4"  
D4V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  4(4Q32.1) MUTATED         7        3         3        3
  AMP PEAK  4(4Q32.1) WILD-TYPE     237       53       123       76
D4V3, multiclass
           clus
vv          AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  STAGE I                             7                           237
  STAGE II                            3                            53
  STAGE III                           3                           123
  STAGE IV                            3                            76
[1] 4 2
[1] 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(4Q32.1) MUTATED     7   3   5   1
  AMP PEAK  4(4Q32.1) WILD-TYPE 243  64 172  10
D4V4, multiclass
    clus
vv   AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  T1                           7                           243
  T2                           3                            64
  T3                           5                           172
  T4                           1                            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"
D4V5, binary
                               cls
clus                              0   1
  AMP PEAK  4(4Q32.1) MUTATED    10   1
  AMP PEAK  4(4Q32.1) WILD-TYPE 220  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4Q32.1) MUTATED     10    1
  AMP PEAK  4(4Q32.1) WILD-TYPE  220   17
   clus
vv  AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  0                          10                           220
  1                           1                            17
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  4(4Q32.1) MUTATED    13   3   0
  AMP PEAK  4(4Q32.1) WILD-TYPE 404  75   9
D4V6, multiclass
    clus
vv   AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  M0                          13                           404
  M1                           3                            75
  MX                           0                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
                               cls
clus                              0   1
  AMP PEAK  4(4Q32.1) MUTATED     7   9
  AMP PEAK  4(4Q32.1) WILD-TYPE 171 318
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4Q32.1) MUTATED      7    9
  AMP PEAK  4(4Q32.1) WILD-TYPE  171  318
        clus
vv       AMP PEAK  4(4Q32.1) MUTATED AMP PEAK  4(4Q32.1) WILD-TYPE
  FEMALE                           7                           171
  MALE                             9                           318
[1] 2 2
[1] FALSE
D4V8, continuous
D4V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  4(4Q32.1) MUTATED       0                         1    15
  AMP PEAK  4(4Q32.1) WILD-TYPE     8                        32   442
D4V10, multiclass
                           clus
vv                          AMP PEAK  4(4Q32.1) MUTATED
  ASIAN                                               0
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              15
                           clus
vv                          AMP PEAK  4(4Q32.1) WILD-TYPE
  ASIAN                                                 8
  BLACK OR AFRICAN AMERICAN                            32
  WHITE                                               442
[1] 3 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(4Q32.1) MUTATED     0   9
  AMP PEAK  4(4Q32.1) WILD-TYPE  24 321
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  4(4Q32.1) MUTATED      0    9
  AMP PEAK  4(4Q32.1) WILD-TYPE   24  321
                        clus
vv                       AMP PEAK  4(4Q32.1) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                           9
                        clus
vv                       AMP PEAK  4(4Q32.1) WILD-TYPE
  HISPANIC OR LATINO                                24
  NOT HISPANIC OR LATINO                           321
[1] 2 2
[1] FALSE

Clustering(5) Variable = AMP PEAK  5(5Q35.1) MUTATION ANALYSIS
D5V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  5(5Q35.1) MUTATED   223  13
  AMP PEAK  5(5Q35.1) WILD-TYPE 115  13
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                          236                           128 
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                           13                            13 
$`AMP PEAK  5(5Q35.1) MUTATED`
TCGA-A3-3307 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 
        1436         1493         1491         1508         1478         1186 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 
         751         1137         1485          665         1043         1610 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3370 
         910         2688         1307         2504         1559         2274 
TCGA-A3-3372 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3385 
         735         1314         1070          567          574         1993 
TCGA-A3-3387 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 
         617         2017          480         2044         1745         1471 
TCGA-AK-3445 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 
        1280         1481         1397          874         1168          951 
TCGA-AK-3461 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
         853           96          183          911         1092          359 
TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 
         797           59          493          554         1132          449 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        3431         1487         3076         1727         1835         2583 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1732         1605         3668         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
        2722         1865         2963         1092          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 
         952          358          315          417          656            7 
TCGA-B4-5834 TCGA-B4-5838 TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5159 
          38          166          511          777          636          722 
TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         822          737          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         435           53          256          150           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 
        3377         2881         3074         2839           13         2718 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4330 TCGA-BP-4335 
        1893         1879         1955         1670         1888          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 
        2859         1666         1367          970         2208         2372 
TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4789 
         400         1843          411         1731         2080         1489 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
        1107         1124         1459         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
        1794         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4991 
         454         1014         1413          785          118         1413 
TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5004 TCGA-BP-5006 
         501         1308         1371         1266         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5181 
        1140         1071         2412          932          293         1495 
TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1291         1132          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4635 
         714          603         1063          951           29         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 
        1924         2308         2554         2423         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4890 
        2353         1955         1759         2125         1952         2085 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
        1521          750         1808         1528         1450         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1560         1792         1499         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        1943         2430         2575         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        2038         1855         1906         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4854 
        2226         2017         2378         2271          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
          18         1943         1787         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        1929         1789           25         1712         1683         1732 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
         330          662         1740          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5568 
         386         2067         1997          373         1905          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
         355         1130          723          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

$`AMP PEAK  5(5Q35.1) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3343 
        1120           16          735         1130         1106          945 
TCGA-A3-3349 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3373 TCGA-A3-3378 
        1385          319          873         2270         1621          630 
TCGA-A3-3383 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3431 
         861            3         3343         2566         2223         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3456 
        2192         2087         1423         1217         1779         1143 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         369         1238           43          110           26          616 
TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5399 TCGA-B0-5690 
          18          665          657          535          652         2408 
TCGA-B0-5695 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B2-3923 TCGA-B2-4098 
        1420         2741         1203         2414          992           51 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 
         507          291          175           16          141           11 
TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
           7          826          838          762          750          523 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5546 
         788          700           36           26          522          505 
TCGA-B8-A54D TCGA-B8-A54F TCGA-BP-4161 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4325 
         830          519         2746         3037          701         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4349 TCGA-BP-4756 
        1625          845         1133          645          372          374 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4970 
         354         1854          620          204          211          433 
TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5169 
        1124          177          932          563         1177          193 
TCGA-BP-5174 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5194 
        2257         2263         1165         1133          693          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4640 TCGA-CJ-4642 
         749         1018         1355         1820         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4878 TCGA-CJ-4881 
        1793          646         1498         1435         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4889 TCGA-CJ-4894 TCGA-CJ-4905 TCGA-CJ-5681 TCGA-CJ-6032 
        1883         1946          841         1496          552         2548 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4862 TCGA-CZ-5459 TCGA-CZ-5460 
        3222         2552         3146         1843         1683         1430 
TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 
        1446         2439          435          693         1329         1398 
TCGA-DV-5567 TCGA-DV-5575 
        1470         1729 

  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                            7                             3 
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                         3668                          3343 
  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE 
                       1424.5                        1062.0 
[1] "7.0 - 3668.0 (1424.5)" "3.0 - 3343.0 (1062.0)"
[1] "hr=" "2.1"
D5V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  5(5Q35.1) MUTATED       149       36        82       54
  AMP PEAK  5(5Q35.1) WILD-TYPE      95       20        44       25
D5V3, multiclass
           clus
vv          AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  STAGE I                           149                            95
  STAGE II                           36                            20
  STAGE III                          82                            44
  STAGE IV                           54                            25
[1] 4 2
[1] 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(5Q35.1) MUTATED   154  46 116   5
  AMP PEAK  5(5Q35.1) WILD-TYPE  96  21  61   6
D5V4, multiclass
    clus
vv   AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  T1                         154                            96
  T2                          46                            21
  T3                         116                            61
  T4                           5                             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"
D5V5, binary
                               cls
clus                              0   1
  AMP PEAK  5(5Q35.1) MUTATED   148   9
  AMP PEAK  5(5Q35.1) WILD-TYPE  82   9
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.1) MUTATED    148    9
  AMP PEAK  5(5Q35.1) WILD-TYPE   82    9
   clus
vv  AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  0                         148                            82
  1                           9                             9
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  5(5Q35.1) MUTATED   261  54   5
  AMP PEAK  5(5Q35.1) WILD-TYPE 156  24   4
D5V6, multiclass
    clus
vv   AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  M0                         261                           156
  M1                          54                            24
  MX                           5                             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"
D5V7, binary
                               cls
clus                              0   1
  AMP PEAK  5(5Q35.1) MUTATED   105 216
  AMP PEAK  5(5Q35.1) WILD-TYPE  73 111
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.1) MUTATED    105  216
  AMP PEAK  5(5Q35.1) WILD-TYPE   73  111
        clus
vv       AMP PEAK  5(5Q35.1) MUTATED AMP PEAK  5(5Q35.1) WILD-TYPE
  FEMALE                         105                            73
  MALE                           216                           111
[1] 2 2
[1] FALSE
D5V8, continuous
D5V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  5(5Q35.1) MUTATED       3                        14   299
  AMP PEAK  5(5Q35.1) WILD-TYPE     5                        19   158
D5V10, multiclass
                           clus
vv                          AMP PEAK  5(5Q35.1) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          14
  WHITE                                             299
                           clus
vv                          AMP PEAK  5(5Q35.1) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            19
  WHITE                                               158
[1] 3 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(5Q35.1) MUTATED    16 210
  AMP PEAK  5(5Q35.1) WILD-TYPE   8 120
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  5(5Q35.1) MUTATED     16  210
  AMP PEAK  5(5Q35.1) WILD-TYPE    8  120
                        clus
vv                       AMP PEAK  5(5Q35.1) MUTATED
  HISPANIC OR LATINO                              16
  NOT HISPANIC OR LATINO                         210
                        clus
vv                       AMP PEAK  5(5Q35.1) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           120
[1] 2 2
[1] FALSE

Clustering(6) Variable = AMP PEAK  6(7Q36.3) MUTATION ANALYSIS
D6V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  6(7Q36.3) MUTATED   112  11
  AMP PEAK  6(7Q36.3) WILD-TYPE 226  15
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                          123                           241 
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                           11                            15 
$`AMP PEAK  6(7Q36.3) MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
         735         1493         1491         1478         1186          751 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
        1043         1610         1307          319          735         1314 
TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 
         574         1993          617            3         3343         2566 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3444 
        2017          480         2192         2044         1745         1471 
TCGA-AK-3453 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5698 
        1397           96          183          359          657         2583 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5639 TCGA-B4-5832 
        1732         1203         1865         1092          417            7 
TCGA-B4-5835 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4619 
          16          166           11            7          511          523 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5550 TCGA-B8-A54I TCGA-BP-4158 
         777          788          700          434          150         3377 
TCGA-BP-4162 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        3074           13         2718         1893         1879         1955 
TCGA-BP-4325 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4759 
        2964         1133          461         2859          970         2372 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4803 TCGA-BP-4804 
        1462          400         1843         2080          204         1459 
TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4971 TCGA-BP-4973 
        2172         1785         1834          205         1487         1384 
TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 
         454         1413         1124          118          501         1308 
TCGA-BP-4998 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5198 TCGA-BP-5200 
         932          193         2412          293          603         1063 
TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         951         1416         1924         2423         1435         2259 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4897 TCGA-CJ-4901 
        2353         2014         2125         1946         1808         1450 
TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5683 
        1560         1496         1499         1943         1883         1889 
TCGA-CJ-5684 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6093 TCGA-CZ-4854 TCGA-CZ-4858 
        2231         2017         2271         3146         1404         1943 
TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 
        1868         1712         1683         1430          330         1740 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5988 TCGA-DV-5565 
         685           59          946         2067          693         1329 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5907 
         723         1729          127 

$`AMP PEAK  6(7Q36.3) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3323 
        1120         1436           16         1130         1508         1106 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
        1137         1485          665          945         1385          910 
TCGA-A3-3357 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
        2688         2504         1559          873         2270         2274 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-AK-3428 
        1621         1070          630          567          861         2223 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        1853         2087         1423         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1481          874         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         369         1238           43          110           26          616 
TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 
          18          665          911         1092          797          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1835         2741         1605         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 
        1459         2931         2722         2963          992           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
         374          648          952          358          315          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B8-4148 
         507          291          175           38          141          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         838          762          750          636          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
         822           26          737          522          505          194 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 
         256           66          110         2881         2746         2839 
TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        3037          701         1670         1625          845         1888 
TCGA-BP-4334 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 
         645         1666         1367          372          374         2208 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 
        2361          182         2184         1876         1885          411 
TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        1731          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 
        1124          211         2660         1935         1862         1871 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 
        1746         1794          433         1502         1433         1632 
TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
        1014          785         1413          177         1371         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        2257          932         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
         967          714          408          749         1018         1355 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
          29         1820         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
         646         2554         1498         2283         1955         2186 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        1883         1759         1952         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4912 
         841         1528         1520         1792         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6027 
        1373         2430         2575          552         2038         1855 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 
        1906         2548         2799         2489         2609         2226 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 
        2378         3222         2552          774           18         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1843         1928         2830         1929         1789           25 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5470 TCGA-CZ-5982 
        1732         1683          662         1446          386         2439 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 
        1997          373          435         1905         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
         370          355         1130          551          119          206 
TCGA-GK-A6C7 
          61 

  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                            3                            15 
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                         3377                          3668 
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                         1416                          1143 
[1] "3.0 - 3377.0 (1416.0)"  "15.0 - 3668.0 (1143.0)"
[1] "hr=" "1.4"
D6V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  6(7Q36.3) MUTATED        70       16        47       37
  AMP PEAK  6(7Q36.3) WILD-TYPE     174       40        79       42
D6V3, multiclass
           clus
vv          AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  STAGE I                            70                           174
  STAGE II                           16                            40
  STAGE III                          47                            79
  STAGE IV                           37                            42
[1] 4 2
[1] 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(7Q36.3) MUTATED    72  21  73   4
  AMP PEAK  6(7Q36.3) WILD-TYPE 178  46 104   7
D6V4, multiclass
    clus
vv   AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  T1                          72                           178
  T2                          21                            46
  T3                          73                           104
  T4                           4                             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"
D6V5, binary
                               cls
clus                              0   1
  AMP PEAK  6(7Q36.3) MUTATED    79   8
  AMP PEAK  6(7Q36.3) WILD-TYPE 151  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7Q36.3) MUTATED     79    8
  AMP PEAK  6(7Q36.3) WILD-TYPE  151   10
   clus
vv  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  0                          79                           151
  1                           8                            10
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  6(7Q36.3) MUTATED   130  38   2
  AMP PEAK  6(7Q36.3) WILD-TYPE 287  40   7
D6V6, multiclass
    clus
vv   AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  M0                         130                           287
  M1                          38                            40
  MX                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
                               cls
clus                              0   1
  AMP PEAK  6(7Q36.3) MUTATED    48 122
  AMP PEAK  6(7Q36.3) WILD-TYPE 130 205
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7Q36.3) MUTATED     48  122
  AMP PEAK  6(7Q36.3) WILD-TYPE  130  205
        clus
vv       AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE
  FEMALE                          48                           130
  MALE                           122                           205
[1] 2 2
[1] FALSE
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:"      "AMP PEAK  6(7Q36.3) MUTATED"
clus
  AMP PEAK  6(7Q36.3) MUTATED AMP PEAK  6(7Q36.3) WILD-TYPE 
                            2                             6 
                   TCGA-B2-A4SR                    TCGA-B8-5158 
"AMP PEAK  6(7Q36.3) WILD-TYPE" "AMP PEAK  6(7Q36.3) WILD-TYPE" 
                   TCGA-B8-5164                    TCGA-B8-A54F 
"AMP PEAK  6(7Q36.3) WILD-TYPE" "AMP PEAK  6(7Q36.3) WILD-TYPE" 
                   TCGA-B8-A54G                    TCGA-G6-A5PC 
"AMP PEAK  6(7Q36.3) WILD-TYPE" "AMP PEAK  6(7Q36.3) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  6(7Q36.3) MUTATED       4                         6   158
  AMP PEAK  6(7Q36.3) WILD-TYPE     4                        27   299
D6V10, multiclass
                           clus
vv                          AMP PEAK  6(7Q36.3) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             158
                           clus
vv                          AMP PEAK  6(7Q36.3) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            27
  WHITE                                               299
[1] 3 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(7Q36.3) MUTATED     4 105
  AMP PEAK  6(7Q36.3) WILD-TYPE  20 225
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  6(7Q36.3) MUTATED      4  105
  AMP PEAK  6(7Q36.3) WILD-TYPE   20  225
                        clus
vv                       AMP PEAK  6(7Q36.3) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                         105
                        clus
vv                       AMP PEAK  6(7Q36.3) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           225
[1] 2 2
[1] FALSE

Clustering(7) Variable = AMP PEAK  7(8Q24.22) MUTATION ANALYSIS
D7V1, survival
                                sevent
clus2                              0   1
  AMP PEAK  7(8Q24.22) MUTATED    47   7
  AMP PEAK  7(8Q24.22) WILD-TYPE 291  19
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                            54                            310 
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                             7                             19 
$`AMP PEAK  7(8Q24.22) MUTATED`
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 
          16          735         1493         1130          751         1043 
TCGA-AK-3425 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3445 TCGA-AK-3454 TCGA-B0-4813 
        3343         2192         2087         1280          874           18 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5701 TCGA-B0-5703 TCGA-B4-5832 TCGA-B8-5158 
         665          911         1732         1203            7          636 
TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4759 
         822           15          150         1879         2859         2372 
TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4962 TCGA-BP-4983 TCGA-BP-5000 TCGA-BP-5169 
         182          400         1785         1413          563          193 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5198 TCGA-CJ-4871 
         932          293         1132          967          603         2423 
TCGA-CJ-4881 TCGA-CJ-4890 TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-6031 TCGA-CW-5588 
        2014         2085         1450         1657         1906         2017 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5464 
        2271         1404         1943         1868         1712         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 
        1446          685           59          946          386          435 

$`AMP PEAK  7(8Q24.22) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1120         1436         1491         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 
        1186         1137         1485          665          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        1993          617            3         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
         480         1853         2044         1745         1423         1471 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
        1217         1779         1481         1397         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 
         951          853          369         1238           43          110 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5110 TCGA-B0-5113 
          26           96          616          183         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1605         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
         656          507          291          175           38           16 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         700          722           36           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D 
         505          194          434         1046          435          830 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
         519           53          256           66          110         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        2881         2746         3074         2839         3037           13 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
        2718          701         1893         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2361         2184         1462         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
         411         1731         2080          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2660         2172         1935         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4986 
        1384         1433         1632          454         1014          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        1371          932         1266         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5180 TCGA-BP-5181 
        1140         1071         2412         2257         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1165         1291         1133          693          406          822 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
        1011          714          408          749         1018         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        1498         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2186         1883         1759         2125         1952         1946 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 
        1521          750          841         1808         1528         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 
        1560         1792         1496         1499         1531         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1943         2430         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2231         2038         1855         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2609         2226         2378         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
         774           18         1787         1843         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1929         1789           25         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1430          330          662         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         373          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                             7                              3 
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                          3343                           3668 
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                        1131.0                         1321.5 
[1] "7.0 - 3343.0 (1131.0)" "3.0 - 3668.0 (1321.5)"
[1] "hr=" "2.2"
D7V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  7(8Q24.22) MUTATED        23       10        26       18
  AMP PEAK  7(8Q24.22) WILD-TYPE     221       46       100       61
D7V3, multiclass
           clus
vv          AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  STAGE I                             23                            221
  STAGE II                            10                             46
  STAGE III                           26                            100
  STAGE IV                            18                             61
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                                vv
clus                              T1  T2  T3  T4
  AMP PEAK  7(8Q24.22) MUTATED    24  11  40   2
  AMP PEAK  7(8Q24.22) WILD-TYPE 226  56 137   9
D7V4, multiclass
    clus
vv   AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  T1                           24                            226
  T2                           11                             56
  T3                           40                            137
  T4                            2                              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"
D7V5, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q24.22) MUTATED    34   3
  AMP PEAK  7(8Q24.22) WILD-TYPE 196  15
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.22) MUTATED     34    3
  AMP PEAK  7(8Q24.22) WILD-TYPE  196   15
   clus
vv  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  0                           34                            196
  1                            3                             15
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  AMP PEAK  7(8Q24.22) MUTATED    58  18   1
  AMP PEAK  7(8Q24.22) WILD-TYPE 359  60   8
D7V6, multiclass
    clus
vv   AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  M0                           58                            359
  M1                           18                             60
  MX                            1                              8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
                                cls
clus                               0   1
  AMP PEAK  7(8Q24.22) MUTATED    21  56
  AMP PEAK  7(8Q24.22) WILD-TYPE 157 271
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.22) MUTATED     21   56
  AMP PEAK  7(8Q24.22) WILD-TYPE  157  271
        clus
vv       AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE
  FEMALE                           21                            157
  MALE                             56                            271
[1] 2 2
[1] FALSE
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:"       "AMP PEAK  7(8Q24.22) MUTATED"
clus
  AMP PEAK  7(8Q24.22) MUTATED AMP PEAK  7(8Q24.22) WILD-TYPE 
                             1                              7 
                    TCGA-A3-A8CQ                     TCGA-B2-A4SR 
"AMP PEAK  7(8Q24.22) WILD-TYPE" "AMP PEAK  7(8Q24.22) WILD-TYPE" 
                    TCGA-B8-4621                     TCGA-B8-5164 
"AMP PEAK  7(8Q24.22) WILD-TYPE" "AMP PEAK  7(8Q24.22) WILD-TYPE" 
                    TCGA-B8-A54F                     TCGA-B8-A54G 
"AMP PEAK  7(8Q24.22) WILD-TYPE" "AMP PEAK  7(8Q24.22) WILD-TYPE" 
                    TCGA-G6-A5PC 
"AMP PEAK  7(8Q24.22) WILD-TYPE" 
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  7(8Q24.22) MUTATED       2                         3    69
  AMP PEAK  7(8Q24.22) WILD-TYPE     6                        30   388
D7V10, multiclass
                           clus
vv                          AMP PEAK  7(8Q24.22) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            3
  WHITE                                               69
                           clus
vv                          AMP PEAK  7(8Q24.22) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             30
  WHITE                                                388
[1] 3 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(8Q24.22) MUTATED     1  48
  AMP PEAK  7(8Q24.22) WILD-TYPE  23 282
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  AMP PEAK  7(8Q24.22) MUTATED      1   48
  AMP PEAK  7(8Q24.22) WILD-TYPE   23  282
                        clus
vv                       AMP PEAK  7(8Q24.22) MUTATED
  HISPANIC OR LATINO                                1
  NOT HISPANIC OR LATINO                           48
                        clus
vv                       AMP PEAK  7(8Q24.22) WILD-TYPE
  HISPANIC OR LATINO                                 23
  NOT HISPANIC OR LATINO                            282
[1] 2 2
[1] FALSE

Clustering(8) Variable = AMP PEAK  8(10P14) MUTATION ANALYSIS
D8V1, survival
                              sevent
clus2                            0   1
  AMP PEAK  8(10P14) MUTATED    13   1
  AMP PEAK  8(10P14) WILD-TYPE 325  25
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                          14                          350 
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                           1                           25 
$`AMP PEAK  8(10P14) MUTATED`
TCGA-A3-3316 TCGA-AK-3453 TCGA-B4-5832 TCGA-B4-5838 TCGA-BP-4338 TCGA-BP-4768 
        1493         1397            7          166         2859          400 
TCGA-BP-4781 TCGA-BP-4986 TCGA-BP-5175 TCGA-CJ-5675 TCGA-CW-5588 TCGA-CZ-4854 
        2080          785          932         2430         2017         1404 
TCGA-CZ-4866 TCGA-EU-5905 
        1868          119 

$`AMP PEAK  8(10P14) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
         617            3         3343         2566         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
         480         1853         2192         2087         2044         1745 
TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        1423         1471         1280         1217         1779         1481 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
         874         1143         1168          951          853          369 
TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1238           43          110           26           96          616 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          18          183          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          38           16          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        2746         3074         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
         701         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 
        1625          845         1888         1133          645          461 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2372         2361          182         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 
        1885         1843          411         1731          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1014         1413         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         177         1308         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 
        1177         1126          840         1140         1071          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2412         2257          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1416         1924         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         646         2554         1498         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2283         2353         1955         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
         750          841         1808         1528         1450         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        1560         1792         1496         1499         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1373         1943         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2489         2609         2226         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        2552         3146          774           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1843         1928         2830         1929         1789           25 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
        1712         1683         1732         1683         1430          330 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
         662         1740         1446          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
         355         1130          723         1729          551          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                           7                            3 
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                        2859                         3668 
  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE 
                      1400.5                       1285.5 
[1] "7.0 - 2859.0 (1400.5)" "3.0 - 3668.0 (1285.5)"
[1] "hr=" "1"  
D8V2, continuous
                              vv
clus                           STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  8(10P14) MUTATED         9        4         3        4
  AMP PEAK  8(10P14) WILD-TYPE     235       52       123       75
D8V3, multiclass
           clus
vv          AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  STAGE I                            9                          235
  STAGE II                           4                           52
  STAGE III                          3                          123
  STAGE IV                           4                           75
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                              vv
clus                            T1  T2  T3  T4
  AMP PEAK  8(10P14) MUTATED     9   5   4   2
  AMP PEAK  8(10P14) WILD-TYPE 241  62 173   9
D8V4, multiclass
    clus
vv   AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  T1                          9                          241
  T2                          5                           62
  T3                          4                          173
  T4                          2                            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"
D8V5, binary
                              cls
clus                             0   1
  AMP PEAK  8(10P14) MUTATED    10   2
  AMP PEAK  8(10P14) WILD-TYPE 220  16
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  8(10P14) MUTATED     10    2
  AMP PEAK  8(10P14) WILD-TYPE  220   16
   clus
vv  AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  0                         10                          220
  1                          2                           16
[1] 2 2
[1] FALSE
                              vv
clus                            M0  M1  MX
  AMP PEAK  8(10P14) MUTATED    16   4   0
  AMP PEAK  8(10P14) WILD-TYPE 401  74   9
D8V6, multiclass
    clus
vv   AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  M0                         16                          401
  M1                          4                           74
  MX                          0                            9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
                              cls
clus                             0   1
  AMP PEAK  8(10P14) MUTATED     6  14
  AMP PEAK  8(10P14) WILD-TYPE 172 313
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  8(10P14) MUTATED      6   14
  AMP PEAK  8(10P14) WILD-TYPE  172  313
        clus
vv       AMP PEAK  8(10P14) MUTATED AMP PEAK  8(10P14) WILD-TYPE
  FEMALE                          6                          172
  MALE                           14                          313
[1] 2 2
[1] FALSE
D8V8, continuous
D8V9, continuous
                              vv
clus                           ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  8(10P14) MUTATED       0                         0    20
  AMP PEAK  8(10P14) WILD-TYPE     8                        33   437
D8V10, multiclass
                           clus
vv                          AMP PEAK  8(10P14) MUTATED
  ASIAN                                              0
  BLACK OR AFRICAN AMERICAN                          0
  WHITE                                             20
                           clus
vv                          AMP PEAK  8(10P14) WILD-TYPE
  ASIAN                                                8
  BLACK OR AFRICAN AMERICAN                           33
  WHITE                                              437
[1] 3 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
  AMP PEAK  8(10P14) MUTATED     1  12
  AMP PEAK  8(10P14) WILD-TYPE  23 318
[1] "tbl2"
                              cls
clus                           [,1] [,2]
  AMP PEAK  8(10P14) MUTATED      1   12
  AMP PEAK  8(10P14) WILD-TYPE   23  318
                        clus
vv                       AMP PEAK  8(10P14) MUTATED
  HISPANIC OR LATINO                              1
  NOT HISPANIC OR LATINO                         12
                        clus
vv                       AMP PEAK  8(10P14) WILD-TYPE
  HISPANIC OR LATINO                               23
  NOT HISPANIC OR LATINO                          318
[1] 2 2
[1] FALSE

Clustering(9) Variable = AMP PEAK  9(XP22.2) MUTATION ANALYSIS
D9V1, survival
                               sevent
clus2                             0   1
  AMP PEAK  9(XP22.2) MUTATED    18   3
  AMP PEAK  9(XP22.2) WILD-TYPE 320  23
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                           21                           343 
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                            3                            23 
$`AMP PEAK  9(XP22.2) MUTATED`
TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3453 TCGA-BP-4162 
         574         2017         2044         1280         1397         3074 
TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4756 TCGA-BP-4969 TCGA-BP-4989 TCGA-CJ-4642 
        1879         2859          374         1794          118         1628 
TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-5681 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 
        2125         1528          552         2271         1404         1712 
TCGA-CZ-5464 TCGA-CZ-5468 TCGA-EU-5905 
        1740           59          119 

$`AMP PEAK  9(XP22.2) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
        1314         1070          630          567          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
         617            3         3343         2566         2223          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        1853         2192         2087         1745         1423         1471 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1217         1779         1481          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 
         951          853          369         1238           43          110 
TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
          26           96          616           18          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         911         1092          359          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 
         648          952          358          315          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 
         507          291          175            7           38           16 
TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         141          166           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         838          762          750          523          777          788 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         700          636          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
         737          522          505          194          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         150           66          110         3377         2881         2746 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          645          461         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         970         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1462          400         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
         205         1746          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        1124         1413          501          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        2308         1998         1793          646         2554         1498 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2423         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4889 
        2186         2014         1883         1759         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 
        2085         1521          750          841         1808         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 
        1657         1373         1943         2430         2575         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 
        3222         2552         3146          774           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 
        1787         1843         1928         2830         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1789           25         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 
         330          662         1446          685          946          386 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
        2439         2067         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
        1130          723         1729          551          206          127 
TCGA-GK-A6C7 
          61 

  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                           59                             3 
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                         3074                          3668 
  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE 
                         1628                          1217 
[1] "59.0 - 3074.0 (1628.0)" "3.0 - 3668.0 (1217.0)" 
[1] "hr=" "1.9"
D9V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK  9(XP22.2) MUTATED         9        5         7        9
  AMP PEAK  9(XP22.2) WILD-TYPE     235       51       119       70
D9V3, multiclass
           clus
vv          AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  STAGE I                             9                           235
  STAGE II                            5                            51
  STAGE III                           7                           119
  STAGE IV                            9                            70
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK  9(XP22.2) MUTATED     9   6  14   1
  AMP PEAK  9(XP22.2) WILD-TYPE 241  61 163  10
D9V4, multiclass
    clus
vv   AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  T1                           9                           241
  T2                           6                            61
  T3                          14                           163
  T4                           1                            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"
D9V5, binary
                               cls
clus                              0   1
  AMP PEAK  9(XP22.2) MUTATED    17   1
  AMP PEAK  9(XP22.2) WILD-TYPE 213  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(XP22.2) MUTATED     17    1
  AMP PEAK  9(XP22.2) WILD-TYPE  213   17
   clus
vv  AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  0                          17                           213
  1                           1                            17
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK  9(XP22.2) MUTATED    22   8   0
  AMP PEAK  9(XP22.2) WILD-TYPE 395  70   9
D9V6, multiclass
    clus
vv   AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  M0                          22                           395
  M1                           8                            70
  MX                           0                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
                               cls
clus                              0   1
  AMP PEAK  9(XP22.2) MUTATED    11  19
  AMP PEAK  9(XP22.2) WILD-TYPE 167 308
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(XP22.2) MUTATED     11   19
  AMP PEAK  9(XP22.2) WILD-TYPE  167  308
        clus
vv       AMP PEAK  9(XP22.2) MUTATED AMP PEAK  9(XP22.2) WILD-TYPE
  FEMALE                          11                           167
  MALE                            19                           308
[1] 2 2
[1] FALSE
D9V8, continuous
D9V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK  9(XP22.2) MUTATED       2                         0    28
  AMP PEAK  9(XP22.2) WILD-TYPE     6                        33   429
D9V10, multiclass
                           clus
vv                          AMP PEAK  9(XP22.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           0
  WHITE                                              28
                           clus
vv                          AMP PEAK  9(XP22.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            33
  WHITE                                               429
[1] 3 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
  AMP PEAK  9(XP22.2) MUTATED     0  15
  AMP PEAK  9(XP22.2) WILD-TYPE  24 315
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK  9(XP22.2) MUTATED      0   15
  AMP PEAK  9(XP22.2) WILD-TYPE   24  315
                        clus
vv                       AMP PEAK  9(XP22.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          15
                        clus
vv                       AMP PEAK  9(XP22.2) WILD-TYPE
  HISPANIC OR LATINO                                24
  NOT HISPANIC OR LATINO                           315
[1] 2 2
[1] FALSE

Clustering(10) Variable = AMP PEAK 10(XP11.4) MUTATION ANALYSIS
D10V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 10(XP11.4) MUTATED    21   3
  AMP PEAK 10(XP11.4) WILD-TYPE 317  23
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                           24                           340 
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                            3                            23 
$`AMP PEAK 10(XP11.4) MUTATED`
TCGA-A3-3325 TCGA-A3-3382 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3453 
         751          574         2017         2044         1280         1397 
TCGA-B8-A54I TCGA-BP-4162 TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4756 TCGA-BP-4969 
         150         3074         1879         2859          374         1794 
TCGA-BP-4989 TCGA-BP-5199 TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-5681 
         118         1355         2125         1528         1520          552 
TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-EU-5905 
        2271         1404         1712         1740           59          119 

$`AMP PEAK 10(XP11.4) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1130         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 
        1485          665         1043          945         1610         1385 
TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
         910         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          567          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
           3         3343         2566         2223          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
        2192         2087         1745         1423         1471         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1779         1481          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
        1092          359          797          657          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2583         2741         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2414         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        2963          992         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J 
         435          830          519           53          256           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4165 
         110         3377         2881         2746         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4176 TCGA-BP-4177 
          13         2718          701         1893         1955         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
        2964         1625          845         1888         1133          645 
TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4758 
         461         1666         1367          372          970         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2372         2361          182         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 
         354         1854         1489          620         1107         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
         204         1459          211         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4991 
         454         1014         1413          785         1124         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 
         193         2412         2257          932          293         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
         749         1018          603         1063          951           29 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
        1820         1416         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793          646         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        2259         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1883         1759         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 
         750          841         1808         1450         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1496         1499         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2430         2575         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2226         2017         2378         3222         2552         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
         774           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 
        2830         1868         1929         1789           25         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 
        1732         1683         1430          330          662         1446 
TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
         685          946          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130          723         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         551          206          127           61 

  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                           59                             3 
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                         3074                          3668 
  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE 
                       1462.0                        1227.5 
[1] "59.0 - 3074.0 (1462.0)" "3.0 - 3668.0 (1227.5)" 
[1] "hr=" "1.7"
D10V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 10(XP11.4) MUTATED        10        5         7       10
  AMP PEAK 10(XP11.4) WILD-TYPE     234       51       119       69
D10V3, multiclass
           clus
vv          AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  STAGE I                            10                           234
  STAGE II                            5                            51
  STAGE III                           7                           119
  STAGE IV                           10                            69
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 10(XP11.4) MUTATED    10   6  15   1
  AMP PEAK 10(XP11.4) WILD-TYPE 240  61 162  10
D10V4, multiclass
    clus
vv   AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  T1                          10                           240
  T2                           6                            61
  T3                          15                           162
  T4                           1                            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"
D10V5, binary
                               cls
clus                              0   1
  AMP PEAK 10(XP11.4) MUTATED    17   1
  AMP PEAK 10(XP11.4) WILD-TYPE 213  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP11.4) MUTATED     17    1
  AMP PEAK 10(XP11.4) WILD-TYPE  213   17
   clus
vv  AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  0                          17                           213
  1                           1                            17
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 10(XP11.4) MUTATED    22   9   1
  AMP PEAK 10(XP11.4) WILD-TYPE 395  69   8
D10V6, multiclass
    clus
vv   AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  M0                          22                           395
  M1                           9                            69
  MX                           1                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
                               cls
clus                              0   1
  AMP PEAK 10(XP11.4) MUTATED    11  21
  AMP PEAK 10(XP11.4) WILD-TYPE 167 306
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP11.4) MUTATED     11   21
  AMP PEAK 10(XP11.4) WILD-TYPE  167  306
        clus
vv       AMP PEAK 10(XP11.4) MUTATED AMP PEAK 10(XP11.4) WILD-TYPE
  FEMALE                          11                           167
  MALE                            21                           306
[1] 2 2
[1] FALSE
D10V8, continuous
D10V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 10(XP11.4) MUTATED       2                         1    29
  AMP PEAK 10(XP11.4) WILD-TYPE     6                        32   428
D10V10, multiclass
                           clus
vv                          AMP PEAK 10(XP11.4) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              29
                           clus
vv                          AMP PEAK 10(XP11.4) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            32
  WHITE                                               428
[1] 3 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
  AMP PEAK 10(XP11.4) MUTATED     0  19
  AMP PEAK 10(XP11.4) WILD-TYPE  24 311
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 10(XP11.4) MUTATED      0   19
  AMP PEAK 10(XP11.4) WILD-TYPE   24  311
                        clus
vv                       AMP PEAK 10(XP11.4) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          19
                        clus
vv                       AMP PEAK 10(XP11.4) WILD-TYPE
  HISPANIC OR LATINO                                24
  NOT HISPANIC OR LATINO                           311
[1] 2 2
[1] FALSE

Clustering(11) Variable = AMP PEAK 11(XQ11.2) MUTATION ANALYSIS
D11V1, survival
                               sevent
clus2                             0   1
  AMP PEAK 11(XQ11.2) MUTATED    19   1
  AMP PEAK 11(XQ11.2) WILD-TYPE 319  25
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                           20                           344 
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                            1                            25 
$`AMP PEAK 11(XQ11.2) MUTATED`
TCGA-A3-3363 TCGA-AK-3429 TCGA-AK-3436 TCGA-AK-3453 TCGA-B8-A54I TCGA-BP-4162 
         319         2017         2044         1397          150         3074 
TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4969 TCGA-BP-4989 
        1879         2859         1876         1885         1794          118 
TCGA-CJ-4885 TCGA-CJ-4899 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5458 
        2125         1528         2271         1404         1712         1732 
TCGA-CZ-5464 TCGA-EU-5905 
        1740          119 

$`AMP PEAK 11(XQ11.2) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 
         617            3         3343         2566         2223          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 
        1853         2192         2087         1745         1423         1471 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 
        1280         1217         1779         1481          874         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         110           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 
         665          911         1092          359          797          657 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
        1203         3668         2414         3117         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        2722         1865         2963          992         1092           51 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
         374          648          952          358          315          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
          16          141          166           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         256           66          110         3377         2881         2746 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          645          461         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        2184         1462          400         1843          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        2080          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1746          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1632          454         1014         1413          785         1124 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 
        1413          501          177         1308         1371          932 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
        1266          563         1177         1126          840         1140 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 
        1071          193         2412         2257          932          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2263         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        2423         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 TCGA-CJ-4889 
        2186         2014         1883         1759         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 
        2085         1521          750          841         1808         1450 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1520         1560         1792         1496         1499         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1883         1889         2231         2038         1855         1906 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2548         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
        2378         3222         2552         3146          774           18 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
        1943         1787         1843         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 
        1929         1789           25         1683         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
         330          662         1446          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
         355         1130          723         1729          551          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                          118                             3 
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                         3074                          3668 
  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE 
                       1767.0                        1194.5 
[1] "118.0 - 3074.0 (1767.0)" "3.0 - 3668.0 (1194.5)"  
[1] "hr=" "1.8"
D11V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 11(XQ11.2) MUTATED        11        5         6        6
  AMP PEAK 11(XQ11.2) WILD-TYPE     233       51       120       73
D11V3, multiclass
           clus
vv          AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  STAGE I                            11                           233
  STAGE II                            5                            51
  STAGE III                           6                           120
  STAGE IV                            6                            73
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  AMP PEAK 11(XQ11.2) MUTATED    11   6  11   0
  AMP PEAK 11(XQ11.2) WILD-TYPE 239  61 166  11
D11V4, multiclass
    clus
vv   AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  T1                          11                           239
  T2                           6                            61
  T3                          11                           166
  T4                           0                            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"
D11V5, binary
                               cls
clus                              0   1
  AMP PEAK 11(XQ11.2) MUTATED    15   1
  AMP PEAK 11(XQ11.2) WILD-TYPE 215  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XQ11.2) MUTATED     15    1
  AMP PEAK 11(XQ11.2) WILD-TYPE  215   17
   clus
vv  AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  0                          15                           215
  1                           1                            17
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  AMP PEAK 11(XQ11.2) MUTATED    21   6   1
  AMP PEAK 11(XQ11.2) WILD-TYPE 396  72   8
D11V6, multiclass
    clus
vv   AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  M0                          21                           396
  M1                           6                            72
  MX                           1                             8
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
                               cls
clus                              0   1
  AMP PEAK 11(XQ11.2) MUTATED    10  18
  AMP PEAK 11(XQ11.2) WILD-TYPE 168 309
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XQ11.2) MUTATED     10   18
  AMP PEAK 11(XQ11.2) WILD-TYPE  168  309
        clus
vv       AMP PEAK 11(XQ11.2) MUTATED AMP PEAK 11(XQ11.2) WILD-TYPE
  FEMALE                          10                           168
  MALE                            18                           309
[1] 2 2
[1] FALSE
D11V8, continuous
D11V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 11(XQ11.2) MUTATED       2                         1    25
  AMP PEAK 11(XQ11.2) WILD-TYPE     6                        32   432
D11V10, multiclass
                           clus
vv                          AMP PEAK 11(XQ11.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           1
  WHITE                                              25
                           clus
vv                          AMP PEAK 11(XQ11.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            32
  WHITE                                               432
[1] 3 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
  AMP PEAK 11(XQ11.2) MUTATED     0  14
  AMP PEAK 11(XQ11.2) WILD-TYPE  24 316
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  AMP PEAK 11(XQ11.2) MUTATED      0   14
  AMP PEAK 11(XQ11.2) WILD-TYPE   24  316
                        clus
vv                       AMP PEAK 11(XQ11.2) MUTATED
  HISPANIC OR LATINO                               0
  NOT HISPANIC OR LATINO                          14
                        clus
vv                       AMP PEAK 11(XQ11.2) WILD-TYPE
  HISPANIC OR LATINO                                24
  NOT HISPANIC OR LATINO                           316
[1] 2 2
[1] FALSE

Clustering(12) Variable = AMP PEAK 12(XQ28) MUTATION ANALYSIS
D12V1, survival
                             sevent
clus2                           0   1
  AMP PEAK 12(XQ28) MUTATED    24   2
  AMP PEAK 12(XQ28) WILD-TYPE 314  24
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                         26                         338 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                          2                          24 
$`AMP PEAK 12(XQ28) MUTATED`
TCGA-A3-3317 TCGA-A3-3336 TCGA-A3-3383 TCGA-AK-3428 TCGA-AK-3436 TCGA-AK-3453 
        1491         1043          861         2223         2044         1397 
TCGA-B0-5120 TCGA-B0-5705 TCGA-B8-5159 TCGA-B8-A54D TCGA-B8-A54I TCGA-BP-4162 
         493         3668          722          830          150         3074 
TCGA-BP-4174 TCGA-BP-4338 TCGA-BP-4959 TCGA-BP-4969 TCGA-BP-4989 TCGA-CJ-4885 
        1879         2859         2660         1794          118         2125 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CZ-4854 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5461 
        2271         3222         1404         1712         1732          330 
TCGA-CZ-5464 TCGA-EU-5905 
        1740          119 

$`AMP PEAK 12(XQ28) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 
        1120         1436           16          735         1493         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
        1485          665          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 
        2270         2274          735         1621         1314         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         630          567          574         1993          617            3 
TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
        3343         2566         2017          480         1853         2192 
TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        2087         1745         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1779         1481          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 
        1092          359          797          657          535           59 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5709 
        2741         1732         1605         1203         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 
           7           38           16          141          166           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5162 
         523          777          788          700          636           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
         822           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54F TCGA-B8-A54G 
         434           15         1046          435          519           53 
TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 
         256           66          110         3377         2881         2746 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
        2839         3037           13         2718          701         1893 
TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1955         1670         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          645          461         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         970          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 
        2184         1462          400         1876         1885         1843 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
         411         1731         2080          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
         620         1107         1124          204         1459          211 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
        2172         1935         1785         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
         205         1746          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 
        1124         1413          501          177         1308         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
         714          408          749         1018          603         1355 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1063          951           29         1820         1416         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
        1955         2186         2014         1883         1759         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1946         2085         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
        1528         1450         1520         1560         1792         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1499         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2575          552         1883         1889         2231         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        1855         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
        2226         2017         2378         2552         3146          774 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 
        1868         1929         1789           25         1683         1683 
TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
        1430          662         1446          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
         355         1130          723         1729          551          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                        118                           3 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                       3668                        3431 
  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE 
                     1722.0                      1227.5 
[1] "118.0 - 3668.0 (1722.0)" "3.0 - 3431.0 (1227.5)"  
[1] "hr=" "1.1"
D12V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  AMP PEAK 12(XQ28) MUTATED        14        4         9        8
  AMP PEAK 12(XQ28) WILD-TYPE     230       52       117       71
D12V3, multiclass
           clus
vv          AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  STAGE I                          14                         230
  STAGE II                          4                          52
  STAGE III                         9                         117
  STAGE IV                          8                          71
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                             vv
clus                           T1  T2  T3  T4
  AMP PEAK 12(XQ28) MUTATED    15   5  14   1
  AMP PEAK 12(XQ28) WILD-TYPE 235  62 163  10
D12V4, multiclass
    clus
vv   AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  T1                        15                         235
  T2                         5                          62
  T3                        14                         163
  T4                         1                          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"
D12V5, binary
                             cls
clus                            0   1
  AMP PEAK 12(XQ28) MUTATED    20   1
  AMP PEAK 12(XQ28) WILD-TYPE 210  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED     20    1
  AMP PEAK 12(XQ28) WILD-TYPE  210   17
   clus
vv  AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  0                        20                         210
  1                         1                          17
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  AMP PEAK 12(XQ28) MUTATED    25   8   2
  AMP PEAK 12(XQ28) WILD-TYPE 392  70   7
D12V6, multiclass
    clus
vv   AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  M0                        25                         392
  M1                         8                          70
  MX                         2                           7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
                             cls
clus                            0   1
  AMP PEAK 12(XQ28) MUTATED    13  22
  AMP PEAK 12(XQ28) WILD-TYPE 165 305
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED     13   22
  AMP PEAK 12(XQ28) WILD-TYPE  165  305
        clus
vv       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  FEMALE                        13                         165
  MALE                          22                         305
[1] 2 2
[1] FALSE
D12V8, continuous
D12V9, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  AMP PEAK 12(XQ28) MUTATED       0                         2    32
  AMP PEAK 12(XQ28) WILD-TYPE     8                        31   425
D12V10, multiclass
                           clus
vv                          AMP PEAK 12(XQ28) MUTATED
  ASIAN                                             0
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            32
                           clus
vv                          AMP PEAK 12(XQ28) WILD-TYPE
  ASIAN                                               8
  BLACK OR AFRICAN AMERICAN                          31
  WHITE                                             425
[1] 3 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
  AMP PEAK 12(XQ28) MUTATED     0  22
  AMP PEAK 12(XQ28) WILD-TYPE  24 308
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  AMP PEAK 12(XQ28) MUTATED      0   22
  AMP PEAK 12(XQ28) WILD-TYPE   24  308
                        clus
vv                       AMP PEAK 12(XQ28) MUTATED AMP PEAK 12(XQ28) WILD-TYPE
  HISPANIC OR LATINO                             0                          24
  NOT HISPANIC OR LATINO                        22                         308
[1] 2 2
[1] FALSE

Clustering(13) Variable = DEL PEAK  1(1P36.23) MUTATION ANALYSIS
D13V1, survival
                                sevent
clus2                              0   1
  DEL PEAK  1(1P36.23) MUTATED    57   9
  DEL PEAK  1(1P36.23) WILD-TYPE 281  17
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                            66                            298 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             9                             17 
$`DEL PEAK  1(1P36.23) MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3347 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 
         735         1493         1610         1621         1314          567 
TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3453 
        2566         2192         2044         1745         1217         1397 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5117 
         369         1238          110          616           18          535 
TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5709 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5641 
        1732         1203         3117          992           51          656 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5162 TCGA-B8-5164 
           7           16          166          523           36           26 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4338 
         194          434           15         1955          645         2859 
TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4986 
         400         1843         2080         1871         1746          785 
TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5185 TCGA-BP-5201 TCGA-CJ-4635 
         118         1308         1126         1132          951         1416 
TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4876 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4901 
        1998         2554         1955          841         1808         1450 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5588 TCGA-CW-6090 
        1560         1499         1855         1906         2017         2552 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 TCGA-EU-5907 TCGA-GK-A6C7 
        2830         1868         1683          946          127           61 

$`DEL PEAK  1(1P36.23) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        1120         1436           16         1491         1130         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1478         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
         665         1043          945         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 
        2274          735         1070          630          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
        1993          617            3         3343         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
         480         1853         2087         1423         1471         1280 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1779         1481          874         1143         1168          951 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5097 
         853           43           26           96          183          665 
TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
         911         1092          359          797          657           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         493          554          652         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 
        2583         2741         1605         3668         2414         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 
        2931         2722         1865         2963         1092          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR 
         648          952          358          315          417          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
         291          175           38          141           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
         511          826          838          762          750          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 
         788          700          636          722          822          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         522          505         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
          53          256          150           66          110         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        2881         2746         3074         2839         3037           13 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 
        2718          701         1893         1879         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4344 
        1625          845         1888         1133          461         1666 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1367          372          970          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 
        2361          182         2184         1462         1876         1885 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
         411         1731          354         1854         1489          620 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
        2172         1935         1785         1834         1862          205 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 
        1794          433         1487         1502         1384         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4991 
        1632          454         1014         1413         1124         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         501          177         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1177          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1291         1133          693          406          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         967          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 
        1355         1063           29         1820         1924         2308 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1628         1793          646         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2259         2283         2353         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
         750         1528         1520         1792         1496         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1657         1373         1943         2430         2575          552 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 
        1883         1889         2231         2038         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2489         2609         2226         2378         2271         3222 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 
        1843         1928         1929         1789           25         1712 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1446          685           59          386         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
        1997          373          435          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1729          551          119          206 

  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             7                              3 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                          3117                           3668 
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                          1273                           1299 
[1] "7.0 - 3117.0 (1273.0)" "3.0 - 3668.0 (1299.0)"
[1] "hr=" "2.5"
D13V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  1(1P36.23) MUTATED        43       12        25       21
  DEL PEAK  1(1P36.23) WILD-TYPE     201       44       101       58
D13V3, multiclass
           clus
vv          DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  STAGE I                             43                            201
  STAGE II                            12                             44
  STAGE III                           25                            101
  STAGE IV                            21                             58
[1] 4 2
[1] 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(1P36.23) MUTATED    46  17  33   5
  DEL PEAK  1(1P36.23) WILD-TYPE 204  50 144   6
D13V4, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  T1                           46                            204
  T2                           17                             50
  T3                           33                            144
  T4                            5                              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"
D13V5, binary
                                cls
clus                               0   1
  DEL PEAK  1(1P36.23) MUTATED    50   4
  DEL PEAK  1(1P36.23) WILD-TYPE 180  14
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     50    4
  DEL PEAK  1(1P36.23) WILD-TYPE  180   14
   clus
vv  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  0                           50                            180
  1                            4                             14
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK  1(1P36.23) MUTATED    80  20   1
  DEL PEAK  1(1P36.23) WILD-TYPE 337  58   8
D13V6, multiclass
    clus
vv   DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  M0                           80                            337
  M1                           20                             58
  MX                            1                              8
[1] 3 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  1(1P36.23) MUTATED    29  72
  DEL PEAK  1(1P36.23) WILD-TYPE 149 255
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED     29   72
  DEL PEAK  1(1P36.23) WILD-TYPE  149  255
        clus
vv       DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE
  FEMALE                           29                            149
  MALE                             72                            255
[1] 2 2
[1] FALSE
D13V8, continuous
D13V9, continuous
[1] "Remove cluster labels:"       "DEL PEAK  1(1P36.23) MUTATED"
clus
  DEL PEAK  1(1P36.23) MUTATED DEL PEAK  1(1P36.23) WILD-TYPE 
                             1                              7 
                    TCGA-A3-A8CQ                     TCGA-B2-A4SR 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-B8-4621                     TCGA-B8-5158 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-B8-A54F                     TCGA-B8-A54G 
"DEL PEAK  1(1P36.23) WILD-TYPE" "DEL PEAK  1(1P36.23) WILD-TYPE" 
                    TCGA-G6-A5PC 
"DEL PEAK  1(1P36.23) WILD-TYPE" 
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  1(1P36.23) MUTATED       1                         8    91
  DEL PEAK  1(1P36.23) WILD-TYPE     7                        25   366
D13V10, multiclass
                           clus
vv                          DEL PEAK  1(1P36.23) MUTATED
  ASIAN                                                1
  BLACK OR AFRICAN AMERICAN                            8
  WHITE                                               91
                           clus
vv                          DEL PEAK  1(1P36.23) WILD-TYPE
  ASIAN                                                  7
  BLACK OR AFRICAN AMERICAN                             25
  WHITE                                                366
[1] 3 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  1(1P36.23) MUTATED     8  69
  DEL PEAK  1(1P36.23) WILD-TYPE  16 261
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK  1(1P36.23) MUTATED      8   69
  DEL PEAK  1(1P36.23) WILD-TYPE   16  261
                        clus
vv                       DEL PEAK  1(1P36.23) MUTATED
  HISPANIC OR LATINO                                8
  NOT HISPANIC OR LATINO                           69
                        clus
vv                       DEL PEAK  1(1P36.23) WILD-TYPE
  HISPANIC OR LATINO                                 16
  NOT HISPANIC OR LATINO                            261
[1] 2 2
[1] FALSE

Clustering(14) Variable = DEL PEAK  2(1P31.1) MUTATION ANALYSIS
D14V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  2(1P31.1) MUTATED    46   6
  DEL PEAK  2(1P31.1) WILD-TYPE 292  20
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                           52                           312 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                            6                            20 
$`DEL PEAK  2(1P31.1) MUTATED`
TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3380 
         735         1493         1130         1621         1314          567 
TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3447 TCGA-AK-3465 
        2566         2192         2044         1745         1217          369 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 
        1238          110          616          535          449         1203 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 
         992           51            7           16          166          523 
TCGA-B8-5549 TCGA-BP-4176 TCGA-BP-4334 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 
         194         1955          645          400         1843         2080 
TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5175 
        1746         1413          785         1308         1126          932 
TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4876 TCGA-CJ-4894 
         951         1416         1998         2554         1955          841 
TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 
        1808         1450         1499         2017         2271         2552 
TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 TCGA-EU-5907 
        1868         1683          946          127 

$`DEL PEAK  2(1P31.1) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3317 TCGA-A3-3320 TCGA-A3-3322 
        1120         1436           16         1491         1508         1478 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 
        1106         1186          751         1137         1485          665 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1043          945         1610         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 
        2274          735         1070          630          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
        1993          617            3         3343         2223         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
         480         1853         2087         1423         1471         1280 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 
        1779         1481         1397          874         1143         1168 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4813 
         951          853           43           26           96           18 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
         183          665          911         1092          359          797 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         657           59          493          554          652         1132 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        2408         3431         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 
        1835         2583         2741         1732         1605         3668 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2414         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        2963         1092          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          38          141           11            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         838          762          750          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         522          505          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        3037           13         2718          701         1893         1879 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
         461         2859         1666         1367          372          970 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 
        1462         1876         1885          411         1731          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 
        1834         1862         1871          205         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
        1487         1502         1384         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
        1014         1124          118         1413          501          177 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5006 
        1371          932         1266          563         1177          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
        1140         1071          193         2412         2257          293 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        2263         1495         1165         1291         1133         1132 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 
          29         1820         1924         2308         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
         646         1498         2423         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4899 
        1952         1946         2085         1521          750         1528 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
        1520         1560         1792         1496         1531         1657 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1373         1943         2430         2575          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 
        2799         2489         2609         2226         2378         3222 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        3146          774         1404           18         1943         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1843         1928         2830         1929         1789           25 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
        1712         1732         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 
        1740         1446          685           59          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373          435          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
         723         1729          551          119          206           61 

  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                            7                             3 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                         2566                          3668 
  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE 
                       1227.5                        1318.0 
[1] "7.0 - 2566.0 (1227.5)" "3.0 - 3668.0 (1318.0)"
[1] "hr=" "1.9"
D14V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  2(1P31.1) MUTATED        34        9        17       15
  DEL PEAK  2(1P31.1) WILD-TYPE     210       47       109       64
D14V3, multiclass
           clus
vv          DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  STAGE I                            34                           210
  STAGE II                            9                            47
  STAGE III                          17                           109
  STAGE IV                           15                            64
[1] 4 2
[1] 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(1P31.1) MUTATED    36  12  22   5
  DEL PEAK  2(1P31.1) WILD-TYPE 214  55 155   6
D14V4, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  T1                          36                           214
  T2                          12                            55
  T3                          22                           155
  T4                           5                             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"
D14V5, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    34   4
  DEL PEAK  2(1P31.1) WILD-TYPE 196  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     34    4
  DEL PEAK  2(1P31.1) WILD-TYPE  196   14
   clus
vv  DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  0                          34                           196
  1                           4                            14
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  2(1P31.1) MUTATED    62  13   0
  DEL PEAK  2(1P31.1) WILD-TYPE 355  65   9
D14V6, multiclass
    clus
vv   DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  M0                          62                           355
  M1                          13                            65
  MX                           0                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V7, binary
                               cls
clus                              0   1
  DEL PEAK  2(1P31.1) MUTATED    18  57
  DEL PEAK  2(1P31.1) WILD-TYPE 160 270
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED     18   57
  DEL PEAK  2(1P31.1) WILD-TYPE  160  270
        clus
vv       DEL PEAK  2(1P31.1) MUTATED DEL PEAK  2(1P31.1) WILD-TYPE
  FEMALE                          18                           160
  MALE                            57                           270
[1] 2 2
[1] FALSE
D14V8, continuous
D14V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  2(1P31.1) MUTATED       2                         6    66
  DEL PEAK  2(1P31.1) WILD-TYPE     6                        27   391
D14V10, multiclass
                           clus
vv                          DEL PEAK  2(1P31.1) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                              66
                           clus
vv                          DEL PEAK  2(1P31.1) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            27
  WHITE                                               391
[1] 3 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  2(1P31.1) MUTATED     7  48
  DEL PEAK  2(1P31.1) WILD-TYPE  17 282
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  2(1P31.1) MUTATED      7   48
  DEL PEAK  2(1P31.1) WILD-TYPE   17  282
                        clus
vv                       DEL PEAK  2(1P31.1) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                          48
                        clus
vv                       DEL PEAK  2(1P31.1) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           282
[1] 2 2
[1] FALSE

Clustering(15) Variable = DEL PEAK  3(1Q43) MUTATION ANALYSIS
D15V1, survival
                             sevent
clus2                           0   1
  DEL PEAK  3(1Q43) MUTATED    26   4
  DEL PEAK  3(1Q43) WILD-TYPE 312  22
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                         30                         334 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                          4                          22 
$`DEL PEAK  3(1Q43) MUTATED`
TCGA-A3-3370 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 
        2274         1314          567         2566         2192         1745 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5117 TCGA-B0-5703 TCGA-B2-3923 
         369         1238          110          535         1203          992 
TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-5549 TCGA-BP-4329 TCGA-BP-4334 TCGA-BP-4768 
         166          523          194          845          645          400 
TCGA-BP-4775 TCGA-BP-4968 TCGA-BP-4994 TCGA-CJ-4878 TCGA-CJ-4897 TCGA-CJ-4901 
        1843         1746         1308         2186         1808         1450 
TCGA-CJ-4907 TCGA-CW-5585 TCGA-CW-5588 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5469 
        1499         2609         2017         1868         1683          946 

$`DEL PEAK  3(1Q43) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
         319          873         2270          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         630          574          861         1993          617            3 
TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        3343         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 
        2044         1423         1471         1280         1217         1779 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 
         853           43           26           96          616           18 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
         183          665          911         1092          359          797 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         657           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         449         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        3668         2414         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
        1865         2963         1092           51          374          648 
TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR 
         952          358          315          417          656          507 
TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         291          175            7           38           16          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         750          777          788          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
          36          822           26          737          522          505 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         434           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
          53          256          150           66          110         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        2881         2746         3074         2839         3037           13 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 
        2718          701         1893         1879         1955         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 
        2964         1625         1888         1133          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4758 
        1666         1367          372          970          374         2208 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2372         2361          182         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        1885          411         1731         2080          354         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1489          620         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1862         1871          205         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1502         1384         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1413          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
         177         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1126          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
        2257          932          293         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 
        1416         1924         2308         1998         1628         1793 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         646         2554         1498         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
        2283         2353         1955         2014         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
         841         1528         1520         1560         1792         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 
        1531         1657         1373         1943         2430         2575 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
         552         1883         1889         2231         2038         1855 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 
        1906         2548         2799         2489         2226         2378 
TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2271         3222         2552         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 
        1929         1789           25         1712         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 
        1430          330          662         1740         1446          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
          59          386         2439         2067         1997          373 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
         435          693         1905         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         119          206          127           61 

  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                        110                           3 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                       2609                        3668 
  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE 
                     1311.0                      1285.5 
[1] "110.0 - 2609.0 (1311.0)" "3.0 - 3668.0 (1285.5)"  
[1] "hr=" "2"  
D15V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  3(1Q43) MUTATED        20        4        10        6
  DEL PEAK  3(1Q43) WILD-TYPE     224       52       116       73
D15V3, multiclass
           clus
vv          DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  STAGE I                          20                         224
  STAGE II                          4                          52
  STAGE III                        10                         116
  STAGE IV                          6                          73
[1] 4 2
[1] 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(1Q43) MUTATED    20   4  13   3
  DEL PEAK  3(1Q43) WILD-TYPE 230  63 164   8
D15V4, multiclass
    clus
vv   DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  T1                        20                         230
  T2                         4                          63
  T3                        13                         164
  T4                         3                           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"
D15V5, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    21   1
  DEL PEAK  3(1Q43) WILD-TYPE 209  17
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     21    1
  DEL PEAK  3(1Q43) WILD-TYPE  209   17
   clus
vv  DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  0                        21                         209
  1                         1                          17
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK  3(1Q43) MUTATED    35   5   0
  DEL PEAK  3(1Q43) WILD-TYPE 382  73   9
D15V6, multiclass
    clus
vv   DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  M0                        35                         382
  M1                         5                          73
  MX                         0                           9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V7, binary
                             cls
clus                            0   1
  DEL PEAK  3(1Q43) MUTATED    14  26
  DEL PEAK  3(1Q43) WILD-TYPE 164 301
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED     14   26
  DEL PEAK  3(1Q43) WILD-TYPE  164  301
        clus
vv       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  FEMALE                        14                         164
  MALE                          26                         301
[1] 2 2
[1] FALSE
D15V8, continuous
D15V9, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  3(1Q43) MUTATED       1                         2    36
  DEL PEAK  3(1Q43) WILD-TYPE     7                        31   421
D15V10, multiclass
                           clus
vv                          DEL PEAK  3(1Q43) MUTATED
  ASIAN                                             1
  BLACK OR AFRICAN AMERICAN                         2
  WHITE                                            36
                           clus
vv                          DEL PEAK  3(1Q43) WILD-TYPE
  ASIAN                                               7
  BLACK OR AFRICAN AMERICAN                          31
  WHITE                                             421
[1] 3 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  3(1Q43) MUTATED     3  30
  DEL PEAK  3(1Q43) WILD-TYPE  21 300
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK  3(1Q43) MUTATED      3   30
  DEL PEAK  3(1Q43) WILD-TYPE   21  300
                        clus
vv                       DEL PEAK  3(1Q43) MUTATED DEL PEAK  3(1Q43) WILD-TYPE
  HISPANIC OR LATINO                             3                          21
  NOT HISPANIC OR LATINO                        30                         300
[1] 2 2
[1] FALSE

Clustering(16) Variable = DEL PEAK  4(2Q37.3) MUTATION ANALYSIS
D16V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  4(2Q37.3) MUTATED    38   5
  DEL PEAK  4(2Q37.3) WILD-TYPE 300  21
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           43                           321 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                            5                            21 
$`DEL PEAK  4(2Q37.3) MUTATED`
TCGA-A3-3323 TCGA-A3-3336 TCGA-A3-3374 TCGA-AK-3425 TCGA-AK-3433 TCGA-AK-3440 
        1106         1043         1314         3343         2192         1745 
TCGA-AK-3447 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-5116 TCGA-B0-5117 
        1217          369         1238          110          657          535 
TCGA-B0-5120 TCGA-B2-3923 TCGA-B2-5641 TCGA-B8-4620 TCGA-B8-5549 TCGA-B8-A54F 
         493          992          656          777          194          519 
TCGA-B8-A54G TCGA-BP-4166 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4782 
          53           13         1133          645          182          354 
TCGA-BP-4991 TCGA-BP-4994 TCGA-BP-5008 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5199 
        1413         1308         1071          932          293         1355 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4881 TCGA-CJ-4902 TCGA-CJ-6027 
        1793          646         1498         2014         1520         1855 
TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-5453 TCGA-CZ-5468 TCGA-CZ-5985 TCGA-CZ-5988 
        2552         1404           25           59         1997          693 
TCGA-CZ-5989 
        1905 

$`DEL PEAK  4(2Q37.3) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1130         1508         1478         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
        1485          665          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
         567          574          861         1993          617            3 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
        2044         1423         1471         1280         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
          43           26           96          616           18          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 
         665          911         1092          359          797           59 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 
         554          652         1132          449         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2741         1732         1605         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 
         315          417          507          291          175            7 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
          38           16          141          166           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         788          700          636          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 
          26          737          522          505          434           15 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
        1046          435          830          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
         110         3377         2881         2746         3074         2839 
TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        3037         2718          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 
        1670         2964         1625          845         1888          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
        2859         1666         1367          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        2208         2372         2361         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 
        1854         1489          620         1107         1124          204 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        1459          211         2660         2172         1935         1785 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 
        1834         1862         1871          205         1746         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
         433         1487         1502         1384         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 
         454         1014         1413          785         1124          118 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         501          177         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5169 TCGA-BP-5170 
        1177         1126          840         1140          193         2412 
TCGA-BP-5174 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        2257         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
         714          408          749         1018          603         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
        1998         1628         2554         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 
        2283         2353         1955         2186         1883         1759 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 
        2125         1952         1946         2085         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1808         1528         1450         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 
        1496         1499         1531         1657         1373         1943 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2430         2575          552         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        2038         1906         2548         2799         2489         2609 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 
        2226         2017         2378         2271         3222         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
         774           18         1943         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5457 
        2830         1868         1929         1789         1712         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1732         1683         1430          330          662         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        1446          685          946          386         2439         2067 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         373          435         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
         355         1130          723         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                           13                             3 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         3343                          3668 
  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE 
                         1043                          1384 
[1] "13.0 - 3343.0 (1043.0)" "3.0 - 3668.0 (1384.0)" 
[1] "hr=" "2.1"
D16V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  4(2Q37.3) MUTATED        24        8        13        5
  DEL PEAK  4(2Q37.3) WILD-TYPE     220       48       113       74
D16V3, multiclass
           clus
vv          DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  STAGE I                            24                           220
  STAGE II                            8                            48
  STAGE III                          13                           113
  STAGE IV                            5                            74
[1] 4 2
[1] 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    24   9  16   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 226  58 161  10
D16V4, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  T1                          24                           226
  T2                           9                            58
  T3                          16                           161
  T4                           1                            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"
D16V5, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    23   1
  DEL PEAK  4(2Q37.3) WILD-TYPE 207  17
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     23    1
  DEL PEAK  4(2Q37.3) WILD-TYPE  207   17
   clus
vv  DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  0                          23                           207
  1                           1                            17
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  4(2Q37.3) MUTATED    43   5   2
  DEL PEAK  4(2Q37.3) WILD-TYPE 374  73   7
D16V6, multiclass
    clus
vv   DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  M0                          43                           374
  M1                           5                            73
  MX                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D16V7, binary
                               cls
clus                              0   1
  DEL PEAK  4(2Q37.3) MUTATED    13  37
  DEL PEAK  4(2Q37.3) WILD-TYPE 165 290
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED     13   37
  DEL PEAK  4(2Q37.3) WILD-TYPE  165  290
        clus
vv       DEL PEAK  4(2Q37.3) MUTATED DEL PEAK  4(2Q37.3) WILD-TYPE
  FEMALE                          13                           165
  MALE                            37                           290
[1] 2 2
[1] FALSE
D16V8, 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                            36 
                   TCGA-A3-A8CQ                    TCGA-AK-3426 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-AK-3430                    TCGA-B0-4838 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B2-5639                    TCGA-B4-5377 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5378                    TCGA-B4-5832 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5834                    TCGA-B4-5835 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5836                    TCGA-B4-5838 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B4-5843                    TCGA-B4-5844 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-4856                    TCGA-CZ-4858 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-4860                    TCGA-CZ-4861 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-4862                    TCGA-CZ-5456 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-5457                    TCGA-CZ-5465 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-CZ-5469                    TCGA-CZ-5982 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5565                    TCGA-DV-5566 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5567                    TCGA-DV-5568 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5569                    TCGA-DV-5573 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5574                    TCGA-DV-5575 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-DV-5576                    TCGA-EU-5904 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-EU-5905                    TCGA-EU-5907 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
D16V9, 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 
                            2                             6 
                   TCGA-A3-A8CQ                    TCGA-B2-A4SR 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B8-4621                    TCGA-B8-5158 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                   TCGA-B8-5164                    TCGA-G6-A5PC 
"DEL PEAK  4(2Q37.3) WILD-TYPE" "DEL PEAK  4(2Q37.3) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  4(2Q37.3) MUTATED       1                         5    43
  DEL PEAK  4(2Q37.3) WILD-TYPE     7                        28   414
D16V10, multiclass
                           clus
vv                          DEL PEAK  4(2Q37.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                              43
                           clus
vv                          DEL PEAK  4(2Q37.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            28
  WHITE                                               414
[1] 3 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  4(2Q37.3) MUTATED     1  34
  DEL PEAK  4(2Q37.3) WILD-TYPE  23 296
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  4(2Q37.3) MUTATED      1   34
  DEL PEAK  4(2Q37.3) WILD-TYPE   23  296
                        clus
vv                       DEL PEAK  4(2Q37.3) MUTATED
  HISPANIC OR LATINO                               1
  NOT HISPANIC OR LATINO                          34
                        clus
vv                       DEL PEAK  4(2Q37.3) WILD-TYPE
  HISPANIC OR LATINO                                23
  NOT HISPANIC OR LATINO                           296
[1] 2 2
[1] FALSE

Clustering(17) Variable = DEL PEAK  5(3P25.3) MUTATION ANALYSIS
D17V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  5(3P25.3) MUTATED   298  21
  DEL PEAK  5(3P25.3) WILD-TYPE  40   5
  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE 
                          319                            45 
  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE 
                           21                             5 
$`DEL PEAK  5(3P25.3) MUTATED`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1130         1508         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 
        1137         1485          665         1043          945         1610 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 
         873         2270         2274          735         1621         1070 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ 
         630          567          574          861          617            3 
TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
        3343         2223         2017          480         1853         2192 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
        2087         2044         1471         1280         1779         1481 
TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 
         874         1168          951          853           43           26 
TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
          96          616           18          183          665          911 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
        1092          359          797          657           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         554          652          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        1732         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
        1459         2931         2722         1865         2963         1092 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-5641 
         374          648          952          358          417          656 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         507          291            7           38           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         166           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         762          750          777          700          636          722 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5549 TCGA-B8-5550 
          36          822           26          737          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G 
          15         1046          435          830          519           53 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         256          150           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        2746         3074         2839           13         2718          701 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1879         1955         2964         1625          845         1888 
TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1133          461         2859         1666         1367          372 
TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4766 
         970         2208         2372          182         2184         1462 
TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
         400         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 
         354         1489         1107         1124          204          211 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        2660         2172         1935         1785         1834         1862 
TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        1871         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1384         1433          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
        1124          118         1413          501          177         1371 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
         932         1266          563         1177         1126          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 
        1140         1071          193         2412         2257          932 
TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         293         2263         1495         1165         1291         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5192 
        1132          693          406          822         1011          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         408          749         1018          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4639 
         951           29         1820         1416         1924         2308 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 
        2423         1435         2259         2283         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 
        2014         1883         1759         2125         1952         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
         750          841         1808         1528         1450         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4916 
        1560         1792         1496         1499         1531         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        1943         2430         2575         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        2038         1855         1906         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2609         2226         2017         2378         2271         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
        2552         3146          774           18         1943         1787 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1928         2830         1868         1929         1789           25 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
        1712         1683         1732         1683         1430          330 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
         662         1740         1446          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
         693         1905         1329         1398          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
        1130          723         1729          551          206          127 
TCGA-GK-A6C7 
          61 

$`DEL PEAK  5(3P25.3) WILD-TYPE`
TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3443 
         319         1314         1993         2566         1745         1423 
TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 
        1217         1397         1143          369         1238          110 
TCGA-B0-5117 TCGA-B0-5400 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5635 TCGA-B4-5378 
         535         1132          992           51          315          175 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5545 TCGA-B8-5546 TCGA-BP-4165 TCGA-BP-4173 
         523          788          522          505         3037         1893 
TCGA-BP-4177 TCGA-BP-4334 TCGA-BP-4756 TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4784 
        1670          645          374         2361         1876         1854 
TCGA-BP-4795 TCGA-BP-4804 TCGA-BP-4967 TCGA-BP-4976 TCGA-BP-4994 TCGA-BP-5191 
         620         1459          205         1632         1308          967 
TCGA-CJ-4875 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4912 TCGA-CJ-5681 TCGA-CZ-4854 
        2353         1946         2085         1657          552         1404 
TCGA-CZ-4862 TCGA-DV-5567 TCGA-EU-5905 
        1843         1470          119 

  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE 
                            3                            51 
  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE 
                         3668                          3037 
  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE 
                         1307                          1238 
[1] "3.0 - 3668.0 (1307.0)"  "51.0 - 3037.0 (1238.0)"
[1] "hr=" "1.8"
D17V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  5(3P25.3) MUTATED       209       48       119       69
  DEL PEAK  5(3P25.3) WILD-TYPE      35        8         7       10
D17V3, multiclass
           clus
vv          DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE
  STAGE I                           209                            35
  STAGE II                           48                             8
  STAGE III                         119                             7
  STAGE IV                           69                            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(3P25.3) MUTATED   215  59 165   6
  DEL PEAK  5(3P25.3) WILD-TYPE  35   8  12   5
D17V4, multiclass
    clus
vv   DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE
  T1                         215                            35
  T2                          59                             8
  T3                         165                            12
  T4                           6                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V5, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P25.3) MUTATED   200  16
  DEL PEAK  5(3P25.3) WILD-TYPE  30   2
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P25.3) MUTATED    200   16
  DEL PEAK  5(3P25.3) WILD-TYPE   30    2
   clus
vv  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE
  0                         200                            30
  1                          16                             2
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  5(3P25.3) MUTATED   366  70   8
  DEL PEAK  5(3P25.3) WILD-TYPE  51   8   1
D17V6, multiclass
    clus
vv   DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE
  M0                         366                            51
  M1                          70                             8
  MX                           8                             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"
D17V7, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P25.3) MUTATED   159 286
  DEL PEAK  5(3P25.3) WILD-TYPE  19  41
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P25.3) MUTATED    159  286
  DEL PEAK  5(3P25.3) WILD-TYPE   19   41
        clus
vv       DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE
  FEMALE                         159                            19
  MALE                           286                            41
[1] 2 2
[1] FALSE
D17V8, continuous
D17V9, continuous
[1] "Remove cluster labels:"        "DEL PEAK  5(3P25.3) WILD-TYPE"
clus
  DEL PEAK  5(3P25.3) MUTATED DEL PEAK  5(3P25.3) WILD-TYPE 
                            7                             1 
                 TCGA-A3-A8CQ                  TCGA-B2-A4SR 
"DEL PEAK  5(3P25.3) MUTATED" "DEL PEAK  5(3P25.3) MUTATED" 
                 TCGA-B8-5158                  TCGA-B8-5164 
"DEL PEAK  5(3P25.3) MUTATED" "DEL PEAK  5(3P25.3) MUTATED" 
                 TCGA-B8-A54F                  TCGA-B8-A54G 
"DEL PEAK  5(3P25.3) MUTATED" "DEL PEAK  5(3P25.3) MUTATED" 
                 TCGA-G6-A5PC 
"DEL PEAK  5(3P25.3) MUTATED" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  5(3P25.3) MUTATED       6                        21   411
  DEL PEAK  5(3P25.3) WILD-TYPE     2                        12    46
D17V10, multiclass
                           clus
vv                          DEL PEAK  5(3P25.3) MUTATED
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          21
  WHITE                                             411
                           clus
vv                          DEL PEAK  5(3P25.3) WILD-TYPE
  ASIAN                                                 2
  BLACK OR AFRICAN AMERICAN                            12
  WHITE                                                46
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V11, binary
                               cls
clus                              0   1
  DEL PEAK  5(3P25.3) MUTATED    22 286
  DEL PEAK  5(3P25.3) WILD-TYPE   2  44
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  5(3P25.3) MUTATED     22  286
  DEL PEAK  5(3P25.3) WILD-TYPE    2   44
                        clus
vv                       DEL PEAK  5(3P25.3) MUTATED
  HISPANIC OR LATINO                              22
  NOT HISPANIC OR LATINO                         286
                        clus
vv                       DEL PEAK  5(3P25.3) WILD-TYPE
  HISPANIC OR LATINO                                 2
  NOT HISPANIC OR LATINO                            44
[1] 2 2
[1] FALSE

Clustering(18) Variable = DEL PEAK  6(3P12.3) MUTATION ANALYSIS
D18V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  6(3P12.3) MUTATED   215  19
  DEL PEAK  6(3P12.3) WILD-TYPE 123   7
  DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE 
                          234                           130 
  DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE 
                           19                             7 
$`DEL PEAK  6(3P12.3) MUTATED`
TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        1120          735         1493         1491         1130         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3335 
        1478         1106         1186          751         1485          665 
TCGA-A3-3347 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3365 
        1610          910         2688         1307         2504          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3378 TCGA-A3-3380 
        2270         2274          735         1621          630          567 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3429 
         574          861          617            3         3343         2017 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 
         480         1853         2192         2087         2044         1280 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1779         1481          874         1168          951          853 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5110 TCGA-B0-5113 
          43           26          616           18         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5402 
         797          657           59          493          652          449 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 
        1487         3076         1835         2741         1732         1203 
TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-5633 
        2414         3117         1459         2722         1092          358 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
         417          656          507          291            7           38 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4620 
         141           11            7          511          826          777 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-5552 
          36          822           26          194           15         1046 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
        3377         2881         2839         3037           13         2718 
TCGA-BP-4169 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4332 
         701         1879         1955         2964          845         1133 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4761 
        2859         1666         1367          970         2208          182 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1462          400         1885          411         1731         2080 
TCGA-BP-4789 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1489         1124          204          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4971 TCGA-BP-4975 
        1935         1785         1834         1871         1487         1433 
TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
         454         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         501          177         1371          932         1266          563 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5174 TCGA-BP-5180 
        1126          840         1071          193         2257         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5187 
        1495         1165         1291         1133         1132          406 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 
         822         1011          967          408          749          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
        1355         1063          951         1820         1416         1924 
TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 
        1998         1628         1793          646         2554         1498 
TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4886 
        2259         1955         2186         2014         1883         1952 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
        1521          750          841         1528         1450         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1560         1792         1531         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 
        2575          552         1883         1889         2231         1855 
TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2548         2489         2226         2378         2271         3222 
TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 
        2552         1404           18         1943         1787         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        2830         1929         1789           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
        1683         1430          330          662         1740         1446 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
         685           59          946         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1130          723         1729          206          127           61 

$`DEL PEAK  6(3P12.3) WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3326 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 
        1436           16         1137         1043          945         1385 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3427 
        1559          319         1314         1070         1993         2566 
TCGA-AK-3428 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 
        2223         1745         1423         1471         1217         1397 
TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4819 
        1143          369         1238          110           96          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5690 
         665          911          535          554         1132         2408 
TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5702 TCGA-B0-5705 
        3431         1420         1727         2583         1605         3668 
TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 
        2931         1865         2963          992           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5838 
         648          952          315          175           16          166 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 
         838          762          750          523          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
         636          722          737          522          505          434 
TCGA-B8-5553 TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4173 TCGA-BP-4177 
         435          110         2746         3074         1893         1670 
TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4349 TCGA-BP-4756 
        1625         1888          645          461          372          374 
TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4775 TCGA-BP-4782 
        2372         2361         2184         1876         1843          354 
TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4804 TCGA-BP-4964 TCGA-BP-4967 
        1854          620         1107         1459         1862          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4976 
        1746         1794          433         1502         1384         1632 
TCGA-BP-4982 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5175 
        1014         1308         1177         1140         2412          932 
TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5192 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4639 
         293          693          714         1018           29         2308 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4885 
        2423         1435         2283         2353         1759         2125 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4912 
        1946         2085         1808         1496         1499         1657 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-6093 
        2038         1906         2799         2609         2017         3146 
TCGA-CZ-4853 TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5470 TCGA-DV-5567 
         774         1843         1868         1712          386         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-EU-5904 TCGA-EU-5905 
         370          355          551          119 

  DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE 
                            3                            16 
  DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE 
                         3377                          3668 
  DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE 
                         1299                          1273 
[1] "3.0 - 3377.0 (1299.0)"  "16.0 - 3668.0 (1273.0)"
[1] "hr=" "1.5"
D18V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  6(3P12.3) MUTATED       150       38        87       46
  DEL PEAK  6(3P12.3) WILD-TYPE      94       18        39       33
D18V3, multiclass
           clus
vv          DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE
  STAGE I                           150                            94
  STAGE II                           38                            18
  STAGE III                          87                            39
  STAGE IV                           46                            33
[1] 4 2
[1] 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(3P12.3) MUTATED   154  46 118   3
  DEL PEAK  6(3P12.3) WILD-TYPE  96  21  59   8
D18V4, multiclass
    clus
vv   DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE
  T1                         154                            96
  T2                          46                            21
  T3                         118                            59
  T4                           3                             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"
D18V5, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P12.3) MUTATED   144  10
  DEL PEAK  6(3P12.3) WILD-TYPE  86   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P12.3) MUTATED    144   10
  DEL PEAK  6(3P12.3) WILD-TYPE   86    8
   clus
vv  DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE
  0                         144                            86
  1                          10                             8
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  6(3P12.3) MUTATED   266  47   8
  DEL PEAK  6(3P12.3) WILD-TYPE 151  31   1
D18V6, multiclass
    clus
vv   DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE
  M0                         266                           151
  M1                          47                            31
  MX                           8                             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"
D18V7, binary
                               cls
clus                              0   1
  DEL PEAK  6(3P12.3) MUTATED    97 224
  DEL PEAK  6(3P12.3) WILD-TYPE  81 103
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P12.3) MUTATED     97  224
  DEL PEAK  6(3P12.3) WILD-TYPE   81  103
        clus
vv       DEL PEAK  6(3P12.3) MUTATED DEL PEAK  6(3P12.3) WILD-TYPE
  FEMALE                          97                            81
  MALE                           224                           103
[1] 2 2
[1] FALSE
D18V8, continuous
D18V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  6(3P12.3) MUTATED       5                        16   295
  DEL PEAK  6(3P12.3) WILD-TYPE     3                        17   162
D18V10, multiclass
                           clus
vv                          DEL PEAK  6(3P12.3) MUTATED
  ASIAN                                               5
  BLACK OR AFRICAN AMERICAN                          16
  WHITE                                             295
                           clus
vv                          DEL PEAK  6(3P12.3) WILD-TYPE
  ASIAN                                                 3
  BLACK OR AFRICAN AMERICAN                            17
  WHITE                                               162
[1] 3 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  6(3P12.3) MUTATED    16 206
  DEL PEAK  6(3P12.3) WILD-TYPE   8 124
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  6(3P12.3) MUTATED     16  206
  DEL PEAK  6(3P12.3) WILD-TYPE    8  124
                        clus
vv                       DEL PEAK  6(3P12.3) MUTATED
  HISPANIC OR LATINO                              16
  NOT HISPANIC OR LATINO                         206
                        clus
vv                       DEL PEAK  6(3P12.3) WILD-TYPE
  HISPANIC OR LATINO                                 8
  NOT HISPANIC OR LATINO                           124
[1] 2 2
[1] FALSE

Clustering(19) Variable = DEL PEAK  7(3P11.2) MUTATION ANALYSIS
D19V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  7(3P11.2) MUTATED   156  15
  DEL PEAK  7(3P11.2) WILD-TYPE 182  11
  DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE 
                          171                           193 
  DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE 
                           15                            11 
$`DEL PEAK  7(3P11.2) MUTATED`
TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
        1120          735         1491         1130         1508         1478 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3357 
        1106         1186          751         1485         1610         2688 
TCGA-A3-3359 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
        2504          873         2270         2274          735         1621 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3429 
         630          567          574            3         3343         2017 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3445 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 
        1853         2192         1280          874         1168          951 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4813 TCGA-B0-5115 TCGA-B0-5116 
         853           43           26           18          797          657 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5699 
          59          493          652          449         1487         2741 
TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-5633 
        1203         2414         1459         2722         1092          358 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5834 
         417          656          507          291            7           38 
TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5549 
         826          777           36          822           26          194 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
          15         1046          830          519           53          256 
TCGA-B8-A54I TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4176 
         150         3377         2881           13          701         1955 
TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        2964          845         1133         2859         1666         1367 
TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4777 
         970         2208          182          400         1885         1731 
TCGA-BP-4781 TCGA-BP-4789 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 
        2080         1489         1124          204          211         2660 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4975 TCGA-BP-4986 TCGA-BP-4989 
        2172         1935         1785         1433          785          118 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1413          501          177         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5180 TCGA-BP-5181 
         563         1126          840         1071         2263         1495 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5195 TCGA-BP-5198 
        1165         1291         1132          406          749          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4640 
        1355         1063          951         1416         1924         1998 
TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4882 TCGA-CJ-4892 
        1628          646         2554         2259         1883         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6027 
        1792         1531         1943         1883         1889         1855 
TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 
        2548         2489         2378         2271         3222         2552 
TCGA-CZ-4854 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 
        1404         1787         1928         2830         1929         1789 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 
          25         1683         1732         1683          330          662 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 
        1446          685           59          946         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5573 
         373          435         1905         1329          370         1130 
TCGA-DV-5574 TCGA-EU-5907 TCGA-GK-A6C7 
         723          127           61 

$`DEL PEAK  7(3P11.2) WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3326 TCGA-A3-3335 TCGA-A3-3336 
        1436           16         1493         1137          665         1043 
TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 
         945         1385          910         1307         1559          319 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 
        1314         1070          861         1993          617         2566 
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
        2223          480         2087         2044         1745         1423 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 
        1471         1217         1779         1481         1397         1143 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4718 TCGA-B0-4819 
         369         1238          110           96          616          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5117 TCGA-B0-5121 
         665          911         1092          359          535          554 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
        1132         2408         3431         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 
        1835         2583         1732         1605         3668         3117 
TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 
        2931         1865         2963          992           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5836 
         648          952          315          175           16          141 
TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 
         166           11            7          511          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
         750          523          788          700          636          722 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5553 TCGA-B8-A54J 
         737          522          505          434          435           66 
TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 
         110         2746         3074         2839         3037         2718 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4334 
        1893         1879         1670         1625         1888          645 
TCGA-BP-4335 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 
         461          372          374         2372         2361         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 
        1462         1876         1843          411          354         1854 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4804 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 
         620         1107         1459         1834         1862         1871 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
         205         1746         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 
        1384         1632          454         1014         1413         1124 
TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
        1308         1177         1140          193         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5189 TCGA-BP-5190 
         932          293         1133          693          822         1011 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 
         967          714          408         1018           29         1820 
TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4874 
        2308         1793         1498         2423         1435         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         1955         2186         2014         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 
        1952         1946         2085         1808         1496         1499 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5684 
        1657         1373         2430         2575          552         2231 
TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        2038         1906         2799         2609         2226         2017 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4862 TCGA-CZ-4866 
        3146          774           18         1943         1843         1868 
TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5988 
        1712         1430         1740          386         2439          693 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
        1398         1470          355         1729          551          119 
TCGA-EU-5906 
         206 

  DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE 
                            3                             7 
  DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE 
                         3377                          3668 
  DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE 
                         1165                          1397 
[1] "3.0 - 3377.0 (1165.0)" "7.0 - 3668.0 (1397.0)"
[1] "hr=" "1.6"
D19V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  7(3P11.2) MUTATED       118       26        61       32
  DEL PEAK  7(3P11.2) WILD-TYPE     126       30        65       47
D19V3, multiclass
           clus
vv          DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE
  STAGE I                           118                           126
  STAGE II                           26                            30
  STAGE III                          61                            65
  STAGE IV                           32                            47
[1] 4 2
[1] 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(3P11.2) MUTATED   121  31  82   3
  DEL PEAK  7(3P11.2) WILD-TYPE 129  36  95   8
D19V4, multiclass
    clus
vv   DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE
  T1                         121                           129
  T2                          31                            36
  T3                          82                            95
  T4                           3                             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"
D19V5, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P11.2) MUTATED   107   8
  DEL PEAK  7(3P11.2) WILD-TYPE 123  10
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P11.2) MUTATED    107    8
  DEL PEAK  7(3P11.2) WILD-TYPE  123   10
   clus
vv  DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE
  0                         107                           123
  1                           8                            10
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  7(3P11.2) MUTATED   197  33   7
  DEL PEAK  7(3P11.2) WILD-TYPE 220  45   2
D19V6, multiclass
    clus
vv   DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE
  M0                         197                           220
  M1                          33                            45
  MX                           7                             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"
D19V7, binary
                               cls
clus                              0   1
  DEL PEAK  7(3P11.2) MUTATED    60 177
  DEL PEAK  7(3P11.2) WILD-TYPE 118 150
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P11.2) MUTATED     60  177
  DEL PEAK  7(3P11.2) WILD-TYPE  118  150
        clus
vv       DEL PEAK  7(3P11.2) MUTATED DEL PEAK  7(3P11.2) WILD-TYPE
  FEMALE                          60                           118
  MALE                           177                           150
[1] 2 2
[1] FALSE
D19V8, continuous
D19V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  7(3P11.2) MUTATED       3                        13   216
  DEL PEAK  7(3P11.2) WILD-TYPE     5                        20   241
D19V10, multiclass
                           clus
vv                          DEL PEAK  7(3P11.2) MUTATED
  ASIAN                                               3
  BLACK OR AFRICAN AMERICAN                          13
  WHITE                                             216
                           clus
vv                          DEL PEAK  7(3P11.2) WILD-TYPE
  ASIAN                                                 5
  BLACK OR AFRICAN AMERICAN                            20
  WHITE                                               241
[1] 3 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  7(3P11.2) MUTATED    10 150
  DEL PEAK  7(3P11.2) WILD-TYPE  14 180
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  7(3P11.2) MUTATED     10  150
  DEL PEAK  7(3P11.2) WILD-TYPE   14  180
                        clus
vv                       DEL PEAK  7(3P11.2) MUTATED
  HISPANIC OR LATINO                              10
  NOT HISPANIC OR LATINO                         150
                        clus
vv                       DEL PEAK  7(3P11.2) WILD-TYPE
  HISPANIC OR LATINO                                14
  NOT HISPANIC OR LATINO                           180
[1] 2 2
[1] FALSE

Clustering(20) Variable = DEL PEAK  8(3Q11.2) MUTATION ANALYSIS
D20V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  8(3Q11.2) MUTATED   105  11
  DEL PEAK  8(3Q11.2) WILD-TYPE 233  15
  DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE 
                          116                           248 
  DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE 
                           11                            15 
$`DEL PEAK  8(3Q11.2) MUTATED`
TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
        1120          735         1491         1130         1508         1478 
TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3331 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3359 
        1106         1186         1485         1610         2688         2504 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3382 
         873         2270         2274          735          567          574 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3429 TCGA-AK-3433 TCGA-AK-3454 TCGA-AK-3460 
           3         3343         2017         2192          874          951 
TCGA-AK-3461 TCGA-B0-4813 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5399 
         853           18          797          657          493          652 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5706 TCGA-B0-5710 TCGA-B2-3924 TCGA-B2-5633 
        2741         1203         2414         1459         1092          358 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 TCGA-B8-4620 TCGA-B8-5162 TCGA-B8-5163 
         417          656            7          777           36          822 
TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54H TCGA-BP-4158 
          26          194          830          519          256         3377 
TCGA-BP-4166 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4344 TCGA-BP-4347 
          13         1955          845         1133         1666         1367 
TCGA-BP-4351 TCGA-BP-4758 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4777 TCGA-BP-4781 
         970         2208          400         1885         1731         2080 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4975 
        1124          204          211         2172         1935         1433 
TCGA-BP-4986 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 
         785         1413          501          177          932         1266 
TCGA-BP-5000 TCGA-BP-5008 TCGA-BP-5180 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5195 
         563         1071         2263         1132          406          749 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4642 
         603         1355         1063          951         1416         1628 
TCGA-CJ-4868 TCGA-CJ-4873 TCGA-CJ-4892 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         646         2259         1521         1520         1560         1792 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-6027 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4863 
        1883         1889         1855         3222         2552         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        2830         1929         1789           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5985 
        1683          330          662           59          946         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5573 TCGA-DV-5574 
         373          435         1905         1329         1130          723 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

$`DEL PEAK  8(3Q11.2) WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3335 
        1436           16         1493          751         1137          665 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3362 
        1043          945         1385          910         1307         1559 
TCGA-A3-3363 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 
         319         1621         1314         1070          630          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3431 
        1993          617         2566         2223          480         1853 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 
        2087         2044         1745         1423         1471         1280 
TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
        1217         1779         1481         1397         1143         1168 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
         616          183          665          911         1092          359 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 
         535           59          554         1132          449         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5711 
        2583         1732         1605         3668         3117         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 
        2722         1865         2963          992           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         648          952          315          507          291          175 
TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 
          38           16          141          166           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5545 
         788          700          636          722          737          522 
TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54G 
         505          434           15         1046          435           53 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
         150           66          110         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037         2718          701         1893         1879 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4334 TCGA-BP-4335 
        1670         2964         1625         1888          645          461 
TCGA-BP-4338 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
        2859          372          374         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 
        2184         1462         1876         1843          411          354 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4804 TCGA-BP-4959 
        1854         1489          620         1107         1459         2660 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4976 
        1794          433         1487         1502         1384         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4994 
         454         1014         1413         1124          118         1308 
TCGA-BP-4995 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5169 
        1371         1177         1126          840         1140          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 
        2412         2257          932          293         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1291         1133          693          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
         714          408         1018           29         1820         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 
        2308         1998         1793         2554         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        1435         2283         2353         1955         2186         2014 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1883         1759         2125         1952         1946         2085 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4905 
         750          841         1808         1528         1450         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1499         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 
        2575          552         2231         2038         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2799         2489         2609         2226         2017         2378 
TCGA-CW-5591 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 
        2271         3146          774         1404           18         1943 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 
        1787         1843         1868         1712         1430         1740 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5988 
        1446          685          386         2439         2067          693 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5575 TCGA-EU-5904 
        1398         1470          370          355         1729          551 
TCGA-EU-5905 TCGA-EU-5906 
         119          206 

  DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE 
                            3                             7 
  DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE 
                         3377                          3668 
  DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE 
                         1127                          1391 
[1] "3.0 - 3377.0 (1127.0)" "7.0 - 3668.0 (1391.0)"
[1] "hr=" "1.7"
D20V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  8(3Q11.2) MUTATED        74       21        41       20
  DEL PEAK  8(3Q11.2) WILD-TYPE     170       35        85       59
D20V3, multiclass
           clus
vv          DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE
  STAGE I                            74                           170
  STAGE II                           21                            35
  STAGE III                          41                            85
  STAGE IV                           20                            59
[1] 4 2
[1] 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(3Q11.2) MUTATED    77  24  55   0
  DEL PEAK  8(3Q11.2) WILD-TYPE 173  43 122  11
D20V4, multiclass
    clus
vv   DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE
  T1                          77                           173
  T2                          24                            43
  T3                          55                           122
  T4                           0                            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"
D20V5, binary
                               cls
clus                              0   1
  DEL PEAK  8(3Q11.2) MUTATED    69   4
  DEL PEAK  8(3Q11.2) WILD-TYPE 161  14
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3Q11.2) MUTATED     69    4
  DEL PEAK  8(3Q11.2) WILD-TYPE  161   14
   clus
vv  DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE
  0                          69                           161
  1                           4                            14
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  8(3Q11.2) MUTATED   129  22   5
  DEL PEAK  8(3Q11.2) WILD-TYPE 288  56   4
D20V6, multiclass
    clus
vv   DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE
  M0                         129                           288
  M1                          22                            56
  MX                           5                             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"
D20V7, binary
                               cls
clus                              0   1
  DEL PEAK  8(3Q11.2) MUTATED    30 126
  DEL PEAK  8(3Q11.2) WILD-TYPE 148 201
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3Q11.2) MUTATED     30  126
  DEL PEAK  8(3Q11.2) WILD-TYPE  148  201
        clus
vv       DEL PEAK  8(3Q11.2) MUTATED DEL PEAK  8(3Q11.2) WILD-TYPE
  FEMALE                          30                           148
  MALE                           126                           201
[1] 2 2
[1] FALSE
D20V8, continuous
D20V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  8(3Q11.2) MUTATED       2                         6   145
  DEL PEAK  8(3Q11.2) WILD-TYPE     6                        27   312
D20V10, multiclass
                           clus
vv                          DEL PEAK  8(3Q11.2) MUTATED
  ASIAN                                               2
  BLACK OR AFRICAN AMERICAN                           6
  WHITE                                             145
                           clus
vv                          DEL PEAK  8(3Q11.2) WILD-TYPE
  ASIAN                                                 6
  BLACK OR AFRICAN AMERICAN                            27
  WHITE                                               312
[1] 3 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  8(3Q11.2) MUTATED     4  95
  DEL PEAK  8(3Q11.2) WILD-TYPE  20 235
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  8(3Q11.2) MUTATED      4   95
  DEL PEAK  8(3Q11.2) WILD-TYPE   20  235
                        clus
vv                       DEL PEAK  8(3Q11.2) MUTATED
  HISPANIC OR LATINO                               4
  NOT HISPANIC OR LATINO                          95
                        clus
vv                       DEL PEAK  8(3Q11.2) WILD-TYPE
  HISPANIC OR LATINO                                20
  NOT HISPANIC OR LATINO                           235
[1] 2 2
[1] FALSE

Clustering(21) Variable = DEL PEAK  9(4Q34.3) MUTATION ANALYSIS
D21V1, survival
                               sevent
clus2                             0   1
  DEL PEAK  9(4Q34.3) MUTATED    38   4
  DEL PEAK  9(4Q34.3) WILD-TYPE 300  22
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                           42                           322 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                            4                            22 
$`DEL PEAK  9(4Q34.3) MUTATED`
TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3367 TCGA-A3-3380 TCGA-AK-3436 TCGA-AK-3458 
        1493         1508         2270          567         2044         1168 
TCGA-B0-4710 TCGA-B0-4813 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5691 TCGA-B0-5699 
          96           18          359          657         3431         2741 
TCGA-B0-5701 TCGA-B0-5709 TCGA-B4-5838 TCGA-B8-4146 TCGA-B8-5158 TCGA-B8-5162 
        1732         3117          166          511          636           36 
TCGA-B8-5549 TCGA-BP-4161 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-5183 TCGA-BP-5196 
         194         2746          970          400         1291         1018 
TCGA-BP-5198 TCGA-CJ-4636 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4881 TCGA-CJ-4897 
         603         1924         1793         1498         2014         1808 
TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-5676 TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4858 
        1560         1499         2575         2017         2552         1943 
TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-EU-5907 
        1868         1683          330         1446          946          127 

$`DEL PEAK  9(4Q34.3) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3331 
        1478         1106         1186          751         1137         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 
        2274          735         1621         1314         1070          630 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         574          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 
        2566         2223         2017          480         1853         2192 
TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        2087         1745         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 
        1779         1481         1397          874         1143          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 
         853          369         1238           43          110           26 
TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 
         616          183          665          911         1092          797 
TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
         535           59          493          554          652         1132 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
         449         2408         1487         3076         1420         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        1835         2583         1605         1203         3668         2414 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         315          417          656          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 
           7           38           16          141           11            7 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         788          700          722          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         522          505          434           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
         110         3377         2881         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
          13         2718          701         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 
        1462         1876         1885         1843          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4797 
        2080          354         1854         1489          620         1107 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 
        1935         1785         1834         1862         1871          205 
TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        1746         1794          433         1487         1502         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 
        1433         1632          454         1014         1413          785 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 
        1124          118         1413          501          177         1308 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
        1371          932         1266          563         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
         840         1140         1071          193         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 
         932          293         2263         1495         1165         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1132          693          406          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         714          408          749         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
          29         1820         1416         2308         1998         1628 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
         646         2554         2423         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         1955         2186         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1952         1946         2085         1521          750          841 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
        1528         1450         1520         1792         1496         1531 
TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 
        1657         1373         1943         2430          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 
        1889         2231         2038         1855         1906         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
        2799         2489         2609         2226         2378         2271 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4859 
        3222         3146          774         1404           18         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1843         1928         2830         1929         1789           25 
TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 
        1712         1732         1683         1430          662         1740 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
         685           59          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373          435          693         1905         1329         1398 
TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        1470          370          355         1130          723         1729 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
         551          119          206           61 

  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                           18                             3 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                         3431                          3668 
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                       1495.5                        1252.0 
[1] "18.0 - 3431.0 (1495.5)" "3.0 - 3668.0 (1252.0)" 
[1] "hr=" "1.4"
D21V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK  9(4Q34.3) MUTATED        19        7        31       21
  DEL PEAK  9(4Q34.3) WILD-TYPE     225       49        95       58
D21V3, multiclass
           clus
vv          DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  STAGE I                            19                           225
  STAGE II                            7                            49
  STAGE III                          31                            95
  STAGE IV                           21                            58
[1] 4 2
[1] 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(4Q34.3) MUTATED    20   9  43   6
  DEL PEAK  9(4Q34.3) WILD-TYPE 230  58 134   5
D21V4, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  T1                          20                           230
  T2                           9                            58
  T3                          43                           134
  T4                           6                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V5, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    32   3
  DEL PEAK  9(4Q34.3) WILD-TYPE 198  15
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     32    3
  DEL PEAK  9(4Q34.3) WILD-TYPE  198   15
   clus
vv  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  0                          32                           198
  1                           3                            15
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK  9(4Q34.3) MUTATED    59  19   0
  DEL PEAK  9(4Q34.3) WILD-TYPE 358  59   9
D21V6, multiclass
    clus
vv   DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  M0                          59                           358
  M1                          19                            59
  MX                           0                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D21V7, binary
                               cls
clus                              0   1
  DEL PEAK  9(4Q34.3) MUTATED    24  54
  DEL PEAK  9(4Q34.3) WILD-TYPE 154 273
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED     24   54
  DEL PEAK  9(4Q34.3) WILD-TYPE  154  273
        clus
vv       DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE
  FEMALE                          24                           154
  MALE                            54                           273
[1] 2 2
[1] FALSE
D21V8, continuous
D21V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK  9(4Q34.3) MUTATED"
clus
  DEL PEAK  9(4Q34.3) MUTATED DEL PEAK  9(4Q34.3) WILD-TYPE 
                            1                             7 
                   TCGA-A3-A8CQ                    TCGA-B2-A4SR 
"DEL PEAK  9(4Q34.3) WILD-TYPE" "DEL PEAK  9(4Q34.3) WILD-TYPE" 
                   TCGA-B8-4621                    TCGA-B8-5164 
"DEL PEAK  9(4Q34.3) WILD-TYPE" "DEL PEAK  9(4Q34.3) WILD-TYPE" 
                   TCGA-B8-A54F                    TCGA-B8-A54G 
"DEL PEAK  9(4Q34.3) WILD-TYPE" "DEL PEAK  9(4Q34.3) WILD-TYPE" 
                   TCGA-G6-A5PC 
"DEL PEAK  9(4Q34.3) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK  9(4Q34.3) MUTATED       1                         2    73
  DEL PEAK  9(4Q34.3) WILD-TYPE     7                        31   384
D21V10, multiclass
                           clus
vv                          DEL PEAK  9(4Q34.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           2
  WHITE                                              73
                           clus
vv                          DEL PEAK  9(4Q34.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            31
  WHITE                                               384
[1] 3 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  9(4Q34.3) MUTATED     5  54
  DEL PEAK  9(4Q34.3) WILD-TYPE  19 276
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK  9(4Q34.3) MUTATED      5   54
  DEL PEAK  9(4Q34.3) WILD-TYPE   19  276
                        clus
vv                       DEL PEAK  9(4Q34.3) MUTATED
  HISPANIC OR LATINO                               5
  NOT HISPANIC OR LATINO                          54
                        clus
vv                       DEL PEAK  9(4Q34.3) WILD-TYPE
  HISPANIC OR LATINO                                19
  NOT HISPANIC OR LATINO                           276
[1] 2 2
[1] FALSE

Clustering(22) Variable = DEL PEAK 10(6Q26) MUTATION ANALYSIS
D22V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 10(6Q26) MUTATED   100   9
  DEL PEAK 10(6Q26) WILD-TYPE 238  17
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                        109                         255 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                          9                          17 
$`DEL PEAK 10(6Q26) MUTATED`
TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        1120          735         1493         1491         1130         1508 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 
         665         1043         1610         1314          567          574 
TCGA-A3-A8CQ TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
           3          480         2192         2087         2044         1745 
TCGA-AK-3447 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
        1217          874         1168          853          369         1238 
TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5402 
         110           18          911          535           59          449 
TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 
        1605          992          656          291            7           16 
TCGA-B4-5838 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4160 
         166          826          777          636           53         2881 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4768 
        2718         1955         2964          645          182          400 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 
        1843         1731         2080         1107         2660         2172 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1785         1834         1746         1413          785         1124 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 
         501          177         1308          563          193          932 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4634 
        2263         1495         1132          967          951         1820 
TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4876 TCGA-CJ-4878 
        1416         1793         2423         1435         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 
        2014         1521          750         1808         1450         1792 
TCGA-CJ-4907 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-6027 TCGA-CJ-6032 TCGA-CW-5585 
        1499         2430         2575         1855         2548         2609 
TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-4866 
        2017          774         1943         1787         2830         1868 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5984 
        1789         1712         1430         1446         2439         2067 
TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5575 
        1997          435         1329          370         1130         1729 
TCGA-EU-5907 
         127 

$`DEL PEAK 10(6Q26) WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1436           16         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1137         1485          945         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 
        2274          735         1621         1070          630          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        1993          617         3343         2566         2223         2017 
TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
        1853         1423         1471         1280         1779         1481 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 
        1397         1143          951           43           26           96 
TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
         616          183          665         1092          359          797 
TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
         657          493          554          652         1132         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2583         2741         1732         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
         315          417          507          175           38          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
          11            7          511          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         523          788          700          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54H 
          15         1046          435          830          519          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4162 
         150           66          110         3377         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037           13          701         1893         1879 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
        1670         1625          845         1888         1133          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
        2859         1666         1367          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2208         2372         2361         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1885          411          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 
        1124          204         1459          211         1935         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        1871          205         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4989 
        1384         1433         1632          454         1014          118 
TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
        1413         1371          932         1266         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
         840         1140         1071         2412         2257          293 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1165         1291         1133          693          406          822 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
        1011          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
        1355         1063           29         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 
        1628          646         2554         1498         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2353         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
        2085          841         1528         1520         1560         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5681 TCGA-CJ-5682 
        1531         1657         1373         1943          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5583 
        1889         2231         2038         1906         2799         2489 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2226         2378         2271         3222         2552         3146 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-5451 TCGA-CZ-5453 
        1404           18         1843         1928         1929           25 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1683         1732         1683          330          662         1740 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 
         685           59          946          386          373          693 
TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-EU-5904 
        1905         1398         1470          355          723          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
         119          206           61 

  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                          3                           7 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                       2964                        3668 
  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE 
                       1413                        1203 
[1] "3.0 - 2964.0 (1413.0)" "7.0 - 3668.0 (1203.0)"
[1] "hr=" "1.2"
D22V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 10(6Q26) MUTATED        65       20        35       27
  DEL PEAK 10(6Q26) WILD-TYPE     179       36        91       52
D22V3, multiclass
           clus
vv          DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  STAGE I                          65                         179
  STAGE II                         20                          36
  STAGE III                        35                          91
  STAGE IV                         27                          52
[1] 4 2
[1] 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(6Q26) MUTATED    67  22  54   4
  DEL PEAK 10(6Q26) WILD-TYPE 183  45 123   7
D22V4, multiclass
    clus
vv   DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  T1                        67                         183
  T2                        22                          45
  T3                        54                         123
  T4                         4                           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"
D22V5, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q26) MUTATED    54  10
  DEL PEAK 10(6Q26) WILD-TYPE 176   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q26) MUTATED     54   10
  DEL PEAK 10(6Q26) WILD-TYPE  176    8
   clus
vv  DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  0                        54                         176
  1                        10                           8
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 10(6Q26) MUTATED   120  25   2
  DEL PEAK 10(6Q26) WILD-TYPE 297  53   7
D22V6, multiclass
    clus
vv   DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  M0                       120                         297
  M1                        25                          53
  MX                         2                           7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V7, binary
                             cls
clus                            0   1
  DEL PEAK 10(6Q26) MUTATED    40 107
  DEL PEAK 10(6Q26) WILD-TYPE 138 220
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q26) MUTATED     40  107
  DEL PEAK 10(6Q26) WILD-TYPE  138  220
        clus
vv       DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  FEMALE                        40                         138
  MALE                         107                         220
[1] 2 2
[1] FALSE
D22V8, continuous
D22V9, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 10(6Q26) MUTATED       2                         5   137
  DEL PEAK 10(6Q26) WILD-TYPE     6                        28   320
D22V10, multiclass
                           clus
vv                          DEL PEAK 10(6Q26) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                           137
                           clus
vv                          DEL PEAK 10(6Q26) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          28
  WHITE                                             320
[1] 3 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 10(6Q26) MUTATED    10  94
  DEL PEAK 10(6Q26) WILD-TYPE  14 236
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 10(6Q26) MUTATED     10   94
  DEL PEAK 10(6Q26) WILD-TYPE   14  236
                        clus
vv                       DEL PEAK 10(6Q26) MUTATED DEL PEAK 10(6Q26) WILD-TYPE
  HISPANIC OR LATINO                            10                          14
  NOT HISPANIC OR LATINO                        94                         236
[1] 2 2
[1] FALSE

Clustering(23) Variable = DEL PEAK 11(6Q26) MUTATION ANALYSIS
D23V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 11(6Q26) MUTATED   100  10
  DEL PEAK 11(6Q26) WILD-TYPE 238  16
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                        110                         254 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                         10                          16 
$`DEL PEAK 11(6Q26) MUTATED`
TCGA-A3-3306 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        1120          735         1493         1491         1130         1508 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3374 TCGA-A3-3380 TCGA-A3-3382 
         665         1043         1610         1314          567          574 
TCGA-A3-A8CQ TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 
           3          480         2192         2087         2044         1745 
TCGA-AK-3447 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 
        1217          874         1168          853          369         1238 
TCGA-B0-4699 TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5402 
         110           18          911          535           59          449 
TCGA-B0-5702 TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5835 
        1605          992          656          291            7           16 
TCGA-B4-5838 TCGA-B8-4148 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-A54G TCGA-BP-4160 
         166          826          777          636           53         2881 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4334 TCGA-BP-4761 TCGA-BP-4768 
        2718         1955         2964          645          182          400 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 
        1843         1731         2080         1107         2660         2172 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 
        1785         1834         1746         1413          785         1124 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 
         501          177         1308          563          193          932 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5185 TCGA-BP-5191 TCGA-BP-5201 TCGA-CJ-4634 
        2263         1495         1132          967          951         1820 
TCGA-CJ-4635 TCGA-CJ-4643 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4876 TCGA-CJ-4878 
        1416         1793         2423         1435         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4904 
        2014         1521          750         1808         1450         1792 
TCGA-CJ-4907 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-6027 TCGA-CJ-6032 TCGA-CW-5585 
        1499         2430         2575         1855         2548         2609 
TCGA-CW-5588 TCGA-CZ-4853 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-4866 
        2017          774         1943         1787         2830         1868 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5468 TCGA-CZ-5982 
        1789         1712         1430         1446           59         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5573 
        2067         1997          435         1329          370         1130 
TCGA-DV-5575 TCGA-EU-5907 
        1729          127 

$`DEL PEAK 11(6Q26) WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 
        1436           16         1478         1106         1186          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
        1137         1485          945         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        1307         2504         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3383 
        2274          735         1621         1070          630          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 
        1993          617         3343         2566         2223         2017 
TCGA-AK-3431 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
        1853         1423         1471         1280         1779         1481 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 
        1397         1143          951           43           26           96 
TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
         616          183          665         1092          359          797 
TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 
         657          493          554          652         1132         2408 
TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        3431         1487         3076         1420         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        2583         2741         1732         1203         3668         2414 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        3117         1459         2931         2722         1865         2963 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 
         315          417          507          175           38          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
          11            7          511          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         523          788          700          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
          26          737          522          505          194          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54H 
          15         1046          435          830          519          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4162 
         150           66          110         3377         2746         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037           13          701         1893         1879 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
        1670         1625          845         1888         1133          461 
TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
        2859         1666         1367          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2208         2372         2361         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1885          411          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4964 
        1124          204         1459          211         1935         1862 
TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
        1871          205         1794          433         1487         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4989 
        1384         1433         1632          454         1014          118 
TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
        1413         1371          932         1266         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
         840         1140         1071         2412         2257          293 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1165         1291         1133          693          406          822 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
        1011          714          408          749         1018          603 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 
        1355         1063           29         1924         2308         1998 
TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 
        1628          646         2554         1498         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2353         1883         1759         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4905 
        2085          841         1528         1520         1560         1496 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5681 TCGA-CJ-5682 
        1531         1657         1373         1943          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5583 
        1889         2231         2038         1906         2799         2489 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
        2226         2378         2271         3222         2552         3146 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-5451 TCGA-CZ-5453 
        1404           18         1843         1928         1929           25 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1683         1732         1683          330          662         1740 
TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
         685          946          386          373          693         1905 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5574 TCGA-EU-5904 TCGA-EU-5905 
        1398         1470          355          723          551          119 
TCGA-EU-5906 TCGA-GK-A6C7 
         206           61 

  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                          3                           7 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                       2964                        3668 
  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE 
                     1371.0                      1234.5 
[1] "3.0 - 2964.0 (1371.0)" "7.0 - 3668.0 (1234.5)"
[1] "hr=" "1.4"
D23V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 11(6Q26) MUTATED        65       20        35       27
  DEL PEAK 11(6Q26) WILD-TYPE     179       36        91       52
D23V3, multiclass
           clus
vv          DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  STAGE I                          65                         179
  STAGE II                         20                          36
  STAGE III                        35                          91
  STAGE IV                         27                          52
[1] 4 2
[1] 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(6Q26) MUTATED    67  22  54   4
  DEL PEAK 11(6Q26) WILD-TYPE 183  45 123   7
D23V4, multiclass
    clus
vv   DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  T1                        67                         183
  T2                        22                          45
  T3                        54                         123
  T4                         4                           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"
D23V5, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED    54  10
  DEL PEAK 11(6Q26) WILD-TYPE 176   8
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     54   10
  DEL PEAK 11(6Q26) WILD-TYPE  176    8
   clus
vv  DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  0                        54                         176
  1                        10                           8
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 11(6Q26) MUTATED   120  25   2
  DEL PEAK 11(6Q26) WILD-TYPE 297  53   7
D23V6, multiclass
    clus
vv   DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  M0                       120                         297
  M1                        25                          53
  MX                         2                           7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V7, binary
                             cls
clus                            0   1
  DEL PEAK 11(6Q26) MUTATED    39 108
  DEL PEAK 11(6Q26) WILD-TYPE 139 219
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     39  108
  DEL PEAK 11(6Q26) WILD-TYPE  139  219
        clus
vv       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  FEMALE                        39                         139
  MALE                         108                         219
[1] 2 2
[1] FALSE
D23V8, continuous
D23V9, continuous
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 11(6Q26) MUTATED       2                         5   137
  DEL PEAK 11(6Q26) WILD-TYPE     6                        28   320
D23V10, multiclass
                           clus
vv                          DEL PEAK 11(6Q26) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                           137
                           clus
vv                          DEL PEAK 11(6Q26) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          28
  WHITE                                             320
[1] 3 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 11(6Q26) MUTATED    10  94
  DEL PEAK 11(6Q26) WILD-TYPE  14 236
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 11(6Q26) MUTATED     10   94
  DEL PEAK 11(6Q26) WILD-TYPE   14  236
                        clus
vv                       DEL PEAK 11(6Q26) MUTATED DEL PEAK 11(6Q26) WILD-TYPE
  HISPANIC OR LATINO                            10                          14
  NOT HISPANIC OR LATINO                        94                         236
[1] 2 2
[1] FALSE

Clustering(24) Variable = DEL PEAK 12(8P23.2) MUTATION ANALYSIS
D24V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 12(8P23.2) MUTATED    95  10
  DEL PEAK 12(8P23.2) WILD-TYPE 243  16
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                          105                           259 
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                           10                            16 
$`DEL PEAK 12(8P23.2) MUTATED`
TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3373 
        1130          751         1043          873          735         1621 
TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3445 
         574         3343         2087         2044         1745         1280 
TCGA-AK-3447 TCGA-AK-3458 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 
        1217         1168         1238          110          616           18 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5712 
         183          665          911         1420         1727         2722 
TCGA-B0-5713 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4151 
        1865          507          291            7          166          838 
TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5551 
         636          822           26          522          194           15 
TCGA-B8-A54H TCGA-B8-A54I TCGA-BP-4169 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 
         256          150          701         1879         1955         1625 
TCGA-BP-4338 TCGA-BP-4347 TCGA-BP-4351 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4781 
        2859         1367          970          400         1843         2080 
TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4967 
         354          620          211         2660         2172          205 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4973 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4994 
        1746          433         1384         1413          785         1308 
TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5177 
         932          563         1126          193          932          293 
TCGA-BP-5182 TCGA-BP-5196 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4640 TCGA-CJ-4642 
        1165         1018         1063          951         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
        1793          646         1498         1955         2186         2014 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 
        1759         2125         1946          841         1808         1560 
TCGA-CJ-4904 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-6027 TCGA-CW-6088 TCGA-CW-6090 
        1792         1499         1657         1855         3222         2552 
TCGA-CZ-4854 TCGA-CZ-4862 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5463 TCGA-CZ-5465 
        1404         1843           25         1683          662         1446 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
         685           59          386          373          435          693 
TCGA-DV-5565 TCGA-DV-5574 TCGA-DV-5575 
        1329          723         1729 

$`DEL PEAK 12(8P23.2) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 
        1508         1478         1106         1186         1137         1485 
TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
         665          945         1610         1385          910         2688 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3367 TCGA-A3-3370 
        1307         2504         1559          319         2270         2274 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
        1314         1070          630          567          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
         617            3         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3451 
        1853         2192         1423         1471         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 
        1397          874         1143          951          853          369 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
          43           26           96         1092          359          797 
TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         657          535           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
        1132          449         2408         3431         1487         3076 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 
        1835         2583         2741         1732         1605         1203 
TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5812 
        3668         2414         3117         1459         2931         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
         992         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5834 
         358          315          417          656          175           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
          16          141           11            7          511          826 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 
         722           36          737          505          434         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54J TCGA-B8-A7U6 
         435          830          519           53           66          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 
        3377         2881         2746         3074         2839         3037 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4329 
          13         2718         1893         1670         2964          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4349 
        1888         1133          645          461         1666          372 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
        1462         1876         1885          411         1731         1854 
TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4961 
        1489         1107         1124          204         1459         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4971 
        1785         1834         1862         1871         1794         1487 
TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4987 
        1502         1433         1632          454         1014         1124 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
         118         1413          501          177         1371         1266 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 
        1177          840         1140         1071         2412         2257 
TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        2263         1495         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
         749          603         1355           29         1820         1416 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
        1924         2308         2554         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4890 TCGA-CJ-4892 
        2283         2353         1883         1952         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
         750         1528         1450         1520         1496         1531 
TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 
        1373         1943         2430         2575          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        1889         2231         2038         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
        2489         2609         2226         2017         2378         2271 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4863 
        3146          774           18         1943         1787         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5458 
        2830         1868         1929         1789         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5469 TCGA-CZ-5982 
        1683         1430          330         1740          946         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
        2067         1997         1905         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         355         1130          551          119          206          127 
TCGA-GK-A6C7 
          61 

  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                            7                             3 
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                         3343                          3668 
  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE 
                         1126                          1397 
[1] "7.0 - 3343.0 (1126.0)" "3.0 - 3668.0 (1397.0)"
[1] "hr=" "1.7"
D24V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 12(8P23.2) MUTATED        61       18        44       28
  DEL PEAK 12(8P23.2) WILD-TYPE     183       38        82       51
D24V3, multiclass
           clus
vv          DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  STAGE I                            61                           183
  STAGE II                           18                            38
  STAGE III                          44                            82
  STAGE IV                           28                            51
[1] 4 2
[1] 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(8P23.2) MUTATED    63  22  62   4
  DEL PEAK 12(8P23.2) WILD-TYPE 187  45 115   7
D24V4, multiclass
    clus
vv   DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  T1                          63                           187
  T2                          22                            45
  T3                          62                           115
  T4                           4                             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"
D24V5, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.2) MUTATED    66   5
  DEL PEAK 12(8P23.2) WILD-TYPE 164  13
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.2) MUTATED     66    5
  DEL PEAK 12(8P23.2) WILD-TYPE  164   13
   clus
vv  DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  0                          66                           164
  1                           5                            13
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 12(8P23.2) MUTATED   120  29   2
  DEL PEAK 12(8P23.2) WILD-TYPE 297  49   7
D24V6, multiclass
    clus
vv   DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  M0                         120                           297
  M1                          29                            49
  MX                           2                             7
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V7, binary
                               cls
clus                              0   1
  DEL PEAK 12(8P23.2) MUTATED    48 103
  DEL PEAK 12(8P23.2) WILD-TYPE 130 224
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.2) MUTATED     48  103
  DEL PEAK 12(8P23.2) WILD-TYPE  130  224
        clus
vv       DEL PEAK 12(8P23.2) MUTATED DEL PEAK 12(8P23.2) WILD-TYPE
  FEMALE                          48                           130
  MALE                           103                           224
[1] 2 2
[1] FALSE
D24V8, continuous
D24V9, continuous
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 12(8P23.2) MUTATED       4                         7   137
  DEL PEAK 12(8P23.2) WILD-TYPE     4                        26   320
D24V10, multiclass
                           clus
vv                          DEL PEAK 12(8P23.2) MUTATED
  ASIAN                                               4
  BLACK OR AFRICAN AMERICAN                           7
  WHITE                                             137
                           clus
vv                          DEL PEAK 12(8P23.2) WILD-TYPE
  ASIAN                                                 4
  BLACK OR AFRICAN AMERICAN                            26
  WHITE                                               320
[1] 3 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 12(8P23.2) MUTATED    12  86
  DEL PEAK 12(8P23.2) WILD-TYPE  12 244
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 12(8P23.2) MUTATED     12   86
  DEL PEAK 12(8P23.2) WILD-TYPE   12  244
                        clus
vv                       DEL PEAK 12(8P23.2) MUTATED
  HISPANIC OR LATINO                              12
  NOT HISPANIC OR LATINO                          86
                        clus
vv                       DEL PEAK 12(8P23.2) WILD-TYPE
  HISPANIC OR LATINO                                12
  NOT HISPANIC OR LATINO                           244
[1] 2 2
[1] FALSE

Clustering(25) Variable = DEL PEAK 13(9P23) MUTATION ANALYSIS
D25V1, survival
                             sevent
clus2                           0   1
  DEL PEAK 13(9P23) MUTATED    77   9
  DEL PEAK 13(9P23) WILD-TYPE 261  17
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                         86                         278 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                          9                          17 
$`DEL PEAK 13(9P23) MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 
        1120         1493         1491         1130          751         1610 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 
         735          574         3343         2044         1280         1779 
TCGA-AS-3777 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5113 TCGA-B0-5116 
        1238           96          183          665          359          657 
TCGA-B0-5402 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 
         449         1732          358          656            7          166 
TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4161 
         777          700          636          194           15         2746 
TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4351 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 
        2718         1955          970         1462          400         2080 
TCGA-BP-4782 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 
         354         1107          204         2172         1785         1834 
TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 
        1862         1384         1413          785         1308         1371 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5189 
         563          193          932         2263         1291          822 
TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4871 
         967         1018          603          951         1416         2423 
TCGA-CJ-4881 TCGA-CJ-4890 TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
        2014         2085         1450         1499         1531         1657 
TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5588 
        1943         2575         1883         1855         1906         2017 
TCGA-CW-5591 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5461 
        2271         2552         1404         1943         1712          330 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 
        1446          685           59          946          386         2067 
TCGA-CZ-5985 TCGA-CZ-5987 
        1997          435 

$`DEL PEAK 13(9P23) WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1436           16          735         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
        1186         1137         1485          665         1043          945 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
         319          873         2270         2274         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          567          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
           3         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
        2192         2087         1745         1423         1471         1217 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         853          369           43          110           26          616 
TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
          18          911         1092          797          535           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 
         493          554          652         1132         2408         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        1487         3076         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 
        2741         1605         1203         3668         2414         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 
        1092           51          374          648          952          315 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 
         417          507          291          175           38           16 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 
         762          750          523          788          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 
         822           26          737          522          505          434 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 
         150           66          110         3377         2881         3074 
TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
        2839         3037           13          701         1893         1879 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 
        1670         2964         1625          845         1888         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
         645          461         2859         1666         1367          372 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4765 
         374         2208         2372         2361          182         2184 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4784 
        1876         1885         1843          411         1731         1854 
TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1489          620         1124         1459          211         2660 
TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1935         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1487         1502         1433         1632          454         1014 
TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 
        1124          118         1413          501          177          932 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
        1266         1177         1126          840         1140         1071 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 
        2412         2257          293         1495         1165         1133 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
        1132          693          406         1011          714          408 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
         749         1355         1063           29         1820         1924 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        2308         1998         1628         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        1498         1435         2259         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        2186         1883         1759         2125         1952         1946 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 
        1521          750          841         1808         1528         1520 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 
        1560         1792         1496         1373         2430          552 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 
        1889         2231         2038         2548         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
        2609         2226         2378         3222         3146          774 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
          18         1787         1843         1928         2830         1868 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        1929         1789           25         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 
        1430          662         1740         2439          373          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 
        1905         1329         1398         1470          370          355 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        1130          723         1729          551          119          206 
TCGA-EU-5907 TCGA-GK-A6C7 
         127           61 

  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                          7                           3 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                       3343                        3668 
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                     1299.5                      1286.5 
[1] "7.0 - 3343.0 (1299.5)" "3.0 - 3668.0 (1286.5)"
[1] "hr=" "1.8"
D25V2, continuous
                             vv
clus                          STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 13(9P23) MUTATED        47       12        51       36
  DEL PEAK 13(9P23) WILD-TYPE     197       44        75       43
D25V3, multiclass
           clus
vv          DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  STAGE I                          47                         197
  STAGE II                         12                          44
  STAGE III                        51                          75
  STAGE IV                         36                          43
[1] 4 2
[1] 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(9P23) MUTATED    51  16  74   5
  DEL PEAK 13(9P23) WILD-TYPE 199  51 103   6
D25V4, multiclass
    clus
vv   DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  T1                        51                         199
  T2                        16                          51
  T3                        74                         103
  T4                         5                           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"
D25V5, binary
                             cls
clus                            0   1
  DEL PEAK 13(9P23) MUTATED    59   8
  DEL PEAK 13(9P23) WILD-TYPE 171  10
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(9P23) MUTATED     59    8
  DEL PEAK 13(9P23) WILD-TYPE  171   10
   clus
vv  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  0                        59                         171
  1                         8                          10
[1] 2 2
[1] FALSE
                             vv
clus                           M0  M1  MX
  DEL PEAK 13(9P23) MUTATED   111  35   0
  DEL PEAK 13(9P23) WILD-TYPE 306  43   9
D25V6, multiclass
    clus
vv   DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  M0                       111                         306
  M1                        35                          43
  MX                         0                           9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V7, binary
                             cls
clus                            0   1
  DEL PEAK 13(9P23) MUTATED    36 110
  DEL PEAK 13(9P23) WILD-TYPE 142 217
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(9P23) MUTATED     36  110
  DEL PEAK 13(9P23) WILD-TYPE  142  217
        clus
vv       DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  FEMALE                        36                         142
  MALE                         110                         217
[1] 2 2
[1] FALSE
D25V8, continuous
D25V9, continuous
[1] "Remove cluster labels:"    "DEL PEAK 13(9P23) MUTATED"
clus
  DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE 
                          2                           6 
                 TCGA-A3-A8CQ                  TCGA-B2-A4SR 
"DEL PEAK 13(9P23) WILD-TYPE" "DEL PEAK 13(9P23) WILD-TYPE" 
                 TCGA-B8-4621                  TCGA-B8-5164 
"DEL PEAK 13(9P23) WILD-TYPE" "DEL PEAK 13(9P23) WILD-TYPE" 
                 TCGA-B8-A54F                  TCGA-B8-A54G 
"DEL PEAK 13(9P23) WILD-TYPE" "DEL PEAK 13(9P23) WILD-TYPE" 
                             vv
clus                          ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 13(9P23) MUTATED       2                         5   134
  DEL PEAK 13(9P23) WILD-TYPE     6                        28   323
D25V10, multiclass
                           clus
vv                          DEL PEAK 13(9P23) MUTATED
  ASIAN                                             2
  BLACK OR AFRICAN AMERICAN                         5
  WHITE                                           134
                           clus
vv                          DEL PEAK 13(9P23) WILD-TYPE
  ASIAN                                               6
  BLACK OR AFRICAN AMERICAN                          28
  WHITE                                             323
[1] 3 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 13(9P23) MUTATED     6  95
  DEL PEAK 13(9P23) WILD-TYPE  18 235
[1] "tbl2"
                             cls
clus                          [,1] [,2]
  DEL PEAK 13(9P23) MUTATED      6   95
  DEL PEAK 13(9P23) WILD-TYPE   18  235
                        clus
vv                       DEL PEAK 13(9P23) MUTATED DEL PEAK 13(9P23) WILD-TYPE
  HISPANIC OR LATINO                             6                          18
  NOT HISPANIC OR LATINO                        95                         235
[1] 2 2
[1] FALSE

Clustering(26) Variable = DEL PEAK 14(9P21.3) MUTATION ANALYSIS
D26V1, survival
                               sevent
clus2                             0   1
  DEL PEAK 14(9P21.3) MUTATED    78  10
  DEL PEAK 14(9P21.3) WILD-TYPE 260  16
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                           88                           276 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                           10                            16 
$`DEL PEAK 14(9P21.3) MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3347 
        1120         1493         1491         1130          751         1610 
TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 
         735          574         3343         2044         1280         1779 
TCGA-AS-3777 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5113 TCGA-B0-5116 
        1238           96          183          665          359          657 
TCGA-B0-5121 TCGA-B0-5402 TCGA-B0-5701 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 
         554          449         1732          358          656            7 
TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5550 
         166          777          700          636          194          434 
TCGA-B8-5551 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4176 TCGA-BP-4351 
          15         2881         2746         2718         1955          970 
TCGA-BP-4761 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4797 
         182         1462          400         2080          354         1107 
TCGA-BP-4803 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4973 
         204         2172         1785         1834         1862         1384 
TCGA-BP-4986 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 
         785         1308         1371          563          193          932 
TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 
        2263         1291          822          967         1018          603 
TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4881 TCGA-CJ-4890 
         951         1416          646         2423         2014         2085 
TCGA-CJ-4901 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 
        1450         1499         1531         1657         1943         2575 
TCGA-CJ-5682 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4854 
        1883         1855         1906         2017         2552         1404 
TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
        1943         1712          330         1446          685           59 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
         946         2067         1997          435 

$`DEL PEAK 14(9P21.3) WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1436           16          735         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 
        1186         1137         1485          665         1043          945 
TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1385          910         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3374 
         319          873         2270         2274         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 
        1070          630          567          861         1993          617 
TCGA-A3-A8CQ TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
           3         2566         2223         2017          480         1853 
TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 
        2192         2087         1745         1423         1471         1217 
TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
        1481         1397          874         1143         1168          951 
TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4718 
         853          369           43          110           26          616 
TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 
          18          911         1092          797          535           59 
TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         493          652         1132         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
        3076         1420         1727         1835         2583         2741 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 
          51          374          648          952          315          417 
TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 
         507          291          175           38           16          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 
         750          523          788          722           36          822 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-5553 
          26          737          522          505         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
         110         3377         3074         2839         3037           13 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
         701         1893         1879         1670         2964         1625 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
         845         1888         1133          645          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2361         2184         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 
        1731         1854         1489          620         1124         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
         211         2660         1935         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 
        1794          433         1487         1502         1433         1632 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
         454         1014         1413         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
         501          177          932         1266         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5177 
         840         1140         1071         2412         2257          293 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
        1495         1165         1133         1132          693          406 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 
        1011          714          408          749         1355         1063 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4642 
          29         1820         1924         2308         1998         1628 
TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
        1793         2554         1498         1435         2259         2283 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        2353         1955         2186         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        1952         1946         1521          750          841         1808 
TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 
        1528         1520         1560         1792         1496         1373 
TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 
        2430          552         1889         2231         2038         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 
        2799         2489         2609         2226         2378         2271 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 
        3222         3146          774           18         1787         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        1928         2830         1868         1929         1789           25 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5464 
        1683         1732         1683         1430          662         1740 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
         386         2439          373          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        1398         1470          370          355         1130          723 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
        1729          551          119          206          127           61 

  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                            7                             3 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                         3343                          3668 
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                       1259.0                        1321.5 
[1] "7.0 - 3343.0 (1259.0)" "3.0 - 3668.0 (1321.5)"
[1] "hr=" "2.1"
D26V2, continuous
                               vv
clus                            STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 14(9P21.3) MUTATED        48       11        55       40
  DEL PEAK 14(9P21.3) WILD-TYPE     196       45        71       39
D26V3, multiclass
           clus
vv          DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  STAGE I                            48                           196
  STAGE II                           11                            45
  STAGE III                          55                            71
  STAGE IV                           40                            39
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
                               vv
clus                             T1  T2  T3  T4
  DEL PEAK 14(9P21.3) MUTATED    52  15  81   6
  DEL PEAK 14(9P21.3) WILD-TYPE 198  52  96   5
D26V4, multiclass
    clus
vv   DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  T1                          52                           198
  T2                          15                            52
  T3                          81                            96
  T4                           6                             5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V5, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED    65  10
  DEL PEAK 14(9P21.3) WILD-TYPE 165   8
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED     65   10
  DEL PEAK 14(9P21.3) WILD-TYPE  165    8
   clus
vv  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  0                          65                           165
  1                          10                             8
[1] 2 2
[1] FALSE
                               vv
clus                             M0  M1  MX
  DEL PEAK 14(9P21.3) MUTATED   115  39   0
  DEL PEAK 14(9P21.3) WILD-TYPE 302  39   9
D26V6, multiclass
    clus
vv   DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  M0                         115                           302
  M1                          39                            39
  MX                           0                             9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D26V7, binary
                               cls
clus                              0   1
  DEL PEAK 14(9P21.3) MUTATED    37 117
  DEL PEAK 14(9P21.3) WILD-TYPE 141 210
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED     37  117
  DEL PEAK 14(9P21.3) WILD-TYPE  141  210
        clus
vv       DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE
  FEMALE                          37                           141
  MALE                           117                           210
[1] 2 2
[1] FALSE
D26V8, continuous
D26V9, continuous
[1] "Remove cluster labels:"      "DEL PEAK 14(9P21.3) MUTATED"
clus
  DEL PEAK 14(9P21.3) MUTATED DEL PEAK 14(9P21.3) WILD-TYPE 
                            2                             6 
                   TCGA-A3-A8CQ                    TCGA-B2-A4SR 
"DEL PEAK 14(9P21.3) WILD-TYPE" "DEL PEAK 14(9P21.3) WILD-TYPE" 
                   TCGA-B8-4621                    TCGA-B8-5164 
"DEL PEAK 14(9P21.3) WILD-TYPE" "DEL PEAK 14(9P21.3) WILD-TYPE" 
                   TCGA-B8-A54F                    TCGA-B8-A54G 
"DEL PEAK 14(9P21.3) WILD-TYPE" "DEL PEAK 14(9P21.3) WILD-TYPE" 
                               vv
clus                            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 14(9P21.3) MUTATED       1                         5   144
  DEL PEAK 14(9P21.3) WILD-TYPE     7                        28   313
D26V10, multiclass
                           clus
vv                          DEL PEAK 14(9P21.3) MUTATED
  ASIAN                                               1
  BLACK OR AFRICAN AMERICAN                           5
  WHITE                                             144
                           clus
vv                          DEL PEAK 14(9P21.3) WILD-TYPE
  ASIAN                                                 7
  BLACK OR AFRICAN AMERICAN                            28
  WHITE                                               313
[1] 3 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 14(9P21.3) MUTATED     7 102
  DEL PEAK 14(9P21.3) WILD-TYPE  17 228
[1] "tbl2"
                               cls
clus                            [,1] [,2]
  DEL PEAK 14(9P21.3) MUTATED      7  102
  DEL PEAK 14(9P21.3) WILD-TYPE   17  228
                        clus
vv                       DEL PEAK 14(9P21.3) MUTATED
  HISPANIC OR LATINO                               7
  NOT HISPANIC OR LATINO                         102
                        clus
vv                       DEL PEAK 14(9P21.3) WILD-TYPE
  HISPANIC OR LATINO                                17
  NOT HISPANIC OR LATINO                           228
[1] 2 2
[1] FALSE

Clustering(27) Variable = DEL PEAK 15(10Q23.31) MUTATION ANALYSIS
D27V1, survival
                                 sevent
clus2                               0   1
  DEL PEAK 15(10Q23.31) MUTATED    60   7
  DEL PEAK 15(10Q23.31) WILD-TYPE 278  19
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             67                             297 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                              7                              19 
$`DEL PEAK 15(10Q23.31) MUTATED`
TCGA-A3-3316 TCGA-A3-3331 TCGA-A3-3374 TCGA-A3-3380 TCGA-AK-3430 TCGA-AK-3433 
        1493         1485         1314          567          480         2192 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3458 TCGA-AK-3461 TCGA-AK-3465 TCGA-B0-4699 
        1745         1423         1168          853          369          110 
TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5117 TCGA-B0-5402 TCGA-B0-5703 TCGA-B0-5706 
         616          183          535          449         1203         2414 
TCGA-B2-3923 TCGA-B2-5641 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-5158 TCGA-B8-5549 
         992          656           16          166          636          194 
TCGA-B8-5550 TCGA-B8-A7U6 TCGA-BP-4161 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4329 
         434          110         2746           13         2718          845 
TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4766 TCGA-BP-4775 TCGA-BP-4797 TCGA-BP-4803 
         645          970         1462         1843         1107          204 
TCGA-BP-4960 TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-5169 TCGA-BP-5180 TCGA-BP-5185 
        2172         1384         1308          193         2263         1132 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4642 TCGA-CJ-4872 
        1018          603          951         1416         1628         1435 
TCGA-CJ-4874 TCGA-CJ-4882 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4901 TCGA-CJ-4907 
        2283         1883          750         1808         1450         1499 
TCGA-CJ-5676 TCGA-CJ-6032 TCGA-CW-6090 TCGA-CZ-5457 TCGA-CZ-5460 TCGA-CZ-5465 
        2575         2548         2552         1683         1430         1446 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-DV-5565 TCGA-DV-5566 
          59          946          386         2439         1329         1398 
TCGA-EU-5907 
         127 

$`DEL PEAK 15(10Q23.31) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3319 
        1120         1436           16          735         1491         1130 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
         665         1043          945         1610         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 
        2270         2274          735         1621         1070          630 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         574          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 
        2566         2223         2017         1853         2087         2044 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
        1471         1280         1217         1779         1481         1397 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4706 
         874         1143          951         1238           43           26 
TCGA-B0-4710 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
          96           18          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
         797          657           59          493          554          652 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
        1132         2408         3431         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
        1727         1835         2583         2741         1732         1605 
TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        3668         3117         1459         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
        2963         1092           51          374          648          952 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 
         358          315          417          507          291          175 
TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
           7           38          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 
         826          838          762          750          523          777 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         788          700          722           36          822           26 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         737          522          505           15         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         830          519           53          256          150           66 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4169 
        3377         2881         3074         2839         3037          701 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 
        1893         1879         1955         1670         2964         1625 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4347 
        1888         1133          461         2859         1666         1367 
TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 
         372          374         2208         2372         2361          182 
TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 
        2184          400         1876         1885          411         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 
        2080          354         1854         1489          620         1124 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
        1459          211         2660         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 
        1487         1502         1433         1632          454         1014 
TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
        1413          785         1124          118         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
         177         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5174 
        1126          840         1140         1071         2412         2257 
TCGA-BP-5175 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         932          293         1495         1165         1291         1133 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
         693          406          822         1011          967          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
         408          749         1355         1063           29         1820 
TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4869 
        1924         2308         1998         1793          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1498         2423         2259         2353         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        2014         1759         2125         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
        1521          841         1528         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1496         1531         1657         1373         1943         2430 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
         552         1883         1889         2231         2038         1855 
TCGA-CJ-6031 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 
        1906         2799         2489         2609         2226         2017 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
        2378         2271         3222         3146          774         1404 
TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
          18         1943         1787         1843         1928         2830 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 
        1868         1929         1789           25         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5984 
        1683          330          662         1740          685         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5567 
        1997          373          435          693         1905         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
         370          355         1130          723         1729          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-GK-A6C7 
         119          206           61 

  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                             13                               3 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                           2746                            3668 
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                           1168                            1355 
[1] "13.0 - 2746.0 (1168.0)" "3.0 - 3668.0 (1355.0)" 
[1] "hr=" "1.9"
D27V2, continuous
                                 vv
clus                              STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 15(10Q23.31) MUTATED        32       11        32       19
  DEL PEAK 15(10Q23.31) WILD-TYPE     212       45        94       60
D27V3, multiclass
           clus
vv          DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  STAGE I                              32                             212
  STAGE II                             11                              45
  STAGE III                            32                              94
  STAGE IV                             19                              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"
                                 vv
clus                               T1  T2  T3  T4
  DEL PEAK 15(10Q23.31) MUTATED    32  12  44   6
  DEL PEAK 15(10Q23.31) WILD-TYPE 218  55 133   5
D27V4, multiclass
    clus
vv   DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  T1                            32                             218
  T2                            12                              55
  T3                            44                             133
  T4                             6                               5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V5, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED    40   3
  DEL PEAK 15(10Q23.31) WILD-TYPE 190  15
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     40    3
  DEL PEAK 15(10Q23.31) WILD-TYPE  190   15
   clus
vv  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  0                            40                             190
  1                             3                              15
[1] 2 2
[1] FALSE
                                 vv
clus                               M0  M1  MX
  DEL PEAK 15(10Q23.31) MUTATED    76  17   0
  DEL PEAK 15(10Q23.31) WILD-TYPE 341  61   9
D27V6, multiclass
    clus
vv   DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  M0                            76                             341
  M1                            17                              61
  MX                             0                               9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V7, binary
                                 cls
clus                                0   1
  DEL PEAK 15(10Q23.31) MUTATED    25  69
  DEL PEAK 15(10Q23.31) WILD-TYPE 153 258
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED     25   69
  DEL PEAK 15(10Q23.31) WILD-TYPE  153  258
        clus
vv       DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE
  FEMALE                            25                             153
  MALE                              69                             258
[1] 2 2
[1] FALSE
D27V8, continuous
D27V9, continuous
[1] "Remove cluster labels:"        "DEL PEAK 15(10Q23.31) MUTATED"
clus
  DEL PEAK 15(10Q23.31) MUTATED DEL PEAK 15(10Q23.31) WILD-TYPE 
                              1                               7 
                     TCGA-A3-A8CQ                      TCGA-B2-A4SR 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-B8-4621                      TCGA-B8-5164 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-B8-A54F                      TCGA-B8-A54G 
"DEL PEAK 15(10Q23.31) WILD-TYPE" "DEL PEAK 15(10Q23.31) WILD-TYPE" 
                     TCGA-G6-A5PC 
"DEL PEAK 15(10Q23.31) WILD-TYPE" 
                                 vv
clus                              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 15(10Q23.31) MUTATED       0                         4    87
  DEL PEAK 15(10Q23.31) WILD-TYPE     8                        29   370
D27V10, multiclass
                           clus
vv                          DEL PEAK 15(10Q23.31) MUTATED
  ASIAN                                                 0
  BLACK OR AFRICAN AMERICAN                             4
  WHITE                                                87
                           clus
vv                          DEL PEAK 15(10Q23.31) WILD-TYPE
  ASIAN                                                   8
  BLACK OR AFRICAN AMERICAN                              29
  WHITE                                                 370
[1] 3 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 15(10Q23.31) MUTATED     6  58
  DEL PEAK 15(10Q23.31) WILD-TYPE  18 272
[1] "tbl2"
                                 cls
clus                              [,1] [,2]
  DEL PEAK 15(10Q23.31) MUTATED      6   58
  DEL PEAK 15(10Q23.31) WILD-TYPE   18  272
                        clus
vv                       DEL PEAK 15(10Q23.31) MUTATED
  HISPANIC OR LATINO                                 6
  NOT HISPANIC OR LATINO                            58
                        clus
vv                       DEL PEAK 15(10Q23.31) WILD-TYPE
  HISPANIC OR LATINO                                  18
  NOT HISPANIC OR LATINO                             272
[1] 2 2
[1] FALSE

Clustering(28) Variable = DEL PEAK 16(13Q13.3) MUTATION ANALYSIS
D28V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 16(13Q13.3) MUTATED    43   8
  DEL PEAK 16(13Q13.3) WILD-TYPE 295  18
  DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE 
                            51                            313 
  DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE 
                             8                             18 
$`DEL PEAK 16(13Q13.3) MUTATED`
TCGA-A3-3319 TCGA-A3-3347 TCGA-A3-3370 TCGA-A3-3374 TCGA-AK-3433 TCGA-AK-3440 
        1130         1610         2274         1314         2192         1745 
TCGA-AK-3445 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4819 
        1280          369         1238          110           96          183 
TCGA-B0-5113 TCGA-B0-5117 TCGA-B0-5696 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 
         359          535         1727            7           16          166 
TCGA-B8-4146 TCGA-B8-5163 TCGA-B8-5549 TCGA-BP-4167 TCGA-BP-4334 TCGA-BP-4351 
         511          822          194         2718          645          970 
TCGA-BP-4761 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4797 TCGA-BP-4964 TCGA-BP-4968 
         182         2184          400         1107         1862         1746 
TCGA-BP-4973 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5175 TCGA-BP-5191 TCGA-BP-5196 
        1384         1308         1126          932          967         1018 
TCGA-CJ-4639 TCGA-CJ-4868 TCGA-CJ-4881 TCGA-CJ-4901 TCGA-CW-5588 TCGA-CW-6090 
        2308          646         2014         1450         2017         2552 
TCGA-CZ-4854 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5465 TCGA-CZ-5468 
        1404         1928         1868         1683         1446           59 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-DV-5568 
         946         2067          370 

$`DEL PEAK 16(13Q13.3) WILD-TYPE`
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 
        1120         1436           16          735         1493         1491 
TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1508         1478         1106         1186          751         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
        1485          665         1043          945         1385          910 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 
        2688         1307         2504         1559          319          873 
TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2270          735         1621         1070          630          567 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3425 
         574          861         1993          617            3         3343 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 
        2566         2223         2017          480         1853         2087 
TCGA-AK-3436 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 
        2044         1423         1471         1217         1779         1481 
TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
        1397          874         1143         1168          951          853 
TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5108 
          43           26          616           18          665          911 
TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
        1092          797          657           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
        3076         1420         1835         2583         2741         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5710 
        1605         1203         3668         2414         3117         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 
        2931         2722         1865         2963          992         1092 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 
          51          374          648          952          358          315 
TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5834 
         417          656          507          291          175           38 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
         141           11            7          826          838          762 
TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         750          523          777          788          700          636 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
         722           36           26          737          522          505 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F 
         434           15         1046          435          830          519 
TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
          53          256          150           66          110         3377 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        2881         2746         3074         2839         3037           13 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
         701         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4338 
        1625          845         1888         1133          461         2859 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
        1666         1367          372          374         2208         2372 
TCGA-BP-4760 TCGA-BP-4766 TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        2361         1462         1876         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 
        1731         2080          354         1854         1489          620 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 
        1124          204         1459          211         2660         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 
        1935         1785         1834         1871          205         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
         433         1487         1502         1433         1632          454 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4989 TCGA-BP-4991 
        1014         1413          785         1124          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
         501          177         1371          932         1266          563 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 
        1177          840         1140         1071          193         2412 
TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 
        2257          293         2263         1495         1165         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1133         1132          693          406          822         1011 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         714          408          749          603         1355         1063 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4640 
         951           29         1820         1416         1924         1998 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1628         1793         2554         1498         2423         1435 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4882 
        2259         2283         2353         1955         2186         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 
        1759         2125         1952         1946         2085         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1808         1528         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 
        1792         1496         1499         1531         1657         1373 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
        1943         2430         2575          552         1883         1889 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
        2231         2038         1855         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 
        2489         2609         2226         2378         2271         3222 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 
        3146          774           18         1943         1787         1843 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5456 TCGA-CZ-5458 
        2830         1929         1789           25         1712         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 
        1683         1430          330          662         1740          685 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
         386         2439         1997          373          435          693 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 
        1905         1329         1398         1470          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         723         1729          551          119          206          127 
TCGA-GK-A6C7 
          61 

  DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE 
                             7                              3 
  DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE 
                          2718                           3668 
  DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE 
                          1130                           1355 
[1] "7.0 - 2718.0 (1130.0)" "3.0 - 3668.0 (1355.0)"
[1] "hr=" "3.1"
D28V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 16(13Q13.3) MUTATED        25        3        31       20
  DEL PEAK 16(13Q13.3) WILD-TYPE     219       53        95       59
D28V3, multiclass
           clus
vv          DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE
  STAGE I                             25                            219
  STAGE II                             3                             53
  STAGE III                           31                             95
  STAGE IV                            20                             59
[1] 4 2
[1] 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(13Q13.3) MUTATED    27   4  42   6
  DEL PEAK 16(13Q13.3) WILD-TYPE 223  63 135   5
D28V4, multiclass
    clus
vv   DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE
  T1                           27                            223
  T2                            4                             63
  T3                           42                            135
  T4                            6                              5
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V5, binary
                                cls
clus                               0   1
  DEL PEAK 16(13Q13.3) MUTATED    37   5
  DEL PEAK 16(13Q13.3) WILD-TYPE 193  13
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(13Q13.3) MUTATED     37    5
  DEL PEAK 16(13Q13.3) WILD-TYPE  193   13
   clus
vv  DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE
  0                           37                            193
  1                            5                             13
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 16(13Q13.3) MUTATED    61  18   0
  DEL PEAK 16(13Q13.3) WILD-TYPE 356  60   9
D28V6, multiclass
    clus
vv   DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE
  M0                           61                            356
  M1                           18                             60
  MX                            0                              9
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D28V7, binary
                                cls
clus                               0   1
  DEL PEAK 16(13Q13.3) MUTATED    27  52
  DEL PEAK 16(13Q13.3) WILD-TYPE 151 275
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(13Q13.3) MUTATED     27   52
  DEL PEAK 16(13Q13.3) WILD-TYPE  151  275
        clus
vv       DEL PEAK 16(13Q13.3) MUTATED DEL PEAK 16(13Q13.3) WILD-TYPE
  FEMALE                           27                            151
  MALE                             52                            275
[1] 2 2
[1] FALSE
D28V8, continuous
D28V9, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 16(13Q13.3) MUTATED       0                         2    76
  DEL PEAK 16(13Q13.3) WILD-TYPE     8                        31   381
D28V10, multiclass
                           clus
vv                          DEL PEAK 16(13Q13.3) MUTATED
  ASIAN                                                0
  BLACK OR AFRICAN AMERICAN                            2
  WHITE                                               76
                           clus
vv                          DEL PEAK 16(13Q13.3) WILD-TYPE
  ASIAN                                                  8
  BLACK OR AFRICAN AMERICAN                             31
  WHITE                                                381
[1] 3 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 16(13Q13.3) MUTATED     2  53
  DEL PEAK 16(13Q13.3) WILD-TYPE  22 277
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 16(13Q13.3) MUTATED      2   53
  DEL PEAK 16(13Q13.3) WILD-TYPE   22  277
                        clus
vv                       DEL PEAK 16(13Q13.3) MUTATED
  HISPANIC OR LATINO                                2
  NOT HISPANIC OR LATINO                           53
                        clus
vv                       DEL PEAK 16(13Q13.3) WILD-TYPE
  HISPANIC OR LATINO                                 22
  NOT HISPANIC OR LATINO                            277
[1] 2 2
[1] FALSE

Clustering(29) Variable = DEL PEAK 17(14Q31.1) MUTATION ANALYSIS
D29V1, survival
                                sevent
clus2                              0   1
  DEL PEAK 17(14Q31.1) MUTATED   130  15
  DEL PEAK 17(14Q31.1) WILD-TYPE 208  11
  DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE 
                           145                            219 
  DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE 
                            15                             11 
$`DEL PEAK 17(14Q31.1) MUTATED`
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3324 
        1120         1493         1491         1130         1508         1186 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 TCGA-A3-3357 
         665         1043         1610         1385          910         2688 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3429 TCGA-AK-3430 
         630          574          617         2566         2017          480 
TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
        1853         2044         1280         1779         1481          874 
TCGA-AK-3458 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5400 
        1168          183          665         1092          359         1132 
TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5710 TCGA-B0-5711 
        1487         1835         2583         1732         1459         2931 
TCGA-B0-5712 TCGA-B2-4098 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
        2722           51          952          358          315          417 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B8-4619 
         656            7          141          166           11          523 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 
         636          722           36           26          434           15 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4167 
         435          830           53          150         2839         2718 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4347 TCGA-BP-4761 TCGA-BP-4768 
        1893         1879         1955         1367          182          400 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4962 
        1731         2080         1107          204         2660         1785 
TCGA-BP-4965 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4983 
        1871          433         1487         1384          454         1413 
TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5004 TCGA-BP-5169 
         785          118          501          563         1126          193 
TCGA-BP-5170 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5185 
        2412         2257          932         2263         1291         1132 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
         822         1011          967          749         1018          603 
TCGA-BP-5201 TCGA-CJ-4636 TCGA-CJ-4640 TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 
         951         1924         1998         1628          646         2554 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 
        2423         2259         2283         2353         1955         2014 
TCGA-CJ-4884 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 
        1759          750          841         1808         1560         1792 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5671 TCGA-CJ-5675 
        1499         1531         1657         1373         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CW-5587 TCGA-CW-5588 
        2575         1883         2038         1855         2226         2017 
TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
        2552         1404         1943         1928         2830         1868 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5468 
        1789         1712          330          662         1446           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5989 
         946          386         2067         1997          435         1905 
TCGA-DV-5573 
        1130 

$`DEL PEAK 17(14Q31.1) WILD-TYPE`
TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3325 
        1436           16          735         1478         1106          751 
TCGA-A3-3326 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1137         1485          945         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ 
        1314         1070          567          861         1993            3 
TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3440 TCGA-AK-3443 
        3343         2223         2192         2087         1745         1423 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 
        1471         1217         1397         1143          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4699 TCGA-B0-4706 TCGA-B0-4710 
         369         1238           43          110           26           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5108 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
         616           18          911          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 
          59          493          554          652          449         2408 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5702 
        3431         3076         1420         1727         2741         1605 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5709 TCGA-B0-5713 TCGA-B0-5812 
        1203         3668         2414         3117         1865         2963 
TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-A4SR TCGA-B4-5377 
         992         1092          374          648          507          291 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 
         175           38           16            7          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         838          762          750          777          788          700 
TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5552 
         822          737          522          505          194         1046 
TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         519          256           66          110         3377         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4177 
        2746         3074         3037           13          701         1670 
TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4334 
        2964         1625          845         1888         1133          645 
TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4756 
         461         2859         1666          372          970          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4769 
        2208         2372         2361         2184         1462         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4789 
        1885         1843          411          354         1854         1489 
TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
         620         1124         1459          211         2172         1935 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 
        1834         1862          205         1746         1794         1502 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4993 
        1433         1632         1014         1124         1413          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5006 
        1308         1371          932         1266         1177          840 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5184 
        1140         1071          293         1495         1165         1133 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5199 TCGA-BP-5200 
         693          406          714          408         1355         1063 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 
          29         1820         1416         2308         1793         1498 
TCGA-CJ-4872 TCGA-CJ-4878 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
        1435         2186         1883         2125         1952         1946 
TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 
        2085         1521         1528         1450         1520         1496 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 
         552         1889         2231         1906         2548         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 
        2489         2609         2378         2271         3222         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-5451 TCGA-CZ-5453 
         774           18         1787         1843         1929           25 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5466 
        1683         1732         1683         1430         1740          685 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        2439          373          693         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
         370          355          723         1729          551          119 
TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         206          127           61 

  DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE 
                             7                              3 
  DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE 
                          2931                           3668 
  DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE 
                          1373                           1238 
[1] "7.0 - 2931.0 (1373.0)" "3.0 - 3668.0 (1238.0)"
[1] "hr=" "2.1"
D29V2, continuous
                                vv
clus                             STAGE I STAGE II STAGE III STAGE IV
  DEL PEAK 17(14Q31.1) MUTATED        80       27        67       47
  DEL PEAK 17(14Q31.1) WILD-TYPE     164       29        59       32
D29V3, multiclass
           clus
vv          DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE
  STAGE I                             80                            164
  STAGE II                            27                             29
  STAGE III                           67                             59
  STAGE IV                            47                             32
[1] 4 2
[1] 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(14Q31.1) MUTATED    86  35  96   4
  DEL PEAK 17(14Q31.1) WILD-TYPE 164  32  81   7
D29V4, multiclass
    clus
vv   DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE
  T1                           86                            164
  T2                           35                             32
  T3                           96                             81
  T4                            4                              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"
D29V5, binary
                                cls
clus                               0   1
  DEL PEAK 17(14Q31.1) MUTATED    97  16
  DEL PEAK 17(14Q31.1) WILD-TYPE 133   2
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q31.1) MUTATED     97   16
  DEL PEAK 17(14Q31.1) WILD-TYPE  133    2
   clus
vv  DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE
  0                           97                            133
  1                           16                              2
[1] 2 2
[1] FALSE
                                vv
clus                              M0  M1  MX
  DEL PEAK 17(14Q31.1) MUTATED   170  48   3
  DEL PEAK 17(14Q31.1) WILD-TYPE 247  30   6
D29V6, multiclass
    clus
vv   DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE
  M0                          170                            247
  M1                           48                             30
  MX                            3                              6
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V7, binary
                                cls
clus                               0   1
  DEL PEAK 17(14Q31.1) MUTATED    71 150
  DEL PEAK 17(14Q31.1) WILD-TYPE 107 177
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q31.1) MUTATED     71  150
  DEL PEAK 17(14Q31.1) WILD-TYPE  107  177
        clus
vv       DEL PEAK 17(14Q31.1) MUTATED DEL PEAK 17(14Q31.1) WILD-TYPE
  FEMALE                           71                            107
  MALE                            150                            177
[1] 2 2
[1] FALSE
D29V8, continuous
D29V9, continuous
                                vv
clus                             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DEL PEAK 17(14Q31.1) MUTATED       2                         9   206
  DEL PEAK 17(14Q31.1) WILD-TYPE     6                        24   251
D29V10, multiclass
                           clus
vv                          DEL PEAK 17(14Q31.1) MUTATED
  ASIAN                                                2
  BLACK OR AFRICAN AMERICAN                            9
  WHITE                                              206
                           clus
vv                          DEL PEAK 17(14Q31.1) WILD-TYPE
  ASIAN                                                  6
  BLACK OR AFRICAN AMERICAN                             24
  WHITE                                                251
[1] 3 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 17(14Q31.1) MUTATED    12 152
  DEL PEAK 17(14Q31.1) WILD-TYPE  12 178
[1] "tbl2"
                                cls
clus                             [,1] [,2]
  DEL PEAK 17(14Q31.1) MUTATED     12  152
  DEL PEAK 17(14Q31.1) WILD-TYPE   12  178
                        clus
vv                       DEL PEAK 17(14Q31.1) MUTATED
  HISPANIC OR LATINO                               12
  NOT HISPANIC OR LATINO                          152
                        clus
vv                       DEL PEAK 17(14Q31.1) WILD-TYPE
  HISPANIC OR LATINO                                 12
  NOT HISPANIC OR LATINO                            178
[1] 2 2
[1] FALSE
