[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/11541492/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_Correlate_Genomic_Events_Preprocess/KIRC-TP/10686177/transformed.cor.cli.txt"

nPatients in clinical file=525, in cluster file=491, common to both=417
[1]  29 417
[1] "SETD2 MUTATION ANALYSIS"
[1] 3
  SETD2 MUTATED SETD2 WILD-TYPE 
             44             373 
  SETD2 MUTATED SETD2 WILD-TYPE 
             44             373 
[1] "BAP1 MUTATION ANALYSIS"
[1] 3
  BAP1 MUTATED BAP1 WILD-TYPE 
            41            376 
  BAP1 MUTATED BAP1 WILD-TYPE 
            41            376 
[1] "PTEN MUTATION ANALYSIS"
[1] 3
  PTEN MUTATED PTEN WILD-TYPE 
            18            399 
  PTEN MUTATED PTEN WILD-TYPE 
            18            399 
[1] "PBRM1 MUTATION ANALYSIS"
[1] 3
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            136             281 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            136             281 
[1] "KDM5C MUTATION ANALYSIS"
[1] 3
  KDM5C MUTATED KDM5C WILD-TYPE 
             26             391 
  KDM5C MUTATED KDM5C WILD-TYPE 
             26             391 
[1] "VHL MUTATION ANALYSIS"
[1] 3
  VHL MUTATED VHL WILD-TYPE 
          166           251 
  VHL MUTATED VHL WILD-TYPE 
          166           251 
[1] "FAM200A MUTATION ANALYSIS"
[1] 3
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               412 
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               412 
[1] "TP53 MUTATION ANALYSIS"
[1] 3
  TP53 MUTATED TP53 WILD-TYPE 
             9            408 
  TP53 MUTATED TP53 WILD-TYPE 
             9            408 
[1] "NEFH MUTATION ANALYSIS"
[1] 3
  NEFH MUTATED NEFH WILD-TYPE 
             5            412 
  NEFH MUTATED NEFH WILD-TYPE 
             5            412 
[1] "CCDC120 MUTATION ANALYSIS"
[1] 3
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               413 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               413 
[1] "MTOR MUTATION ANALYSIS"
[1] 3
  MTOR MUTATED MTOR WILD-TYPE 
            23            394 
  MTOR MUTATED MTOR WILD-TYPE 
            23            394 
[1] "GUSB MUTATION ANALYSIS"
[1] 3
  GUSB MUTATED GUSB WILD-TYPE 
             4            413 
  GUSB MUTATED GUSB WILD-TYPE 
             4            413 
[1] "PIK3CA MUTATION ANALYSIS"
[1] 3
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              405 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              405 
[1] "PCK1 MUTATION ANALYSIS"
[1] 3
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            412 
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            412 
[1] "ARID1A MUTATION ANALYSIS"
[1] 3
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              405 
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              405 
[1] "ATM MUTATION ANALYSIS"
[1] 3
  ATM MUTATED ATM WILD-TYPE 
           11           406 
  ATM MUTATED ATM WILD-TYPE 
           11           406 
[1] "DPCR1 MUTATION ANALYSIS"
[1] 3
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             411 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             411 
[1] "FGFR3 MUTATION ANALYSIS"
[1] 3
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4             413 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4             413 
[1] "PTCH1 MUTATION ANALYSIS"
[1] 3
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7             410 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7             410 
[1] "RBMX MUTATION ANALYSIS"
[1] 3
  RBMX MUTATED RBMX WILD-TYPE 
             4            413 
  RBMX MUTATED RBMX WILD-TYPE 
             4            413 
[1] "ARAP3 MUTATION ANALYSIS"
[1] 3
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             414 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             414 
[1] "GPR172B MUTATION ANALYSIS"
[1] 3
  GPR172B MUTATED GPR172B WILD-TYPE 
                4               413 
  GPR172B MUTATED GPR172B WILD-TYPE 
                4               413 
[1] "EGFR MUTATION ANALYSIS"
[1] 3
  EGFR MUTATED EGFR WILD-TYPE 
             7            410 
  EGFR MUTATED EGFR WILD-TYPE 
             7            410 
[1] "IL1RAP MUTATION ANALYSIS"
[1] 3
  IL1RAP MUTATED IL1RAP WILD-TYPE 
               4              413 
  IL1RAP MUTATED IL1RAP WILD-TYPE 
               4              413 
[1] "BCL6 MUTATION ANALYSIS"
[1] 3
  BCL6 MUTATED BCL6 WILD-TYPE 
             5            412 
  BCL6 MUTATED BCL6 WILD-TYPE 
             5            412 
[1] "NFAT5 MUTATION ANALYSIS"
[1] 3
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              6             411 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              6             411 
[1] "LARP1 MUTATION ANALYSIS"
[1] 3
  LARP1 MUTATED LARP1 WILD-TYPE 
              5             412 
  LARP1 MUTATED LARP1 WILD-TYPE 
              5             412 
[1] "KIAA1751 MUTATION ANALYSIS"
[1] 3
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 6                411 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 6                411 
[1] "INSRR MUTATION ANALYSIS"
[1] 3
  INSRR MUTATED INSRR WILD-TYPE 
              4             413 
  INSRR MUTATED INSRR WILD-TYPE 
              4             413 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 417 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
          16           NA         1493         1491         1130         1508 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
        1478         1106         1137           NA         1610         1385 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
        2688         1307         1559          319          873         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
        2274          735         1621         1070          630          567 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
         574          861         1993          617         3343         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
        2017          480         1853         2087         2044         1471 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
        1280         1779         1481          874           NA         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
        1168          951          853           43           NA           NA 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
          NA           NA           NA           NA           NA           26 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
          NA           96           NA           NA           NA          616 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
          NA           NA           18           NA           NA           NA 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
          NA           NA          183           NA           NA           NA 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
          NA           NA           NA           NA          665           NA 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
          NA           NA           NA           NA           NA          911 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
          NA         1092          359          797          657           59 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
         493          554          652         1132          449         3431 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
        1487         3076           NA         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-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
        2414         2828         3117         1459         2931         1865 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
        2963         1092           51          374          648          358 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
         315          656          291           NA          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-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
         636          722          822           26          737          522 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
         505          194          434           15         1046          435 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
        3377           NA         2881         2746         3074         2839 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
          NA         3037           13         2718          701           NA 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
        1893         1879         1955         1625          845         1888 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
          NA           NA         2859           NA           NA           NA 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
          NA         1516           NA         1367          372          970 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
          NA           NA           NA          374         2208         2372 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
         182           NA           NA         2184         1462          400 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
          NA           NA         1885         1843         1731         2080 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
         354           NA         1489           NA         1107           NA 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
          NA         1124          204         1459          211         2172 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
        1935         1785         1834         1862          205         1746 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
         433         1487         1502         1384           NA         1433 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
        1632          454           NA         1014         1413           NA 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
         785         1124           NA          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-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-5182 TCGA-BP-5183 
          NA          293           NA         2263         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-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
        1924           NA           NA         2308         1998           NA 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
        1793           NA          646         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-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
        1883         1759         2125         1952           NA           NA 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        1946         2085           NA         1521          750          841 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
          NA         1808         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
        1792         1496         1499         1531         1657           NA 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
        1373           NA           NA           NA         1943           NA 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
        2430         2575           NA           NA           NA           NA 
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-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
          NA           NA         1906         2548           NA           NA 
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-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
          NA         2552         3146          774         1404           18 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
          NA         1943         1787           NA         1843         1928 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
          NA         1868         1929         1789           25           NA 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
          NA         1712         1683         1732         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
         330           NA          662         1446          685           NA 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
          59           NA          386         2439         2067         1997 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
         373           NA          693         1905         1329         1398 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
         370          355         2016         1729           NA          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
         119          206          127 
Variable 1:'AGE':	nDistinctValues=56,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=135,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=271,	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=2,	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=13,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=46,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=3,	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=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=1,	numeric=FALSE,	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=11,	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" "RACE"                       
[9] "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 417 columns, 1 survival variables, and 9 non-survival variables.
AGE, nv=56, 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 
202  49 160   6 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
202  49 160   6 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
202  49 160   6 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
202  49 160   6 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=2, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=3, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = SETD2 MUTATION ANALYSIS
D1V1, survival
                 sevent
clus2               0   1
  SETD2 MUTATED    24  20
  SETD2 WILD-TYPE 251 122
  SETD2 MUTATED SETD2 WILD-TYPE 
             44             373 
  SETD2 MUTATED SETD2 WILD-TYPE 
             20             122 
$`SETD2 MUTATED`
TCGA-A3-3311 TCGA-A3-3358 TCGA-A3-3383 TCGA-AK-3431 TCGA-AK-3455 TCGA-B0-4703 
       39.16        42.97        28.31        60.92        22.45         5.98 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4814 TCGA-B0-4822 
        3.16        43.96        20.25        46.59         5.52        36.53 
TCGA-B0-4837 TCGA-B0-4845 TCGA-B0-4852 TCGA-B0-5081 TCGA-B0-5121 TCGA-B0-5399 
       45.30        65.29        36.85        11.90        18.21        21.44 
TCGA-B0-5402 TCGA-B0-5699 TCGA-BP-4161 TCGA-BP-4329 TCGA-BP-4343 TCGA-BP-4759 
       14.76        90.12        90.28        27.78        62.86        77.98 
TCGA-BP-4774 TCGA-BP-4790 TCGA-BP-4983 TCGA-BP-5006 TCGA-BP-5169 TCGA-BP-5178 
       61.97        36.53        46.45        27.62         6.35        62.86 
TCGA-BP-5198 TCGA-CJ-4872 TCGA-CJ-4891 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5678 
       19.82        47.18        26.93        63.88        84.66        18.87 
TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CW-5580 TCGA-CW-5591 TCGA-CZ-4861 TCGA-CZ-5459 
       61.91        73.35        64.57        74.66        14.66        55.33 
TCGA-CZ-5461 TCGA-CZ-5470 
       10.85        12.69 

$`SETD2 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
        0.53        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38         4.50        52.93        45.53        88.37 
TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
       51.25        10.49        28.70        74.63        74.76        24.16 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3385 
       53.29        35.18        20.71        18.64        18.87        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 
       20.28       109.91        73.08        66.31        15.78        68.61 
TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       67.20        48.36        42.08        58.49        48.69        28.73 
TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 
       37.58        38.40        31.27        28.04         1.41         1.41 
TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4706 
        4.57         2.53         3.48        19.00        65.10         0.85 
TCGA-B0-4707 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4813 TCGA-B0-4815 
       19.73         6.64         3.25        15.72         0.59        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 
       45.07        33.50        16.77         6.02        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
       29.10        10.09        78.44        40.70        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        10.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        70.52        20.94        43.30        11.24 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
       25.32        18.51        15.09        10.95         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 
       21.86        15.95        62.89        90.87        90.48        52.54 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5692 
       21.60         1.94        16.21        37.22       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
      102.48        47.97        96.36        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        9.57        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       24.66        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.49        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       94.72       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       53.42        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        74.17        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       10.82         5.33        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       15.78        48.95        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       36.07        33.34        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5008 
       41.62        18.51        38.70        37.02        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       36.23        28.87        48.10        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       30.64        52.27         9.63        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 
       31.79        23.47        13.41        24.62        33.47        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4874 
       11.05        21.24        49.25        79.66        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 TCGA-CJ-5679 TCGA-CJ-5680 
       18.81        72.00        79.89        25.71        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       18.15        62.10        67.00        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       62.66        83.77         7.36        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       66.31        78.18         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 
       46.16         0.59        47.08        63.88        58.75        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 
       23.74        18.44        56.28        55.33        56.94        47.01 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       31.10        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 
        4.18 

  SETD2 MUTATED SETD2 WILD-TYPE 
           3.16            0.07 
  SETD2 MUTATED SETD2 WILD-TYPE 
          90.28          120.59 
  SETD2 MUTATED SETD2 WILD-TYPE 
         38.005          37.250 
[1] "3.2 - 90.3 (38.0)"  "0.1 - 120.6 (37.2)"
[1] "hr=" "1.4"
D1V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  SETD2 MUTATED        15        5        13       11
  SETD2 WILD-TYPE     182       35       100       56
D1V3, multiclass
           clus
vv          SETD2 MUTATED SETD2 WILD-TYPE
  STAGE I              15             182
  STAGE II              5              35
  STAGE III            13             100
  STAGE IV             11              56
[1] 4 2
[1] 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
  SETD2 MUTATED    16   6  20   2
  SETD2 WILD-TYPE 186  43 140   4
D1V4, multiclass
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  T1            16             186
  T2             6              43
  T3            20             140
  T4             2               4
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
                 cls
clus                0   1
  SETD2 MUTATED    21   0
  SETD2 WILD-TYPE 171  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     21    0
  SETD2 WILD-TYPE  171   12
   clus
vv  SETD2 MUTATED SETD2 WILD-TYPE
  0            21             171
  1             0              12
[1] 2 2
[1] FALSE
D1V6, binary
                 cls
clus                0   1
  SETD2 MUTATED    34  10
  SETD2 WILD-TYPE 316  57
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     34   10
  SETD2 WILD-TYPE  316   57
    clus
vv   SETD2 MUTATED SETD2 WILD-TYPE
  M0            34             316
  M1            10              57
[1] 2 2
[1] FALSE
D1V7, binary
                 cls
clus                0   1
  SETD2 MUTATED    11  33
  SETD2 WILD-TYPE 135 238
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED     11   33
  SETD2 WILD-TYPE  135  238
        clus
vv       SETD2 MUTATED SETD2 WILD-TYPE
  FEMALE            11             135
  MALE              33             238
[1] 2 2
[1] FALSE
D1V8, continuous
[1] "Remove cluster labels:" "SETD2 MUTATED"         
clus
  SETD2 MUTATED SETD2 WILD-TYPE 
              1              22 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-CZ-4854 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4862      TCGA-CZ-5456 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-DV-5574      TCGA-DV-5575      TCGA-DV-5576      TCGA-EU-5904 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
     TCGA-EU-5905      TCGA-EU-5907 
"SETD2 WILD-TYPE" "SETD2 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  SETD2 MUTATED       1                         1    40
  SETD2 WILD-TYPE     6                        13   350
D1V9, multiclass
                           clus
vv                          SETD2 MUTATED SETD2 WILD-TYPE
  ASIAN                                 1               6
  BLACK OR AFRICAN AMERICAN             1              13
  WHITE                                40             350
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
                 cls
clus                0   1
  SETD2 MUTATED     1  28
  SETD2 WILD-TYPE  20 237
[1] "tbl2"
                 cls
clus              [,1] [,2]
  SETD2 MUTATED      1   28
  SETD2 WILD-TYPE   20  237
                        clus
vv                       SETD2 MUTATED SETD2 WILD-TYPE
  HISPANIC OR LATINO                 1              20
  NOT HISPANIC OR LATINO            28             237
[1] 2 2
[1] FALSE

Clustering(2) Variable = BAP1 MUTATION ANALYSIS
D2V1, survival
                sevent
clus2              0   1
  BAP1 MUTATED    18  23
  BAP1 WILD-TYPE 257 119
  BAP1 MUTATED BAP1 WILD-TYPE 
            41            376 
  BAP1 MUTATED BAP1 WILD-TYPE 
            23            119 
$`BAP1 MUTATED`
TCGA-A3-3317 TCGA-AK-3451 TCGA-B0-4691 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4713 
       49.02        48.69         4.57         5.98        19.73         6.64 
TCGA-B0-4827 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       29.10        18.51        15.09         8.05         2.24        21.86 
TCGA-B0-5107 TCGA-B0-5699 TCGA-B8-4143 TCGA-B8-4151 TCGA-B8-5551 TCGA-BP-4163 
       30.48        90.12        23.31        27.55         0.49        93.34 
TCGA-BP-4337 TCGA-BP-4340 TCGA-BP-4352 TCGA-BP-4355 TCGA-BP-4798 TCGA-BP-4962 
        0.07        18.48        11.31        31.33        10.98        58.68 
TCGA-BP-5174 TCGA-BP-5182 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4641 
       74.20        38.30        63.25        73.22        14.17        54.61 
TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4923 TCGA-CJ-5680 TCGA-CW-5580 
       74.27        66.21        61.91        18.81        25.25        64.57 
TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5985 
       61.41        58.82        31.10        12.69        65.65 

$`BAP1 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
        0.53        39.16        49.08        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38         4.50        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        35.18        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
       28.31        65.52        20.28       109.91        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       58.49        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
       28.04         1.41         1.41         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4718 
       65.10         0.85         3.16        43.96         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5094 TCGA-B0-5099 
       43.30        11.24        11.90        25.32        10.95        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 
       62.89        90.87        90.48        52.54        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
      102.48        47.97        96.36        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
        9.57        16.80        27.16        25.05        24.66        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.91        23.01        20.91        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
       24.23        17.16        16.60         6.38        14.27        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        64.27        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4338 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       80.68        93.99        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4354 TCGA-BP-4756 
       49.08        44.94        12.23        31.89        33.99        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       36.39        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       71.41        63.62        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5175 TCGA-BP-5176 
       48.10         6.35        79.30         1.78        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
        9.63        62.86        74.40        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 
       31.27         0.95        59.84        46.55        75.88        65.69 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        11.05        21.24        49.25        79.66        47.18 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 
       75.06        77.36        64.27        71.87        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       22.32        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        1.35        83.90       103.43        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        63.88        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
        5.46        63.42         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5982 
       21.76        47.54        22.52         2.40         1.94        80.19 
TCGA-CZ-5984 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       67.96        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  BAP1 MUTATED BAP1 WILD-TYPE 
          0.07           0.43 
  BAP1 MUTATED BAP1 WILD-TYPE 
         93.34         120.59 
  BAP1 MUTATED BAP1 WILD-TYPE 
         29.10          37.99 
[1] "0.1 - 93.3 (29.1)"  "0.4 - 120.6 (38.0)"
[1] "hr=" "2"  
D2V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  BAP1 MUTATED         7        7        15       12
  BAP1 WILD-TYPE     190       33        98       55
D2V3, multiclass
           clus
vv          BAP1 MUTATED BAP1 WILD-TYPE
  STAGE I              7            190
  STAGE II             7             33
  STAGE III           15             98
  STAGE IV            12             55
[1] 4 2
[1] 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
  BAP1 MUTATED     8  10  23   0
  BAP1 WILD-TYPE 194  39 137   6
D2V4, multiclass
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  T1            8            194
  T2           10             39
  T3           23            137
  T4            0              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"
D2V5, binary
                cls
clus               0   1
  BAP1 MUTATED    26   2
  BAP1 WILD-TYPE 166  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     26    2
  BAP1 WILD-TYPE  166   10
   clus
vv  BAP1 MUTATED BAP1 WILD-TYPE
  0           26            166
  1            2             10
[1] 2 2
[1] FALSE
D2V6, binary
                cls
clus               0   1
  BAP1 MUTATED    28  13
  BAP1 WILD-TYPE 322  54
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     28   13
  BAP1 WILD-TYPE  322   54
    clus
vv   BAP1 MUTATED BAP1 WILD-TYPE
  M0           28            322
  M1           13             54
[1] 2 2
[1] FALSE
D2V7, binary
                cls
clus               0   1
  BAP1 MUTATED    24  17
  BAP1 WILD-TYPE 122 254
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED     24   17
  BAP1 WILD-TYPE  122  254
        clus
vv       BAP1 MUTATED BAP1 WILD-TYPE
  FEMALE           24            122
  MALE             17            254
[1] 2 2
[1] FALSE
D2V8, continuous
[1] "Remove cluster labels:" "BAP1 MUTATED"          
clus
  BAP1 MUTATED BAP1 WILD-TYPE 
             1             22 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-CZ-4854 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-CZ-5456     TCGA-CZ-5457     TCGA-CZ-5465     TCGA-CZ-5982 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-DV-5574     TCGA-DV-5575     TCGA-DV-5576     TCGA-EU-5904 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
    TCGA-EU-5905     TCGA-EU-5907 
"BAP1 WILD-TYPE" "BAP1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BAP1 MUTATED       0                         2    37
  BAP1 WILD-TYPE     7                        12   353
D2V9, multiclass
                           clus
vv                          BAP1 MUTATED BAP1 WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            2             12
  WHITE                               37            353
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, binary
                cls
clus               0   1
  BAP1 MUTATED     2  31
  BAP1 WILD-TYPE  19 234
[1] "tbl2"
                cls
clus             [,1] [,2]
  BAP1 MUTATED      2   31
  BAP1 WILD-TYPE   19  234
                        clus
vv                       BAP1 MUTATED BAP1 WILD-TYPE
  HISPANIC OR LATINO                2             19
  NOT HISPANIC OR LATINO           31            234
[1] 2 2
[1] FALSE

Clustering(3) Variable = PTEN MUTATION ANALYSIS
D3V1, survival
                sevent
clus2              0   1
  PTEN MUTATED    11   7
  PTEN WILD-TYPE 264 135
  PTEN MUTATED PTEN WILD-TYPE 
            18            399 
  PTEN MUTATED PTEN WILD-TYPE 
             7            135 
$`PTEN MUTATED`
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3346 TCGA-B0-4694 TCGA-B0-4810 TCGA-B0-4843 
        0.53        49.08         4.50         3.48        15.72        11.64 
TCGA-B8-4621 TCGA-B8-5158 TCGA-BP-4161 TCGA-BP-4326 TCGA-BP-4345 TCGA-BP-4351 
       25.91        20.91        90.28        53.42        49.84        31.89 
TCGA-BP-5010 TCGA-BP-5199 TCGA-CJ-4871 TCGA-CZ-4858 TCGA-DV-5568 TCGA-EU-5907 
       28.87        44.55        79.66        63.88        12.16         4.18 

$`PTEN WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
       39.16        49.02        37.15        49.58        48.59        36.36 
TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 
       37.38        52.93        45.53        88.37        42.97        51.25 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
       10.49        28.70        74.63        74.76        24.16        53.29 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
       35.18        20.71        18.64        18.87        28.31        65.52 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       109.91        73.08        66.31        15.78        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       68.61        67.20        48.36        42.08        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 TCGA-B0-4700 
        1.41         1.41         4.57         2.53        19.00        65.10 
TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 
        5.98         0.85        19.73         3.16        43.96         6.64 
TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
        3.25        20.25        46.59         0.59         5.52        52.21 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       45.07        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 
       54.48        29.10        10.09        78.44        40.70        45.30 
TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4844 TCGA-B0-4845 
       27.42        53.88         6.71        56.68        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        35.90        11.80        26.20        21.60         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
       79.36        92.98       102.48        47.97        96.36        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       97.41        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
       10.36        21.57         9.57        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4622 TCGA-B8-5159 
       27.55        25.05        24.66        25.55        23.01        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.49        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       94.72       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       52.24        74.17        62.86        49.08        44.94        12.23 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       11.64        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5168 
       37.02        27.62        37.48        35.21        36.23        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        62.86        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5200 
       23.47        13.41        24.62        33.47        19.82        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        49.25        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 
       25.45        46.16         0.59        47.08        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       43.69        45.96        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       18.12         3.91         6.77 

  PTEN MUTATED PTEN WILD-TYPE 
          0.53           0.07 
  PTEN MUTATED PTEN WILD-TYPE 
         90.28         120.59 
  PTEN MUTATED PTEN WILD-TYPE 
         27.39          37.48 
[1] "0.5 - 90.3 (27.4)"  "0.1 - 120.6 (37.5)"
[1] "hr=" "1.4"
D3V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PTEN MUTATED         5        3         9        1
  PTEN WILD-TYPE     192       37       104       66
D3V3, multiclass
           clus
vv          PTEN MUTATED PTEN WILD-TYPE
  STAGE I              5            192
  STAGE II             3             37
  STAGE III            9            104
  STAGE IV             1             66
[1] 4 2
[1] 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
  PTEN MUTATED     5   3  10   0
  PTEN WILD-TYPE 197  46 150   6
D3V4, multiclass
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  T1            5            197
  T2            3             46
  T3           10            150
  T4            0              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"
D3V5, binary
                cls
clus               0   1
  PTEN MUTATED     8   2
  PTEN WILD-TYPE 184  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      8    2
  PTEN WILD-TYPE  184   10
   clus
vv  PTEN MUTATED PTEN WILD-TYPE
  0            8            184
  1            2             10
[1] 2 2
[1] FALSE
D3V6, binary
                cls
clus               0   1
  PTEN MUTATED    17   1
  PTEN WILD-TYPE 333  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED     17    1
  PTEN WILD-TYPE  333   66
    clus
vv   PTEN MUTATED PTEN WILD-TYPE
  M0           17            333
  M1            1             66
[1] 2 2
[1] FALSE
D3V7, binary
                cls
clus               0   1
  PTEN MUTATED     3  15
  PTEN WILD-TYPE 143 256
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      3   15
  PTEN WILD-TYPE  143  256
        clus
vv       PTEN MUTATED PTEN WILD-TYPE
  FEMALE            3            143
  MALE             15            256
[1] 2 2
[1] FALSE
D3V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTEN MUTATED       0                         1    17
  PTEN WILD-TYPE     7                        13   373
D3V9, multiclass
                           clus
vv                          PTEN MUTATED PTEN WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            1             13
  WHITE                               17            373
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
                cls
clus               0   1
  PTEN MUTATED     0  12
  PTEN WILD-TYPE  21 253
[1] "tbl2"
                cls
clus             [,1] [,2]
  PTEN MUTATED      0   12
  PTEN WILD-TYPE   21  253
                        clus
vv                       PTEN MUTATED PTEN WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO           12            253
[1] 2 2
[1] FALSE

Clustering(4) Variable = PBRM1 MUTATION ANALYSIS
D4V1, survival
                 sevent
clus2               0   1
  PBRM1 MUTATED    92  44
  PBRM1 WILD-TYPE 183  98
  PBRM1 MUTATED PBRM1 WILD-TYPE 
            136             281 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
             44              98 
$`PBRM1 MUTATED`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 
       39.16        49.08        49.58        48.59        36.36        37.38 
TCGA-A3-3362 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3382 TCGA-A3-3387 
       51.25        74.63        24.16        53.29        18.87        20.28 
TCGA-AK-3425 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3458 
      109.91        60.92        68.61        67.20        42.08        38.40 
TCGA-AK-3460 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4818 
       31.27         0.85        20.25        52.21        45.07        16.77 
TCGA-B0-4822 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4842 TCGA-B0-4845 TCGA-B0-4847 
       36.53        54.48        10.09        56.68        65.29        26.07 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5085 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5104 
        2.27        36.85        25.32        10.95         2.24        90.48 
TCGA-B0-5107 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 
       30.48        35.90        11.80        26.20        21.60        16.21 
TCGA-B0-5399 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 
       21.44       101.13        15.78        46.68        56.78        84.92 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
       90.12        39.55       120.59        47.97        96.36        61.32 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B4-5377 TCGA-B8-4148 TCGA-B8-4154 TCGA-B8-5158 
       12.30        21.30         9.57        27.16        24.66        20.91 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4164 TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4337 
      111.02        85.51        32.61        64.27        27.78         0.07 
TCGA-BP-4341 TCGA-BP-4759 TCGA-BP-4774 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4960 
       52.24        77.98        61.97        36.95         6.71        71.41 
TCGA-BP-4964 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4985 
       61.22        45.50        47.11        36.07        33.34        31.30 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
       36.95        27.22         3.88         5.82        45.07        41.62 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5180 TCGA-BP-5184 TCGA-BP-5186 
       48.10         6.35        79.30        74.40        37.25        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4635 
       13.35        27.02        19.82        34.95        59.84        46.55 
TCGA-CJ-4644 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4887 
       11.05        79.66        47.18        77.36        57.83        30.64 
TCGA-CJ-4888 TCGA-CJ-4903 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       51.52        51.29        49.18        50.33        54.48        38.56 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5682 
        4.57        18.81        84.66        18.87        22.32        61.91 
TCGA-CJ-5684 TCGA-CJ-6030 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5589 TCGA-CW-6093 
       73.35        75.58         7.36        64.57        78.18       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       25.45        46.16         0.82        23.74        18.44        56.28 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 
       47.01        10.85        47.54        22.52        12.69        80.19 
TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 TCGA-EU-5907 
       12.26        62.63        45.96         4.18 

$`PBRM1 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
        0.53        49.02        37.15         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3370 TCGA-A3-3376 
       88.37        42.97        10.49        28.70        74.76        35.18 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3428 TCGA-AK-3429 
       20.71        18.64        28.31        65.52        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 
       15.78        48.36        58.49        48.69        28.73        22.45 
TCGA-AK-3456 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       37.58        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 
        3.48        19.00        65.10         5.98        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       43.96         6.64         3.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4817 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4833 
        5.52        33.50         6.02        14.93        29.10        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4843 
       40.70        45.30        27.42        53.88         6.71        11.64 
TCGA-B0-4844 TCGA-B0-4846 TCGA-B0-4848 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       10.29        39.45        29.03        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5097 
       11.24        11.90        18.51        15.09         8.05        21.86 
TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5108 TCGA-B0-5109 
       15.95        62.89        90.87        52.54        29.95        19.30 
TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
        1.94        18.21        37.22        14.76       112.80        48.89 
TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       60.33        56.94        52.77        79.36        92.98       102.48 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
       97.41        35.90         1.68        11.77        10.36        21.57 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4620 TCGA-B8-4621 
       23.31        16.80        27.55        25.05        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       23.01        23.74        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.49        34.39        14.30 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4326 
       89.36        23.05        77.03        62.24        61.78        53.42 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 TCGA-BP-4343 
       62.07        80.68        93.99        18.48        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4762 
       33.99        31.33        12.30        72.59         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4804 TCGA-BP-4807 
       36.53        36.39        10.98        37.25        47.97         6.94 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       63.62        58.68        60.30         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4974 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4983 
       48.89        49.38         7.23        53.65        14.93        46.45 
TCGA-BP-4986 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5001 
       25.81        46.45        16.47        30.64        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       38.30        42.44        37.22        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5201 TCGA-BP-5202 
       13.41        24.62        33.47        44.55        31.27         0.95 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 
       58.95        21.24        49.25        74.27        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4889 
       71.87        66.21        61.91        69.86        64.18        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4904 TCGA-CJ-4907 
       59.44        50.24        47.67        49.97        58.92        49.28 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5677 
       45.14         3.06        63.88        72.00        79.89        25.71 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       25.25        18.15        62.10        67.00        60.99        53.42 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
       62.66        83.77        92.02        81.83        85.78        66.31 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
       74.66         1.35        83.90         0.59        47.08        63.88 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 
       58.75        14.66        60.59        63.39         5.46        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5462 
       63.42        58.82        55.33        56.94        55.33        10.22 
TCGA-CZ-5463 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 
       21.76         2.40         1.94        31.10        67.96        65.65 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       14.63        22.78        43.69        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       56.84        23.90        18.12         3.91         6.77 

  PBRM1 MUTATED PBRM1 WILD-TYPE 
           0.07            0.43 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
         120.59          112.80 
  PBRM1 MUTATED PBRM1 WILD-TYPE 
          38.86           37.15 
[1] "0.1 - 120.6 (38.9)" "0.4 - 112.8 (37.1)"
[1] "hr=" "1.1"
D4V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PBRM1 MUTATED        66       14        35       21
  PBRM1 WILD-TYPE     131       26        78       46
D4V3, multiclass
           clus
vv          PBRM1 MUTATED PBRM1 WILD-TYPE
  STAGE I              66             131
  STAGE II             14              26
  STAGE III            35              78
  STAGE IV             21              46
[1] 4 2
[1] 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
  PBRM1 MUTATED    67  20  49   0
  PBRM1 WILD-TYPE 135  29 111   6
D4V4, multiclass
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  T1            67             135
  T2            20              29
  T3            49             111
  T4             0               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"
D4V5, binary
                 cls
clus                0   1
  PBRM1 MUTATED    56   2
  PBRM1 WILD-TYPE 136  10
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     56    2
  PBRM1 WILD-TYPE  136   10
   clus
vv  PBRM1 MUTATED PBRM1 WILD-TYPE
  0            56             136
  1             2              10
[1] 2 2
[1] FALSE
D4V6, binary
                 cls
clus                0   1
  PBRM1 MUTATED   114  22
  PBRM1 WILD-TYPE 236  45
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED    114   22
  PBRM1 WILD-TYPE  236   45
    clus
vv   PBRM1 MUTATED PBRM1 WILD-TYPE
  M0           114             236
  M1            22              45
[1] 2 2
[1] FALSE
D4V7, binary
                 cls
clus                0   1
  PBRM1 MUTATED    42  94
  PBRM1 WILD-TYPE 104 177
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED     42   94
  PBRM1 WILD-TYPE  104  177
        clus
vv       PBRM1 MUTATED PBRM1 WILD-TYPE
  FEMALE            42             104
  MALE              94             177
[1] 2 2
[1] FALSE
D4V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PBRM1 MUTATED       1                         2   129
  PBRM1 WILD-TYPE     6                        12   261
D4V9, multiclass
                           clus
vv                          PBRM1 MUTATED PBRM1 WILD-TYPE
  ASIAN                                 1               6
  BLACK OR AFRICAN AMERICAN             2              12
  WHITE                               129             261
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
                 cls
clus                0   1
  PBRM1 MUTATED     4  87
  PBRM1 WILD-TYPE  17 178
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PBRM1 MUTATED      4   87
  PBRM1 WILD-TYPE   17  178
                        clus
vv                       PBRM1 MUTATED PBRM1 WILD-TYPE
  HISPANIC OR LATINO                 4              17
  NOT HISPANIC OR LATINO            87             178
[1] 2 2
[1] FALSE

Clustering(5) Variable = KDM5C MUTATION ANALYSIS
D5V1, survival
                 sevent
clus2               0   1
  KDM5C MUTATED    13  13
  KDM5C WILD-TYPE 262 129
  KDM5C MUTATED KDM5C WILD-TYPE 
             26             391 
  KDM5C MUTATED KDM5C WILD-TYPE 
             13             129 
$`KDM5C MUTATED`
TCGA-AK-3430 TCGA-AK-3458 TCGA-B0-4694 TCGA-B0-4718 TCGA-B0-4816 TCGA-B0-4828 
       15.78        38.40         3.48        20.25        45.07        10.09 
TCGA-B0-4837 TCGA-B0-4844 TCGA-B0-5077 TCGA-B0-5094 TCGA-B0-5106 TCGA-B0-5108 
       45.30        10.29        43.30        10.95        52.54        29.95 
TCGA-B0-5698 TCGA-B2-5641 TCGA-BP-4159 TCGA-BP-4342 TCGA-BP-4351 TCGA-BP-4803 
       84.92        21.57        85.51        74.17        31.89         6.71 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5202 TCGA-CJ-4871 
       18.51         6.35        27.02        33.24         0.95        79.66 
TCGA-CW-5581 TCGA-CZ-5467 
       92.02         2.40 

$`KDM5C WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       66.31        60.92        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3460 
       58.49        48.69        28.73        22.45        37.58        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4697 
       28.04         1.41         1.41         4.57         2.53        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         0.85        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 
        6.64         3.25        15.72        46.59         0.59         5.52 
TCGA-B0-4815 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 
       52.21        33.50        16.77         6.02        36.53        14.93 
TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4838 TCGA-B0-4839 
       54.48        29.10        78.44        40.70        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
        6.71        56.68        11.64        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5080 
       29.03         2.27        36.85        70.52        20.94        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5095 TCGA-B0-5096 
       11.90        25.32        18.51        15.09         8.05         2.24 
TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5107 
       21.86        15.95        62.89        90.87        90.48        30.48 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        35.90        11.80        26.20        21.60         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
       92.98       102.48        47.97        96.36        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        9.57        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       24.66        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4160 
       14.27         0.49        34.39        14.30       111.02        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       18.48        52.24        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       12.23        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        11.64        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       10.98        37.25        36.95        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
        5.82        45.07        30.64        41.62        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       22.78        13.35        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-CJ-4634 
       33.47        19.82        44.55        34.95        31.27        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4872 
       54.61        58.95        11.05        21.24        49.25        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        59.44        50.24        47.67        49.97        51.29 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
       58.92        49.18        49.28        50.33        54.48        38.56 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
       45.14         3.06         4.57        18.81        63.88        72.00 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       79.89        84.66        25.71        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       63.88        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 
       10.22        21.76        47.54        22.52         1.94        31.10 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
       12.69        80.19        67.96        65.65        12.26        14.63 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
       22.78        62.63        43.69        45.96        12.16        11.67 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
       66.28        56.84        23.90        18.12         3.91         6.77 
TCGA-EU-5907 
        4.18 

  KDM5C MUTATED KDM5C WILD-TYPE 
           0.95            0.07 
  KDM5C MUTATED KDM5C WILD-TYPE 
          92.02          120.59 
  KDM5C MUTATED KDM5C WILD-TYPE 
         28.485          37.580 
[1] "0.9 - 92.0 (28.5)"  "0.1 - 120.6 (37.6)"
[1] "hr=" "1.8"
D5V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  KDM5C MUTATED        12        2         8        4
  KDM5C WILD-TYPE     185       38       105       63
D5V3, multiclass
           clus
vv          KDM5C MUTATED KDM5C WILD-TYPE
  STAGE I              12             185
  STAGE II              2              38
  STAGE III             8             105
  STAGE IV              4              63
[1] 4 2
[1] 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
  KDM5C MUTATED    12   3  11   0
  KDM5C WILD-TYPE 190  46 149   6
D5V4, multiclass
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  T1            12             190
  T2             3              46
  T3            11             149
  T4             0               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
  KDM5C MUTATED    13   1
  KDM5C WILD-TYPE 179  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     13    1
  KDM5C WILD-TYPE  179   11
   clus
vv  KDM5C MUTATED KDM5C WILD-TYPE
  0            13             179
  1             1              11
[1] 2 2
[1] FALSE
D5V6, binary
                 cls
clus                0   1
  KDM5C MUTATED    22   4
  KDM5C WILD-TYPE 328  63
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED     22    4
  KDM5C WILD-TYPE  328   63
    clus
vv   KDM5C MUTATED KDM5C WILD-TYPE
  M0            22             328
  M1             4              63
[1] 2 2
[1] FALSE
D5V7, binary
                 cls
clus                0   1
  KDM5C MUTATED     2  24
  KDM5C WILD-TYPE 144 247
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      2   24
  KDM5C WILD-TYPE  144  247
        clus
vv       KDM5C MUTATED KDM5C WILD-TYPE
  FEMALE             2             144
  MALE              24             247
[1] 2 2
[1] FALSE
D5V8, continuous
[1] "Remove cluster labels:" "KDM5C MUTATED"         
clus
  KDM5C MUTATED KDM5C WILD-TYPE 
              1              22 
     TCGA-B0-4838      TCGA-B4-5377      TCGA-CZ-4854      TCGA-CZ-4856 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862      TCGA-CZ-5456 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-CZ-5457      TCGA-CZ-5465      TCGA-CZ-5469      TCGA-CZ-5982 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568      TCGA-DV-5569 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-DV-5574      TCGA-DV-5575      TCGA-DV-5576      TCGA-EU-5904 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
     TCGA-EU-5905      TCGA-EU-5907 
"KDM5C WILD-TYPE" "KDM5C WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KDM5C MUTATED       0                         1    25
  KDM5C WILD-TYPE     7                        13   365
D5V9, multiclass
                           clus
vv                          KDM5C MUTATED KDM5C WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             1              13
  WHITE                                25             365
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
                 cls
clus                0   1
  KDM5C MUTATED     0  19
  KDM5C WILD-TYPE  21 246
[1] "tbl2"
                 cls
clus              [,1] [,2]
  KDM5C MUTATED      0   19
  KDM5C WILD-TYPE   21  246
                        clus
vv                       KDM5C MUTATED KDM5C WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO            19             246
[1] 2 2
[1] FALSE

Clustering(6) Variable = VHL MUTATION ANALYSIS
D6V1, survival
               sevent
clus2             0   1
  VHL MUTATED   113  53
  VHL WILD-TYPE 162  89
  VHL MUTATED VHL WILD-TYPE 
          166           251 
  VHL MUTATED VHL WILD-TYPE 
           53            89 
$`VHL MUTATED`
TCGA-A3-3308 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3380 
        0.53        45.53        51.25        53.29        35.18        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3444 TCGA-AK-3455 TCGA-AK-3458 
       18.87        28.31        65.52        48.36        22.45        38.40 
TCGA-AS-3778 TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 
        1.41        65.10         0.85        19.73        43.96         6.64 
TCGA-B0-4810 TCGA-B0-4814 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4827 
       15.72         5.52        16.77         6.02        14.93        29.10 
TCGA-B0-4828 TCGA-B0-4842 TCGA-B0-4847 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5077 
       10.09        56.68        26.07        36.85        70.52        43.30 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 
       11.90        25.32        18.51         8.05         2.24        21.86 
TCGA-B0-5099 TCGA-B0-5102 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5113 
       15.95        90.87        52.54        30.48        29.95        11.80 
TCGA-B0-5115 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
       26.20        14.76       112.80        48.89       101.13        46.68 
TCGA-B0-5696 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 
       56.78        39.55       120.59       102.48        47.97        96.36 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-5635 TCGA-B8-4148 TCGA-B8-4151 
       61.32        97.41        35.90        10.36        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5549 
       25.05        24.66        23.74        27.02        24.23         6.38 
TCGA-B8-5551 TCGA-BP-4159 TCGA-BP-4164 TCGA-BP-4167 TCGA-BP-4329 TCGA-BP-4341 
        0.49        85.51        32.61        89.36        27.78        52.24 
TCGA-BP-4771 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 
        5.33         6.94        71.41        63.62        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
        6.74        57.40        14.24         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       14.93        33.34        25.81        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
       16.47        45.07        30.64        41.62        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5169 TCGA-BP-5170 
       27.62        37.48        35.21        36.23         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5180 
        1.78        74.20        30.64        52.27         9.63        74.40 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
       42.44        37.25        22.78        33.24        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4634 TCGA-CJ-4636 
       24.62        33.47        19.82        44.55        59.84        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4644 TCGA-CJ-4875 TCGA-CJ-4894 TCGA-CJ-4903 
       73.22        14.17        11.05        77.36        27.65        51.29 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-5672 
       50.33        54.48        45.14         3.06         4.57        72.00 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5680 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       84.66        25.71        25.25        73.35        67.00        60.99 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5583 
       75.58        62.66        83.77         7.36        64.57        81.83 
TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
       66.31        74.66        83.90       103.43        25.45         0.59 
TCGA-CZ-4861 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5465 TCGA-CZ-5469 TCGA-CZ-5470 
       14.66        56.94        47.01        47.54        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 
       80.19        67.96        65.65        12.26        14.63        62.63 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

$`VHL WILD-TYPE`
TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 
       39.16        49.08        49.02        37.15        49.58        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3357 TCGA-A3-3358 
       36.36        37.38         4.50        52.93        88.37        42.97 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3378 
       10.49        28.70        74.63        74.76        24.16        20.71 
TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 
       20.28       109.91        73.08        66.31        15.78        60.92 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 
       68.61        67.20        42.08        58.49        48.69        28.73 
TCGA-AK-3456 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       37.58        31.27        28.04         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4703 TCGA-B0-4710 TCGA-B0-4714 TCGA-B0-4718 
        3.48        19.00         5.98         3.16         3.25        20.25 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4822 
       46.59         0.59        52.21        45.07        33.50        36.53 
TCGA-B0-4824 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       54.48        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4848 
        6.71        11.64        10.29        65.29        39.45        29.03 
TCGA-B0-4849 TCGA-B0-5075 TCGA-B0-5080 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5100 
        2.27        20.94        11.24        15.09        10.95        62.89 
TCGA-B0-5104 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       90.48        19.30        35.90        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5694 TCGA-B0-5697 TCGA-B0-5698 
       18.21        21.44        37.22        15.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5707 TCGA-B2-4098 
       90.12        56.94        52.77        79.36        92.98         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 
       12.30        21.30        11.77        21.57         9.57        23.31 
TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5164 
       16.80        25.55        25.91        23.01        20.91         0.85 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
       17.16        16.60        14.27        34.39        14.30       111.02 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28       101.06        93.34        99.85         0.43 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 
       23.05        77.03        62.24        61.78        64.27        53.42 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4342 
       62.07        80.68         0.07        93.99        18.48        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
       10.82        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4962 TCGA-BP-4971 TCGA-BP-4972 
       36.95         6.71        47.97        58.68        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4981 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4987 TCGA-BP-4993 
       45.50        36.07        46.45        31.30        36.95         5.82 
TCGA-BP-5000 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5178 TCGA-BP-5182 TCGA-BP-5185 
       18.51        28.87        48.10        62.86        38.30        37.22 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       13.35        27.02        31.79        34.95        31.27         0.95 
TCGA-CJ-4635 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       46.55        75.88        65.69        54.61        58.95        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4876 
       49.25        79.66        47.18        74.27        75.06        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        39.45        59.44        50.24        47.67        49.97 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4913 TCGA-CJ-4923 TCGA-CJ-5671 
       58.92        49.18        49.28        38.56        18.81        63.88 
TCGA-CJ-5675 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       79.89        18.87        22.32        18.15        61.91        62.10 
TCGA-CJ-6028 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6087 TCGA-CZ-4854 
       53.42        92.02        85.78        78.18         1.35        46.16 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       47.08        63.88        58.75        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.28        55.33        55.33        10.85        10.22        21.76 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 
       22.52         2.40         1.94        22.78        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       12.16        11.67        66.28        56.84        23.90 

  VHL MUTATED VHL WILD-TYPE 
         0.49          0.07 
  VHL MUTATED VHL WILD-TYPE 
       120.59        111.02 
  VHL MUTATED VHL WILD-TYPE 
       33.405        40.700 
[1] "0.5 - 120.6 (33.4)" "0.1 - 111.0 (40.7)"
[1] "hr=" "1.1"
D6V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  VHL MUTATED        90       12        42       22
  VHL WILD-TYPE     107       28        71       45
D6V3, multiclass
           clus
vv          VHL MUTATED VHL WILD-TYPE
  STAGE I            90           107
  STAGE II           12            28
  STAGE III          42            71
  STAGE IV           22            45
[1] 4 2
[1] 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
  VHL MUTATED    91  16  56   3
  VHL WILD-TYPE 111  33 104   3
D6V4, multiclass
    clus
vv   VHL MUTATED VHL WILD-TYPE
  T1          91           111
  T2          16            33
  T3          56           104
  T4           3             3
[1] 4 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
               cls
clus              0   1
  VHL MUTATED    72   4
  VHL WILD-TYPE 120   8
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     72    4
  VHL WILD-TYPE  120    8
   clus
vv  VHL MUTATED VHL WILD-TYPE
  0          72           120
  1           4             8
[1] 2 2
[1] FALSE
D6V6, binary
               cls
clus              0   1
  VHL MUTATED   144  22
  VHL WILD-TYPE 206  45
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED    144   22
  VHL WILD-TYPE  206   45
    clus
vv   VHL MUTATED VHL WILD-TYPE
  M0         144           206
  M1          22            45
[1] 2 2
[1] FALSE
D6V7, binary
               cls
clus              0   1
  VHL MUTATED    62 104
  VHL WILD-TYPE  84 167
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED     62  104
  VHL WILD-TYPE   84  167
        clus
vv       VHL MUTATED VHL WILD-TYPE
  FEMALE          62            84
  MALE           104           167
[1] 2 2
[1] FALSE
D6V8, continuous
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  VHL MUTATED       2                         2   159
  VHL WILD-TYPE     5                        12   231
D6V9, multiclass
                           clus
vv                          VHL MUTATED VHL WILD-TYPE
  ASIAN                               2             5
  BLACK OR AFRICAN AMERICAN           2            12
  WHITE                             159           231
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
               cls
clus              0   1
  VHL MUTATED     9 104
  VHL WILD-TYPE  12 161
[1] "tbl2"
               cls
clus            [,1] [,2]
  VHL MUTATED      9  104
  VHL WILD-TYPE   12  161
                        clus
vv                       VHL MUTATED VHL WILD-TYPE
  HISPANIC OR LATINO               9            12
  NOT HISPANIC OR LATINO         104           161
[1] 2 2
[1] FALSE

Clustering(7) Variable = FAM200A MUTATION ANALYSIS
D7V1, survival
                   sevent
clus2                 0   1
  FAM200A MUTATED     4   1
  FAM200A WILD-TYPE 271 141
  FAM200A MUTATED FAM200A WILD-TYPE 
                5               412 
  FAM200A MUTATED FAM200A WILD-TYPE 
                1               141 
$`FAM200A MUTATED`
TCGA-B0-4710 TCGA-B8-4154 TCGA-BP-4162 TCGA-BP-4762 TCGA-BP-4775 
        3.16        24.66       101.06        44.15        60.59 

$`FAM200A WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        31.27        28.04         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         0.85 
TCGA-B0-4707 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
       19.73        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
       92.98       102.48        47.97        96.36        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
       21.57         9.57        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       25.05        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.49        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       94.72        90.28        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4763 TCGA-BP-4765 
       12.30        72.59        77.98         5.98        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4777 
       48.07        13.15        10.82         5.33        61.97        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        11.64        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 
       30.64        52.27         9.63        62.86        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        11.05        21.24        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        59.44        50.24        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
       74.66         1.35        83.90       103.43        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        63.88        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  FAM200A MUTATED FAM200A WILD-TYPE 
             3.16              0.07 
  FAM200A MUTATED FAM200A WILD-TYPE 
           101.06            120.59 
  FAM200A MUTATED FAM200A WILD-TYPE 
            44.15             37.25 
[1] "3.2 - 101.1 (44.1)" "0.1 - 120.6 (37.2)"
[1] "hr=" "2"  
D7V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  FAM200A MUTATED         4        0         1        0
  FAM200A WILD-TYPE     193       40       112       67
D7V3, multiclass
           clus
vv          FAM200A MUTATED FAM200A WILD-TYPE
  STAGE I                 4               193
  STAGE II                0                40
  STAGE III               1               112
  STAGE IV                0                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
  FAM200A MUTATED     4   0   1   0
  FAM200A WILD-TYPE 198  49 159   6
D7V4, multiclass
    clus
vv   FAM200A MUTATED FAM200A WILD-TYPE
  T1               4               198
  T2               0                49
  T3               1               159
  T4               0                 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"
D7V5, binary
                   cls
clus                  0   1
  FAM200A MUTATED     3   0
  FAM200A WILD-TYPE 189  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      3    0
  FAM200A WILD-TYPE  189   12
   clus
vv  FAM200A MUTATED FAM200A WILD-TYPE
  0               3               189
  1               0                12
[1] 2 2
[1] FALSE
D7V6, binary
                   cls
clus                  0   1
  FAM200A MUTATED     5   0
  FAM200A WILD-TYPE 345  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      5    0
  FAM200A WILD-TYPE  345   67
    clus
vv   FAM200A MUTATED FAM200A WILD-TYPE
  M0               5               345
  M1               0                67
[1] 2 2
[1] FALSE
D7V7, binary
                   cls
clus                  0   1
  FAM200A MUTATED     4   1
  FAM200A WILD-TYPE 142 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      4    1
  FAM200A WILD-TYPE  142  270
        clus
vv       FAM200A MUTATED FAM200A WILD-TYPE
  FEMALE               4               142
  MALE                 1               270
[1] 2 2
[1] FALSE
D7V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FAM200A MUTATED       0                         0     5
  FAM200A WILD-TYPE     7                        14   385
D7V9, multiclass
                           clus
vv                          FAM200A MUTATED FAM200A WILD-TYPE
  ASIAN                                   0                 7
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   5               385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
                   cls
clus                  0   1
  FAM200A MUTATED     0   2
  FAM200A WILD-TYPE  21 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  FAM200A MUTATED      0    2
  FAM200A WILD-TYPE   21  263
                        clus
vv                       FAM200A MUTATED FAM200A WILD-TYPE
  HISPANIC OR LATINO                   0                21
  NOT HISPANIC OR LATINO               2               263
[1] 2 2
[1] FALSE

Clustering(8) Variable = TP53 MUTATION ANALYSIS
D8V1, survival
                sevent
clus2              0   1
  TP53 MUTATED     3   6
  TP53 WILD-TYPE 272 136
  TP53 MUTATED TP53 WILD-TYPE 
             9            408 
  TP53 MUTATED TP53 WILD-TYPE 
             6            136 
$`TP53 MUTATED`
TCGA-B0-4703 TCGA-B0-4710 TCGA-BP-4176 TCGA-BP-4770 TCGA-BP-4798 TCGA-CJ-5677 
        5.98         3.16        64.27        10.82        10.98        25.71 
TCGA-CZ-4858 TCGA-CZ-4865 TCGA-CZ-5463 
       63.88         5.46        21.76 

$`TP53 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        31.27        28.04         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4706 TCGA-B0-4707 
        2.53         3.48        19.00        65.10         0.85        19.73 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
      102.48        47.97        96.36        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        9.57        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       24.66        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.49        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       71.80        48.07        13.15         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       36.39        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 
       30.64        52.27         9.63        62.86        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        11.05        21.24        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        59.44        50.24        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
       72.00        79.89        84.66        18.87        22.32        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 
       18.15        61.91        62.10        73.35        67.00        60.99 
TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 
       53.42        75.58        62.66        83.77         7.36        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        1.35        83.90       103.43        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4866 
       47.08        58.75        14.66        60.59        63.39        61.41 
TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 
       63.42        58.82         0.82        23.74        18.44        56.28 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 
       55.33        56.94        55.33        47.01        10.85        10.22 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 

  TP53 MUTATED TP53 WILD-TYPE 
          3.16           0.07 
  TP53 MUTATED TP53 WILD-TYPE 
         64.27         120.59 
  TP53 MUTATED TP53 WILD-TYPE 
         10.98          37.53 
[1] "3.2 - 64.3 (11.0)"  "0.1 - 120.6 (37.5)"
[1] "hr=" "3.5"
D8V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  TP53 MUTATED         2        2         2        3
  TP53 WILD-TYPE     195       38       111       64
D8V3, multiclass
           clus
vv          TP53 MUTATED TP53 WILD-TYPE
  STAGE I              2            195
  STAGE II             2             38
  STAGE III            2            111
  STAGE IV             3             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
  TP53 MUTATED     2   2   4   1
  TP53 WILD-TYPE 200  47 156   5
D8V4, multiclass
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  T1            2            200
  T2            2             47
  T3            4            156
  T4            1              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"
D8V5, binary
                cls
clus               0   1
  TP53 MUTATED     4   0
  TP53 WILD-TYPE 188  12
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4    0
  TP53 WILD-TYPE  188   12
   clus
vv  TP53 MUTATED TP53 WILD-TYPE
  0            4            188
  1            0             12
[1] 2 2
[1] FALSE
D8V6, binary
                cls
clus               0   1
  TP53 MUTATED     6   3
  TP53 WILD-TYPE 344  64
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      6    3
  TP53 WILD-TYPE  344   64
    clus
vv   TP53 MUTATED TP53 WILD-TYPE
  M0            6            344
  M1            3             64
[1] 2 2
[1] FALSE
D8V7, binary
                cls
clus               0   1
  TP53 MUTATED     4   5
  TP53 WILD-TYPE 142 266
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      4    5
  TP53 WILD-TYPE  142  266
        clus
vv       TP53 MUTATED TP53 WILD-TYPE
  FEMALE            4            142
  MALE              5            266
[1] 2 2
[1] FALSE
D8V8, continuous
[1] "Remove cluster labels:" "TP53 MUTATED"          
clus
  TP53 MUTATED TP53 WILD-TYPE 
             1             22 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-CZ-4854 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4861     TCGA-CZ-4862     TCGA-CZ-5456 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-DV-5574     TCGA-DV-5575     TCGA-DV-5576     TCGA-EU-5904 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" "TP53 WILD-TYPE" 
    TCGA-EU-5905     TCGA-EU-5907 
"TP53 WILD-TYPE" "TP53 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  TP53 MUTATED       0                         0     9
  TP53 WILD-TYPE     7                        14   381
D8V9, multiclass
                           clus
vv                          TP53 MUTATED TP53 WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             14
  WHITE                                9            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"
D8V10, binary
                cls
clus               0   1
  TP53 MUTATED     0   5
  TP53 WILD-TYPE  21 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  TP53 MUTATED      0    5
  TP53 WILD-TYPE   21  260
                        clus
vv                       TP53 MUTATED TP53 WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            5            260
[1] 2 2
[1] FALSE

Clustering(9) Variable = NEFH MUTATION ANALYSIS
D9V1, survival
                sevent
clus2              0   1
  NEFH MUTATED     3   2
  NEFH WILD-TYPE 272 140
  NEFH MUTATED NEFH WILD-TYPE 
             5            412 
  NEFH MUTATED NEFH WILD-TYPE 
             2            140 
$`NEFH MUTATED`
TCGA-AK-3451 TCGA-B0-4706 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CZ-5456 
       48.69         0.85        18.15        62.10        56.28 

$`NEFH WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       42.08        58.49        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       31.27        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4707 TCGA-B0-4710 
        3.48        19.00        65.10         5.98        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
      102.48        47.97        96.36        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        9.57        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       24.66        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.49        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       64.27        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 
       31.33        12.30        72.59        77.98         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 
       77.36        64.27        71.87        66.21        61.91        57.83 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 
       69.86        64.18        30.64        51.52        63.98        68.55 
TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       26.93        50.01        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
       49.28        50.33        54.48        38.56        45.14         3.06 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
        4.57        18.81        63.88        72.00        79.89        84.66 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5682 TCGA-CJ-5684 
       25.71        18.87        22.32        25.25        61.91        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        63.88        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        0.82        23.74        18.44        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  NEFH MUTATED NEFH WILD-TYPE 
          0.85           0.07 
  NEFH MUTATED NEFH WILD-TYPE 
         62.10         120.59 
  NEFH MUTATED NEFH WILD-TYPE 
         48.69          37.25 
[1] "0.8 - 62.1 (48.7)"  "0.1 - 120.6 (37.2)"
[1] "hr=" "1.3"
D9V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  NEFH MUTATED         1        2         1        1
  NEFH WILD-TYPE     196       38       112       66
D9V3, multiclass
           clus
vv          NEFH MUTATED NEFH WILD-TYPE
  STAGE I              1            196
  STAGE II             2             38
  STAGE III            1            112
  STAGE IV             1             66
[1] 4 2
[1] 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
  NEFH MUTATED     1   2   2   0
  NEFH WILD-TYPE 201  47 158   6
D9V4, multiclass
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  T1            1            201
  T2            2             47
  T3            2            158
  T4            0              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"
D9V5, binary
                cls
clus               0   1
  NEFH MUTATED     2   0
  NEFH WILD-TYPE 190  12
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      2    0
  NEFH WILD-TYPE  190   12
   clus
vv  NEFH MUTATED NEFH WILD-TYPE
  0            2            190
  1            0             12
[1] 2 2
[1] FALSE
D9V6, binary
                cls
clus               0   1
  NEFH MUTATED     4   1
  NEFH WILD-TYPE 346  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      4    1
  NEFH WILD-TYPE  346   66
    clus
vv   NEFH MUTATED NEFH WILD-TYPE
  M0            4            346
  M1            1             66
[1] 2 2
[1] FALSE
D9V7, binary
                cls
clus               0   1
  NEFH MUTATED     1   4
  NEFH WILD-TYPE 145 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      1    4
  NEFH WILD-TYPE  145  267
        clus
vv       NEFH MUTATED NEFH WILD-TYPE
  FEMALE            1            145
  MALE              4            267
[1] 2 2
[1] FALSE
D9V8, continuous
[1] "Remove cluster labels:" "NEFH MUTATED"          
clus
  NEFH MUTATED NEFH WILD-TYPE 
             1             22 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-CZ-4854 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-DV-5574     TCGA-DV-5575     TCGA-DV-5576     TCGA-EU-5904 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" "NEFH WILD-TYPE" 
    TCGA-EU-5905     TCGA-EU-5907 
"NEFH WILD-TYPE" "NEFH WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NEFH MUTATED       0                         0     5
  NEFH WILD-TYPE     7                        14   385
D9V9, multiclass
                           clus
vv                          NEFH MUTATED NEFH WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             14
  WHITE                                5            385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
                cls
clus               0   1
  NEFH MUTATED     0   4
  NEFH WILD-TYPE  21 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  NEFH MUTATED      0    4
  NEFH WILD-TYPE   21  261
                        clus
vv                       NEFH MUTATED NEFH WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            4            261
[1] 2 2
[1] FALSE

Clustering(10) Variable = CCDC120 MUTATION ANALYSIS
D10V1, survival
                   sevent
clus2                 0   1
  CCDC120 MUTATED     4   0
  CCDC120 WILD-TYPE 271 142
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                4               413 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
                0               142 
$`CCDC120 MUTATED`
TCGA-AK-3425 TCGA-BP-4759 TCGA-CJ-4876 TCGA-CZ-5470 
      109.91        77.98        64.27        12.69 

$`CCDC120 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3428 TCGA-AK-3429 
       18.87        28.31        65.52        20.28        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       31.27        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
       92.98       102.48        47.97        96.36        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
       21.57         9.57        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        24.66        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.49        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       61.78        64.27        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4761 TCGA-BP-4762 
       33.99        31.33        12.30        72.59         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       77.36        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        63.88        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5982 
       47.54        22.52         2.40         1.94        31.10        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  CCDC120 MUTATED CCDC120 WILD-TYPE 
            12.69              0.07 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
           109.91            120.59 
  CCDC120 MUTATED CCDC120 WILD-TYPE 
           71.125            37.250 
[1] "12.7 - 109.9 (71.1)" "0.1 - 120.6 (37.2)" 
[1] "hr="     "9200000"
D10V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  CCDC120 MUTATED         2        2         0        0
  CCDC120 WILD-TYPE     195       38       113       67
D10V3, multiclass
           clus
vv          CCDC120 MUTATED CCDC120 WILD-TYPE
  STAGE I                 2               195
  STAGE II                2                38
  STAGE III               0               113
  STAGE IV                0                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
  CCDC120 MUTATED     2   2   0   0
  CCDC120 WILD-TYPE 200  47 160   6
D10V4, multiclass
    clus
vv   CCDC120 MUTATED CCDC120 WILD-TYPE
  T1               2               200
  T2               2                47
  T3               0               160
  T4               0                 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"
D10V5, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     3   0
  CCDC120 WILD-TYPE 189  12
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      3    0
  CCDC120 WILD-TYPE  189   12
   clus
vv  CCDC120 MUTATED CCDC120 WILD-TYPE
  0               3               189
  1               0                12
[1] 2 2
[1] FALSE
D10V6, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     4   0
  CCDC120 WILD-TYPE 346  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      4    0
  CCDC120 WILD-TYPE  346   67
    clus
vv   CCDC120 MUTATED CCDC120 WILD-TYPE
  M0               4               346
  M1               0                67
[1] 2 2
[1] FALSE
D10V7, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     1   3
  CCDC120 WILD-TYPE 145 268
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      1    3
  CCDC120 WILD-TYPE  145  268
        clus
vv       CCDC120 MUTATED CCDC120 WILD-TYPE
  FEMALE               1               145
  MALE                 3               268
[1] 2 2
[1] FALSE
D10V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  CCDC120 MUTATED       0                         0     3
  CCDC120 WILD-TYPE     7                        14   387
D10V9, multiclass
                           clus
vv                          CCDC120 MUTATED CCDC120 WILD-TYPE
  ASIAN                                   0                 7
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   3               387
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
                   cls
clus                  0   1
  CCDC120 MUTATED     1   2
  CCDC120 WILD-TYPE  20 263
[1] "tbl2"
                   cls
clus                [,1] [,2]
  CCDC120 MUTATED      1    2
  CCDC120 WILD-TYPE   20  263
                        clus
vv                       CCDC120 MUTATED CCDC120 WILD-TYPE
  HISPANIC OR LATINO                   1                20
  NOT HISPANIC OR LATINO               2               263
[1] 2 2
[1] FALSE

Clustering(11) Variable = MTOR MUTATION ANALYSIS
D11V1, survival
                sevent
clus2              0   1
  MTOR MUTATED    10  13
  MTOR WILD-TYPE 265 129
  MTOR MUTATED MTOR WILD-TYPE 
            23            394 
  MTOR MUTATED MTOR WILD-TYPE 
            13            129 
$`MTOR MUTATED`
TCGA-A3-3347 TCGA-AK-3429 TCGA-B0-4810 TCGA-B0-4827 TCGA-B0-4846 TCGA-B0-4852 
       52.93        66.31        15.72        29.10        39.45        36.85 
TCGA-B0-5100 TCGA-B0-5119 TCGA-B0-5691 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 
       62.89         1.94       112.80        56.78        60.33        56.94 
TCGA-BP-5175 TCGA-BP-5176 TCGA-CJ-4644 TCGA-CJ-4887 TCGA-CJ-4907 TCGA-CJ-5679 
       30.64        52.27        11.05        30.64        49.28        22.32 
TCGA-CJ-6027 TCGA-CW-5580 TCGA-CZ-4857 TCGA-CZ-4866 TCGA-CZ-5987 
       60.99        64.57        47.08        61.41        14.63 

$`MTOR WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3349 TCGA-A3-3357 
       48.59        36.36        37.38         4.50        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        35.18        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3430 
       28.31        65.52        20.28       109.91        73.08        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 
       60.92        68.61        67.20        48.36        42.08        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       48.69        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       28.04         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         0.85        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4811 TCGA-B0-4813 
       43.96         6.64         3.25        20.25        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 
       36.53        14.93        54.48        10.09        78.44        40.70 
TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 
       45.30        27.42        53.88         6.71        56.68        11.64 
TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4945 
       10.29        65.29        26.07        29.03         2.27        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        21.86        15.95 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 
       35.90        11.80        26.20        21.60        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       21.44        37.22        14.76        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       46.68        84.92        90.12        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
       79.36        92.98       102.48        47.97        96.36        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       97.41        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
       10.36        21.57         9.57        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       27.55        25.05        24.66        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       20.91        23.74        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.49        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        64.27        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       11.64        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5177 
       48.10         6.35        79.30         1.78        74.20         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4868 
       14.17        75.88        65.69        54.61        58.95        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       64.18        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
       24.66        27.65        39.45        59.44        50.24        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-4912 
       49.97        51.29        58.92        49.18        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5680 
       72.00        79.89        84.66        25.71        18.87        25.25 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6028 
       18.15        61.91        62.10        73.35        67.00        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5581 TCGA-CW-5583 
       75.58        62.66        83.77         7.36        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 
      103.43        25.45        46.16         0.59        63.88        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 TCGA-CZ-5452 
       14.66        60.59        63.39         5.46        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       67.96        65.65        12.26        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  MTOR MUTATED MTOR WILD-TYPE 
          1.94           0.07 
  MTOR MUTATED MTOR WILD-TYPE 
        112.80         120.59 
  MTOR MUTATED MTOR WILD-TYPE 
         49.28          37.22 
[1] "1.9 - 112.8 (49.3)" "0.1 - 120.6 (37.2)"
[1] "hr=" "1.6"
D11V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  MTOR MUTATED         7        2         8        6
  MTOR WILD-TYPE     190       38       105       61
D11V3, multiclass
           clus
vv          MTOR MUTATED MTOR WILD-TYPE
  STAGE I              7            190
  STAGE II             2             38
  STAGE III            8            105
  STAGE IV             6             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
  MTOR MUTATED     8   2  13   0
  MTOR WILD-TYPE 194  47 147   6
D11V4, multiclass
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  T1            8            194
  T2            2             47
  T3           13            147
  T4            0              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"
D11V5, binary
                cls
clus               0   1
  MTOR MUTATED    11   2
  MTOR WILD-TYPE 181  10
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     11    2
  MTOR WILD-TYPE  181   10
   clus
vv  MTOR MUTATED MTOR WILD-TYPE
  0           11            181
  1            2             10
[1] 2 2
[1] FALSE
D11V6, binary
                cls
clus               0   1
  MTOR MUTATED    17   6
  MTOR WILD-TYPE 333  61
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     17    6
  MTOR WILD-TYPE  333   61
    clus
vv   MTOR MUTATED MTOR WILD-TYPE
  M0           17            333
  M1            6             61
[1] 2 2
[1] FALSE
D11V7, binary
                cls
clus               0   1
  MTOR MUTATED    10  13
  MTOR WILD-TYPE 136 258
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED     10   13
  MTOR WILD-TYPE  136  258
        clus
vv       MTOR MUTATED MTOR WILD-TYPE
  FEMALE           10            136
  MALE             13            258
[1] 2 2
[1] FALSE
D11V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  MTOR MUTATED       0                         1    22
  MTOR WILD-TYPE     7                        13   368
D11V9, multiclass
                           clus
vv                          MTOR MUTATED MTOR WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            1             13
  WHITE                               22            368
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
                cls
clus               0   1
  MTOR MUTATED     1  20
  MTOR WILD-TYPE  20 245
[1] "tbl2"
                cls
clus             [,1] [,2]
  MTOR MUTATED      1   20
  MTOR WILD-TYPE   20  245
                        clus
vv                       MTOR MUTATED MTOR WILD-TYPE
  HISPANIC OR LATINO                1             20
  NOT HISPANIC OR LATINO           20            245
[1] 2 2
[1] FALSE

Clustering(12) Variable = GUSB MUTATION ANALYSIS
D12V1, survival
                sevent
clus2              0   1
  GUSB MUTATED     2   2
  GUSB WILD-TYPE 273 140
  GUSB MUTATED GUSB WILD-TYPE 
             4            413 
  GUSB MUTATED GUSB WILD-TYPE 
             2            140 
$`GUSB MUTATED`
TCGA-B0-5095 TCGA-BP-4159 TCGA-CJ-4884 TCGA-CJ-4902 
        8.05        85.51        57.83        49.97 

$`GUSB WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        31.27        28.04         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         0.85 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       15.09        10.95         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
       92.98       102.48        47.97        96.36        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
       21.57         9.57        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        24.66        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.49        34.39        14.30       111.02 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       64.27        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 
       31.33        12.30        72.59        77.98         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 
       21.24        49.25        79.66        47.18        74.27        75.06 
TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4885 
       77.36        64.27        71.87        66.21        61.91        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        63.88        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  GUSB MUTATED GUSB WILD-TYPE 
          8.05           0.07 
  GUSB MUTATED GUSB WILD-TYPE 
         85.51         120.59 
  GUSB MUTATED GUSB WILD-TYPE 
         53.90          37.25 
[1] "8.1 - 85.5 (53.9)"  "0.1 - 120.6 (37.2)"
[1] "hr=" "1.1"
D12V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  GUSB MUTATED         1        0         3        0
  GUSB WILD-TYPE     196       40       110       67
D12V3, multiclass
           clus
vv          GUSB MUTATED GUSB WILD-TYPE
  STAGE I              1            196
  STAGE II             0             40
  STAGE III            3            110
  STAGE IV             0             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
  GUSB MUTATED     1   0   3   0
  GUSB WILD-TYPE 201  49 157   6
D12V4, multiclass
    clus
vv   GUSB MUTATED GUSB WILD-TYPE
  T1            1            201
  T2            0             49
  T3            3            157
  T4            0              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"
D12V5, binary
                cls
clus               0   1
  GUSB MUTATED     2   0
  GUSB WILD-TYPE 190  12
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      2    0
  GUSB WILD-TYPE  190   12
   clus
vv  GUSB MUTATED GUSB WILD-TYPE
  0            2            190
  1            0             12
[1] 2 2
[1] FALSE
D12V6, binary
                cls
clus               0   1
  GUSB MUTATED     4   0
  GUSB WILD-TYPE 346  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      4    0
  GUSB WILD-TYPE  346   67
    clus
vv   GUSB MUTATED GUSB WILD-TYPE
  M0            4            346
  M1            0             67
[1] 2 2
[1] FALSE
D12V7, binary
                cls
clus               0   1
  GUSB MUTATED     1   3
  GUSB WILD-TYPE 145 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      1    3
  GUSB WILD-TYPE  145  268
        clus
vv       GUSB MUTATED GUSB WILD-TYPE
  FEMALE            1            145
  MALE              3            268
[1] 2 2
[1] FALSE
D12V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GUSB MUTATED       0                         0     4
  GUSB WILD-TYPE     7                        14   386
D12V9, multiclass
                           clus
vv                          GUSB MUTATED GUSB WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             14
  WHITE                                4            386
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
                cls
clus               0   1
  GUSB MUTATED     0   3
  GUSB WILD-TYPE  21 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  GUSB MUTATED      0    3
  GUSB WILD-TYPE   21  262
                        clus
vv                       GUSB MUTATED GUSB WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            3            262
[1] 2 2
[1] FALSE

Clustering(13) Variable = PIK3CA MUTATION ANALYSIS
D13V1, survival
                  sevent
clus2                0   1
  PIK3CA MUTATED     8   4
  PIK3CA WILD-TYPE 267 138
  PIK3CA MUTATED PIK3CA WILD-TYPE 
              12              405 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
               4              138 
$`PIK3CA MUTATED`
TCGA-A3-3357 TCGA-B0-4693 TCGA-B0-4824 TCGA-B0-5713 TCGA-B8-5159 TCGA-BP-4160 
       88.37         2.53        54.48        61.32        23.74        94.72 
TCGA-BP-4352 TCGA-BP-4960 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4886 TCGA-CJ-6033 
       11.31        71.41        47.18        74.27        64.18         7.36 

$`PIK3CA WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        35.18        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
       28.31        65.52        20.28       109.91        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4694 
       31.27        28.04         1.41         1.41         4.57         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         0.85        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
        6.02        36.53        14.93        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        21.60         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       47.97        96.36        97.41        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 
       21.30        11.77        10.36        21.57         9.57        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        27.55        25.05        24.66        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       25.91        23.01        20.91        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.49        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
       14.30       111.02        85.51        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        64.27        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4962 
       36.95         6.71        47.97         6.94        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       21.24        49.25        79.66        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4887 
       71.87        66.21        61.91        57.83        69.86        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        59.44        50.24        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CW-5580 
       60.99        53.42        75.58        62.66        83.77        64.57 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 
       92.02        81.83        85.78        66.31        78.18        74.66 
TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
        1.35        83.90       103.43        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        63.88        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  PIK3CA MUTATED PIK3CA WILD-TYPE 
            2.53             0.07 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           94.72           120.59 
  PIK3CA MUTATED PIK3CA WILD-TYPE 
           57.90            37.22 
[1] "2.5 - 94.7 (57.9)"  "0.1 - 120.6 (37.2)"
[1] "hr=" "1.3"
D13V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  PIK3CA MUTATED         4        2         4        2
  PIK3CA WILD-TYPE     193       38       109       65
D13V3, multiclass
           clus
vv          PIK3CA MUTATED PIK3CA WILD-TYPE
  STAGE I                4              193
  STAGE II               2               38
  STAGE III              4              109
  STAGE IV               2               65
[1] 4 2
[1] 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
  PIK3CA MUTATED     4   2   6   0
  PIK3CA WILD-TYPE 198  47 154   6
D13V4, multiclass
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  T1              4              198
  T2              2               47
  T3              6              154
  T4              0                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
  PIK3CA MUTATED    11   0
  PIK3CA WILD-TYPE 181  12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     11    0
  PIK3CA WILD-TYPE  181   12
   clus
vv  PIK3CA MUTATED PIK3CA WILD-TYPE
  0             11              181
  1              0               12
[1] 2 2
[1] FALSE
D13V6, binary
                  cls
clus                 0   1
  PIK3CA MUTATED    10   2
  PIK3CA WILD-TYPE 340  65
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED     10    2
  PIK3CA WILD-TYPE  340   65
    clus
vv   PIK3CA MUTATED PIK3CA WILD-TYPE
  M0             10              340
  M1              2               65
[1] 2 2
[1] FALSE
D13V7, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     8   4
  PIK3CA WILD-TYPE 138 267
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      8    4
  PIK3CA WILD-TYPE  138  267
        clus
vv       PIK3CA MUTATED PIK3CA WILD-TYPE
  FEMALE              8              138
  MALE                4              267
[1] 2 2
[1] FALSE
D13V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PIK3CA MUTATED       0                         0    12
  PIK3CA WILD-TYPE     7                        14   378
D13V9, multiclass
                           clus
vv                          PIK3CA MUTATED PIK3CA WILD-TYPE
  ASIAN                                  0                7
  BLACK OR AFRICAN AMERICAN              0               14
  WHITE                                 12              378
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D13V10, binary
                  cls
clus                 0   1
  PIK3CA MUTATED     1  10
  PIK3CA WILD-TYPE  20 255
[1] "tbl2"
                  cls
clus               [,1] [,2]
  PIK3CA MUTATED      1   10
  PIK3CA WILD-TYPE   20  255
                        clus
vv                       PIK3CA MUTATED PIK3CA WILD-TYPE
  HISPANIC OR LATINO                  1               20
  NOT HISPANIC OR LATINO             10              255
[1] 2 2
[1] FALSE

Clustering(14) Variable = PCK1 MUTATION ANALYSIS
D14V1, survival
                sevent
clus2              0   1
  PCK1 MUTATED     5   0
  PCK1 WILD-TYPE 270 142
  PCK1 MUTATED PCK1 WILD-TYPE 
             5            412 
  PCK1 MUTATED PCK1 WILD-TYPE 
             0            142 
$`PCK1 MUTATED`
TCGA-A3-3326 TCGA-AK-3429 TCGA-B0-5119 TCGA-CJ-4902 TCGA-CZ-5456 
       37.38        66.31         1.94        49.97        56.28 

$`PCK1 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       48.59        36.36         4.50        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        35.18        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3430 
       28.31        65.52        20.28       109.91        73.08        15.78 
TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 
       60.92        68.61        67.20        48.36        42.08        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       48.69        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       28.04         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         0.85        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       11.80        26.20        21.60        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
       47.97        96.36        61.32        97.41        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       25.55        25.91        23.01        20.91        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.49        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       47.67        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        63.88        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
        0.82        23.74        18.44        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  PCK1 MUTATED PCK1 WILD-TYPE 
          1.94           0.07 
  PCK1 MUTATED PCK1 WILD-TYPE 
         66.31         120.59 
  PCK1 MUTATED PCK1 WILD-TYPE 
        49.970         37.235 
[1] "1.9 - 66.3 (50.0)"  "0.1 - 120.6 (37.2)"
[1] "hr="     "9100000"
D14V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  PCK1 MUTATED         2        2         1        0
  PCK1 WILD-TYPE     195       38       112       67
D14V3, multiclass
           clus
vv          PCK1 MUTATED PCK1 WILD-TYPE
  STAGE I              2            195
  STAGE II             2             38
  STAGE III            1            112
  STAGE IV             0             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
  PCK1 MUTATED     2   2   1   0
  PCK1 WILD-TYPE 200  47 159   6
D14V4, multiclass
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  T1            2            200
  T2            2             47
  T3            1            159
  T4            0              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
  PCK1 MUTATED     3   0
  PCK1 WILD-TYPE 189  12
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      3    0
  PCK1 WILD-TYPE  189   12
   clus
vv  PCK1 MUTATED PCK1 WILD-TYPE
  0            3            189
  1            0             12
[1] 2 2
[1] FALSE
D14V6, binary
                cls
clus               0   1
  PCK1 MUTATED     5   0
  PCK1 WILD-TYPE 345  67
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      5    0
  PCK1 WILD-TYPE  345   67
    clus
vv   PCK1 MUTATED PCK1 WILD-TYPE
  M0            5            345
  M1            0             67
[1] 2 2
[1] FALSE
D14V7, binary
                cls
clus               0   1
  PCK1 MUTATED     2   3
  PCK1 WILD-TYPE 144 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      2    3
  PCK1 WILD-TYPE  144  268
        clus
vv       PCK1 MUTATED PCK1 WILD-TYPE
  FEMALE            2            144
  MALE              3            268
[1] 2 2
[1] FALSE
D14V8, continuous
[1] "Remove cluster labels:" "PCK1 MUTATED"          
clus
  PCK1 MUTATED PCK1 WILD-TYPE 
             1             22 
    TCGA-AK-3430     TCGA-B0-4838     TCGA-B4-5377     TCGA-CZ-4854 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-4856     TCGA-CZ-4858     TCGA-CZ-4861     TCGA-CZ-4862 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-CZ-5457     TCGA-CZ-5465     TCGA-CZ-5469     TCGA-CZ-5982 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DV-5565     TCGA-DV-5566     TCGA-DV-5568     TCGA-DV-5569 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-DV-5574     TCGA-DV-5575     TCGA-DV-5576     TCGA-EU-5904 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
    TCGA-EU-5905     TCGA-EU-5907 
"PCK1 WILD-TYPE" "PCK1 WILD-TYPE" 
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PCK1 MUTATED       0                         0     5
  PCK1 WILD-TYPE     7                        14   385
D14V9, multiclass
                           clus
vv                          PCK1 MUTATED PCK1 WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             14
  WHITE                                5            385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D14V10, binary
                cls
clus               0   1
  PCK1 MUTATED     0   3
  PCK1 WILD-TYPE  21 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  PCK1 MUTATED      0    3
  PCK1 WILD-TYPE   21  262
                        clus
vv                       PCK1 MUTATED PCK1 WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            3            262
[1] 2 2
[1] FALSE

Clustering(15) Variable = ARID1A MUTATION ANALYSIS
D15V1, survival
                  sevent
clus2                0   1
  ARID1A MUTATED     9   3
  ARID1A WILD-TYPE 266 139
  ARID1A MUTATED ARID1A WILD-TYPE 
              12              405 
  ARID1A MUTATED ARID1A WILD-TYPE 
               3              139 
$`ARID1A MUTATED`
TCGA-A3-3320 TCGA-AK-3444 TCGA-B0-5102 TCGA-B0-5692 TCGA-B0-5713 TCGA-B8-5549 
       49.58        48.36        90.87        48.89        61.32         6.38 
TCGA-BP-5199 TCGA-CJ-4892 TCGA-CJ-4912 TCGA-CJ-6032 TCGA-CZ-4857 TCGA-CZ-4861 
       44.55        50.01        54.48        83.77        47.08        14.66 

$`ARID1A WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3322 
        0.53        39.16        49.08        49.02        37.15        48.59 
TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       36.36        37.38         4.50        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        35.18        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
       28.31        65.52        20.28       109.91        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 
       15.78        60.92        68.61        67.20        42.08        58.49 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 
       48.69        28.73        22.45        37.58        38.40        31.27 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 
       28.04         1.41         1.41         4.57         2.53         3.48 
TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
       19.00        65.10         5.98         0.85        19.73         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
       43.96         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5104 
        8.05         2.24        21.86        15.95        62.89        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        21.60         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       37.22        14.76       112.80       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 
       96.36        97.41        35.90         1.68        12.30        21.30 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 
       11.77        10.36        21.57         9.57        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 
       27.16        27.55        25.05        24.66        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       23.01        20.91        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       17.16        16.60        14.27         0.49        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 
       32.61        99.85         0.43        89.36        23.05        77.03 
TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 
       62.24        61.78        64.27        53.42        27.78        62.07 
TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 
       80.68         0.07        93.99        18.48        52.24        74.17 
TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
       62.86        49.84        49.08        44.94        12.23        31.89 
TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       11.31        33.99        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       11.64        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       52.27         9.63        62.86        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 
       68.55        26.93        24.66        27.65        39.45        59.44 
TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
       50.24        47.67        49.97        51.29        58.92        49.18 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       49.28        50.33        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
       46.16         0.59        63.88        58.75        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  ARID1A MUTATED ARID1A WILD-TYPE 
            6.38             0.07 
  ARID1A MUTATED ARID1A WILD-TYPE 
           90.87           120.59 
  ARID1A MUTATED ARID1A WILD-TYPE 
          49.235           37.150 
[1] "6.4 - 90.9 (49.2)"  "0.1 - 120.6 (37.1)"
[1] "hr=" "1.7"
D15V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  ARID1A MUTATED         5        4         2        1
  ARID1A WILD-TYPE     192       36       111       66
D15V3, multiclass
           clus
vv          ARID1A MUTATED ARID1A WILD-TYPE
  STAGE I                5              192
  STAGE II               4               36
  STAGE III              2              111
  STAGE IV               1               66
[1] 4 2
[1] 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
  ARID1A MUTATED     5   4   3   0
  ARID1A WILD-TYPE 197  45 157   6
D15V4, multiclass
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  T1              5              197
  T2              4               45
  T3              3              157
  T4              0                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"
D15V5, binary
                  cls
clus                 0   1
  ARID1A MUTATED     6   0
  ARID1A WILD-TYPE 186  12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      6    0
  ARID1A WILD-TYPE  186   12
   clus
vv  ARID1A MUTATED ARID1A WILD-TYPE
  0              6              186
  1              0               12
[1] 2 2
[1] FALSE
D15V6, binary
                  cls
clus                 0   1
  ARID1A MUTATED    11   1
  ARID1A WILD-TYPE 339  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED     11    1
  ARID1A WILD-TYPE  339   66
    clus
vv   ARID1A MUTATED ARID1A WILD-TYPE
  M0             11              339
  M1              1               66
[1] 2 2
[1] FALSE
D15V7, binary
                  cls
clus                 0   1
  ARID1A MUTATED     7   5
  ARID1A WILD-TYPE 139 266
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      7    5
  ARID1A WILD-TYPE  139  266
        clus
vv       ARID1A MUTATED ARID1A WILD-TYPE
  FEMALE              7              139
  MALE                5              266
[1] 2 2
[1] FALSE
D15V8, continuous
[1] "Remove cluster labels:" "ARID1A MUTATED"        
clus
  ARID1A MUTATED ARID1A WILD-TYPE 
               1               22 
      TCGA-AK-3430       TCGA-B0-4838       TCGA-B4-5377       TCGA-CZ-4854 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CZ-4856       TCGA-CZ-4858       TCGA-CZ-4862       TCGA-CZ-5456 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-CZ-5457       TCGA-CZ-5465       TCGA-CZ-5469       TCGA-CZ-5982 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DV-5565       TCGA-DV-5566       TCGA-DV-5568       TCGA-DV-5569 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-DV-5574       TCGA-DV-5575       TCGA-DV-5576       TCGA-EU-5904 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
      TCGA-EU-5905       TCGA-EU-5907 
"ARID1A WILD-TYPE" "ARID1A WILD-TYPE" 
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARID1A MUTATED       0                         0    12
  ARID1A WILD-TYPE     7                        14   378
D15V9, multiclass
                           clus
vv                          ARID1A MUTATED ARID1A WILD-TYPE
  ASIAN                                  0                7
  BLACK OR AFRICAN AMERICAN              0               14
  WHITE                                 12              378
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D15V10, binary
                  cls
clus                 0   1
  ARID1A MUTATED     2   8
  ARID1A WILD-TYPE  19 257
[1] "tbl2"
                  cls
clus               [,1] [,2]
  ARID1A MUTATED      2    8
  ARID1A WILD-TYPE   19  257
                        clus
vv                       ARID1A MUTATED ARID1A WILD-TYPE
  HISPANIC OR LATINO                  2               19
  NOT HISPANIC OR LATINO              8              257
[1] 2 2
[1] FALSE

Clustering(16) Variable = ATM MUTATION ANALYSIS
D16V1, survival
               sevent
clus2             0   1
  ATM MUTATED     8   3
  ATM WILD-TYPE 267 139
  ATM MUTATED ATM WILD-TYPE 
           11           406 
  ATM MUTATED ATM WILD-TYPE 
            3           139 
$`ATM MUTATED`
TCGA-B0-4690 TCGA-B0-5097 TCGA-B0-5703 TCGA-BP-4964 TCGA-BP-5173 TCGA-CJ-4639 
        1.41        21.86        39.55        61.22         1.78        75.88 
TCGA-CJ-4904 TCGA-CJ-5686 TCGA-CZ-4861 TCGA-CZ-5451 TCGA-CZ-5986 
       58.92        67.00        14.66        63.42        12.26 

$`ATM WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4691 TCGA-B0-4693 
       38.40        31.27        28.04         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
       10.95         8.05         2.24        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       56.94        52.77       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
       47.97        96.36        61.32        97.41        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       25.55        25.91        23.01        20.91        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.49        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5174 
       36.23        28.87        48.10         6.35        79.30        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 
       30.64        52.27         9.63        62.86        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4640 TCGA-CJ-4641 
       46.55        63.25        73.22        14.17        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 
       58.95        11.05        21.24        49.25        79.66        47.18 
TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 
       74.27        75.06        77.36        64.27        71.87        66.21 
TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 
       61.91        57.83        69.86        64.18        30.64        51.52 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
       63.98        68.55        26.93        50.01        24.66        27.65 
TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
       39.45        59.44        50.24        47.67        49.97        51.29 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 
       61.91        62.10        73.35        60.99        53.42        75.58 
TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 
       62.66        83.77         7.36        64.57        92.02        81.83 
TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       85.78        66.31        78.18        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        25.45        46.16         0.59        47.08        63.88 
TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5452 
       58.75        60.59        63.39         5.46        61.41        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       67.96        65.65        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  ATM MUTATED ATM WILD-TYPE 
         1.41          0.07 
  ATM MUTATED ATM WILD-TYPE 
        75.88        120.59 
  ATM MUTATED ATM WILD-TYPE 
        39.55         37.25 
[1] "1.4 - 75.9 (39.5)"  "0.1 - 120.6 (37.2)"
[1] "hr=" "1.2"
D16V2, continuous
               vv
clus            STAGE I STAGE II STAGE III STAGE IV
  ATM MUTATED         5        3         1        2
  ATM WILD-TYPE     192       37       112       65
D16V3, multiclass
           clus
vv          ATM MUTATED ATM WILD-TYPE
  STAGE I             5           192
  STAGE II            3            37
  STAGE III           1           112
  STAGE IV            2            65
[1] 4 2
[1] 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
  ATM MUTATED     5   3   2   1
  ATM WILD-TYPE 197  46 158   5
D16V4, multiclass
    clus
vv   ATM MUTATED ATM WILD-TYPE
  T1           5           197
  T2           3            46
  T3           2           158
  T4           1             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"
D16V5, binary
               cls
clus              0   1
  ATM MUTATED     7   1
  ATM WILD-TYPE 185  11
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      7    1
  ATM WILD-TYPE  185   11
   clus
vv  ATM MUTATED ATM WILD-TYPE
  0           7           185
  1           1            11
[1] 2 2
[1] FALSE
D16V6, binary
               cls
clus              0   1
  ATM MUTATED     9   2
  ATM WILD-TYPE 341  65
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      9    2
  ATM WILD-TYPE  341   65
    clus
vv   ATM MUTATED ATM WILD-TYPE
  M0           9           341
  M1           2            65
[1] 2 2
[1] FALSE
D16V7, binary
               cls
clus              0   1
  ATM MUTATED     5   6
  ATM WILD-TYPE 141 265
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      5    6
  ATM WILD-TYPE  141  265
        clus
vv       ATM MUTATED ATM WILD-TYPE
  FEMALE           5           141
  MALE             6           265
[1] 2 2
[1] FALSE
D16V8, continuous
[1] "Remove cluster labels:" "ATM MUTATED"           
clus
  ATM MUTATED ATM WILD-TYPE 
            1            22 
   TCGA-AK-3430    TCGA-B0-4838    TCGA-B4-5377    TCGA-CZ-4854    TCGA-CZ-4856 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-4858    TCGA-CZ-4862    TCGA-CZ-5456    TCGA-CZ-5457    TCGA-CZ-5465 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-CZ-5469    TCGA-CZ-5982    TCGA-DV-5565    TCGA-DV-5566    TCGA-DV-5568 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-DV-5569    TCGA-DV-5574    TCGA-DV-5575    TCGA-DV-5576    TCGA-EU-5904 
"ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" "ATM WILD-TYPE" 
   TCGA-EU-5905    TCGA-EU-5907 
"ATM WILD-TYPE" "ATM WILD-TYPE" 
               vv
clus            ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ATM MUTATED       0                         0    11
  ATM WILD-TYPE     7                        14   379
D16V9, multiclass
                           clus
vv                          ATM MUTATED ATM WILD-TYPE
  ASIAN                               0             7
  BLACK OR AFRICAN AMERICAN           0            14
  WHITE                              11           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"
D16V10, binary
               cls
clus              0   1
  ATM MUTATED     1   5
  ATM WILD-TYPE  20 260
[1] "tbl2"
               cls
clus            [,1] [,2]
  ATM MUTATED      1    5
  ATM WILD-TYPE   20  260
                        clus
vv                       ATM MUTATED ATM WILD-TYPE
  HISPANIC OR LATINO               1            20
  NOT HISPANIC OR LATINO           5           260
[1] 2 2
[1] FALSE

Clustering(17) Variable = DPCR1 MUTATION ANALYSIS
D17V1, survival
                 sevent
clus2               0   1
  DPCR1 MUTATED     3   3
  DPCR1 WILD-TYPE 272 139
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              6             411 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              3             139 
$`DPCR1 MUTATED`
TCGA-B0-5080 TCGA-CW-5589 TCGA-CZ-4866 TCGA-CZ-5460 TCGA-CZ-5468 TCGA-DV-5576 
       11.24        78.18        61.41        47.01         1.94        23.90 

$`DPCR1 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        31.27        28.04         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         0.85 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       20.94        43.30        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
       92.98       102.48        47.97        96.36        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 
       35.90         1.68        12.30        21.30        11.77        10.36 
TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
       21.57         9.57        23.31        16.80        27.16        27.55 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
       25.05        24.66        25.55        25.91        23.01        20.91 
TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
       23.74        27.02         0.85        24.23        17.16        16.60 
TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 
        6.38        14.27         0.49        34.39        14.30       111.02 
TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 
       85.51        94.72        90.28       101.06        93.34        32.61 
TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 
       99.85         0.43        89.36        23.05        77.03        62.24 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 
       61.78        64.27        53.42        27.78        62.07        80.68 
TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 
        0.07        93.99        18.48        52.24        74.17        62.86 
TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 
       49.84        49.08        44.94        12.23        31.89        11.31 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 
       33.99        31.33        12.30        72.59        77.98         5.98 
TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 
       44.15        41.75        71.80        48.07        13.15        10.82 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        5.33        61.97        60.59        56.91        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        62.86        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       59.44        50.24        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 
       81.83        85.78        66.31        74.66         1.35        83.90 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 
      103.43        25.45        46.16         0.59        47.08        63.88 
TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-5451 
       58.75        14.66        60.59        63.39         5.46        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       56.94        55.33        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
       22.52         2.40        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
       45.96        12.16        11.67        66.28        56.84        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  DPCR1 MUTATED DPCR1 WILD-TYPE 
           1.94            0.07 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
          78.18          120.59 
  DPCR1 MUTATED DPCR1 WILD-TYPE 
         35.455          37.250 
[1] "1.9 - 78.2 (35.5)"  "0.1 - 120.6 (37.2)"
[1] "hr=" "1.6"
D17V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  DPCR1 MUTATED         3        0         0        3
  DPCR1 WILD-TYPE     194       40       113       64
D17V3, multiclass
           clus
vv          DPCR1 MUTATED DPCR1 WILD-TYPE
  STAGE I               3             194
  STAGE II              0              40
  STAGE III             0             113
  STAGE IV              3              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
  DPCR1 MUTATED     3   0   3   0
  DPCR1 WILD-TYPE 199  49 157   6
D17V4, multiclass
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  T1             3             199
  T2             0              49
  T3             3             157
  T4             0               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"
D17V5, binary
                 cls
clus                0   1
  DPCR1 MUTATED     1   0
  DPCR1 WILD-TYPE 191  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      1    0
  DPCR1 WILD-TYPE  191   12
   clus
vv  DPCR1 MUTATED DPCR1 WILD-TYPE
  0             1             191
  1             0              12
[1] 2 2
[1] FALSE
D17V6, binary
                 cls
clus                0   1
  DPCR1 MUTATED     3   3
  DPCR1 WILD-TYPE 347  64
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      3    3
  DPCR1 WILD-TYPE  347   64
    clus
vv   DPCR1 MUTATED DPCR1 WILD-TYPE
  M0             3             347
  M1             3              64
[1] 2 2
[1] FALSE
D17V7, binary
                 cls
clus                0   1
  DPCR1 MUTATED     2   4
  DPCR1 WILD-TYPE 144 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      2    4
  DPCR1 WILD-TYPE  144  267
        clus
vv       DPCR1 MUTATED DPCR1 WILD-TYPE
  FEMALE             2             144
  MALE               4             267
[1] 2 2
[1] FALSE
D17V8, continuous
[1] "Remove cluster labels:" "DPCR1 MUTATED"         
clus
  DPCR1 MUTATED DPCR1 WILD-TYPE 
              1              22 
     TCGA-AK-3430      TCGA-B0-4838      TCGA-B4-5377      TCGA-CZ-4854 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-4856      TCGA-CZ-4858      TCGA-CZ-4861      TCGA-CZ-4862 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5456      TCGA-CZ-5457      TCGA-CZ-5465      TCGA-CZ-5469 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-CZ-5982      TCGA-DV-5565      TCGA-DV-5566      TCGA-DV-5568 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-DV-5569      TCGA-DV-5574      TCGA-DV-5575      TCGA-EU-5904 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
     TCGA-EU-5905      TCGA-EU-5907 
"DPCR1 WILD-TYPE" "DPCR1 WILD-TYPE" 
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  DPCR1 MUTATED       0                         1     5
  DPCR1 WILD-TYPE     7                        13   385
D17V9, multiclass
                           clus
vv                          DPCR1 MUTATED DPCR1 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             1              13
  WHITE                                 5             385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D17V10, binary
                 cls
clus                0   1
  DPCR1 MUTATED     0   6
  DPCR1 WILD-TYPE  21 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  DPCR1 MUTATED      0    6
  DPCR1 WILD-TYPE   21  259
                        clus
vv                       DPCR1 MUTATED DPCR1 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             6             259
[1] 2 2
[1] FALSE

Clustering(18) Variable = FGFR3 MUTATION ANALYSIS
D18V1, survival
                 sevent
clus2               0   1
  FGFR3 MUTATED     3   1
  FGFR3 WILD-TYPE 272 141
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              4             413 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
              1             141 
$`FGFR3 MUTATED`
TCGA-AK-3445 TCGA-B0-5109 TCGA-B2-4101 TCGA-CJ-4908 
       42.08        19.30        21.30        50.33 

$`FGFR3 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       31.27        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5110 
       90.87        90.48        52.54        30.48        29.95        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
      102.48        47.97        96.36        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
        1.68        12.30        11.77        10.36        21.57         9.57 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       25.55        25.91        23.01        20.91        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.49        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        63.88        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  FGFR3 MUTATED FGFR3 WILD-TYPE 
          19.30            0.07 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          50.33          120.59 
  FGFR3 MUTATED FGFR3 WILD-TYPE 
          31.69           37.25 
[1] "19.3 - 50.3 (31.7)" "0.1 - 120.6 (37.2)"
[1] "hr=" "1.1"
D18V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  FGFR3 MUTATED         1        1         2        0
  FGFR3 WILD-TYPE     196       39       111       67
D18V3, multiclass
           clus
vv          FGFR3 MUTATED FGFR3 WILD-TYPE
  STAGE I               1             196
  STAGE II              1              39
  STAGE III             2             111
  STAGE IV              0              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
  FGFR3 MUTATED     1   1   2   0
  FGFR3 WILD-TYPE 201  48 158   6
D18V4, multiclass
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  T1             1             201
  T2             1              48
  T3             2             158
  T4             0               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"
D18V5, binary
                 cls
clus                0   1
  FGFR3 MUTATED     0   1
  FGFR3 WILD-TYPE 192  11
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      0    1
  FGFR3 WILD-TYPE  192   11
   clus
vv  FGFR3 MUTATED FGFR3 WILD-TYPE
  0             0             192
  1             1              11
[1] 2 2
[1] FALSE
D18V6, binary
                 cls
clus                0   1
  FGFR3 MUTATED     4   0
  FGFR3 WILD-TYPE 346  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      4    0
  FGFR3 WILD-TYPE  346   67
    clus
vv   FGFR3 MUTATED FGFR3 WILD-TYPE
  M0             4             346
  M1             0              67
[1] 2 2
[1] FALSE
D18V7, binary
                 cls
clus                0   1
  FGFR3 MUTATED     0   4
  FGFR3 WILD-TYPE 146 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      0    4
  FGFR3 WILD-TYPE  146  267
        clus
vv       FGFR3 MUTATED FGFR3 WILD-TYPE
  FEMALE             0             146
  MALE               4             267
[1] 2 2
[1] FALSE
D18V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  FGFR3 MUTATED       0                         0     4
  FGFR3 WILD-TYPE     7                        14   386
D18V9, multiclass
                           clus
vv                          FGFR3 MUTATED FGFR3 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              14
  WHITE                                 4             386
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D18V10, binary
                 cls
clus                0   1
  FGFR3 MUTATED     0   4
  FGFR3 WILD-TYPE  21 261
[1] "tbl2"
                 cls
clus              [,1] [,2]
  FGFR3 MUTATED      0    4
  FGFR3 WILD-TYPE   21  261
                        clus
vv                       FGFR3 MUTATED FGFR3 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             4             261
[1] 2 2
[1] FALSE

Clustering(19) Variable = PTCH1 MUTATION ANALYSIS
D19V1, survival
                 sevent
clus2               0   1
  PTCH1 MUTATED     4   3
  PTCH1 WILD-TYPE 271 139
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              7             410 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
              3             139 
$`PTCH1 MUTATED`
TCGA-B0-4713 TCGA-B0-4718 TCGA-B0-4814 TCGA-B8-4153 TCGA-BP-4337 TCGA-BP-4768 
        6.64        20.25         5.52        25.05         0.07        13.15 
TCGA-BP-4777 
       56.91 

$`PTCH1 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        31.27        28.04         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         0.85 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 
       19.73         3.16        43.96         3.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        0.59        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        21.60         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
       47.97        96.36        61.32        97.41        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4154 TCGA-B8-4620 
       23.31        16.80        27.16        27.55        24.66        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.91        23.01        20.91        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.49 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 
       23.05        77.03        62.24        61.78        64.27        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       27.78        62.07        80.68        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4782 
       10.82         5.33        61.97        60.59        68.38        11.64 
TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 
       15.78        48.95        36.53        36.39        10.98        37.25 
TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 
       36.95         6.71        47.97         6.94        71.41        63.62 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 
       58.68        60.30        61.22         6.74        57.40        14.24 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
       48.89        49.38        45.50         7.23        47.11        53.65 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
       14.93        36.07        33.34        46.45        31.30        25.81 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
       36.95        27.22         3.88        46.45        16.47         5.82 
TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 
       45.07        30.64        41.62        18.51        38.70        37.02 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 
       27.62        37.48        35.21        36.23        28.87        48.10 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 
        6.35        79.30         1.78        74.20        30.64        52.27 
TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
        9.63        62.86        74.40        38.30        42.44        37.25 
TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
       37.22        22.78        13.35        27.02        33.24        31.79 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
       23.47        13.41        24.62        33.47        19.82        44.55 
TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 
       34.95        31.27         0.95        59.84        46.55        63.25 
TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 
       73.22        14.17        75.88        65.69        54.61        58.95 
TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       11.05        21.24        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       59.44        50.24        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       63.88        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 
        6.77         4.18 

  PTCH1 MUTATED PTCH1 WILD-TYPE 
           0.07            0.43 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          56.91          120.59 
  PTCH1 MUTATED PTCH1 WILD-TYPE 
          13.15           37.53 
[1] "0.1 - 56.9 (13.2)"  "0.4 - 120.6 (37.5)"
[1] "hr=" "2.9"
D19V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  PTCH1 MUTATED         2        0         4        1
  PTCH1 WILD-TYPE     195       40       109       66
D19V3, multiclass
           clus
vv          PTCH1 MUTATED PTCH1 WILD-TYPE
  STAGE I               2             195
  STAGE II              0              40
  STAGE III             4             109
  STAGE IV              1              66
[1] 4 2
[1] 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
  PTCH1 MUTATED     2   0   4   1
  PTCH1 WILD-TYPE 200  49 156   5
D19V4, multiclass
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  T1             2             200
  T2             0              49
  T3             4             156
  T4             1               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"
D19V5, binary
                 cls
clus                0   1
  PTCH1 MUTATED     3   0
  PTCH1 WILD-TYPE 189  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      3    0
  PTCH1 WILD-TYPE  189   12
   clus
vv  PTCH1 MUTATED PTCH1 WILD-TYPE
  0             3             189
  1             0              12
[1] 2 2
[1] FALSE
D19V6, binary
                 cls
clus                0   1
  PTCH1 MUTATED     6   1
  PTCH1 WILD-TYPE 344  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      6    1
  PTCH1 WILD-TYPE  344   66
    clus
vv   PTCH1 MUTATED PTCH1 WILD-TYPE
  M0             6             344
  M1             1              66
[1] 2 2
[1] FALSE
D19V7, binary
                 cls
clus                0   1
  PTCH1 MUTATED     3   4
  PTCH1 WILD-TYPE 143 267
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      3    4
  PTCH1 WILD-TYPE  143  267
        clus
vv       PTCH1 MUTATED PTCH1 WILD-TYPE
  FEMALE             3             143
  MALE               4             267
[1] 2 2
[1] FALSE
D19V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  PTCH1 MUTATED       0                         0     7
  PTCH1 WILD-TYPE     7                        14   383
D19V9, multiclass
                           clus
vv                          PTCH1 MUTATED PTCH1 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              14
  WHITE                                 7             383
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D19V10, binary
                 cls
clus                0   1
  PTCH1 MUTATED     0   5
  PTCH1 WILD-TYPE  21 260
[1] "tbl2"
                 cls
clus              [,1] [,2]
  PTCH1 MUTATED      0    5
  PTCH1 WILD-TYPE   21  260
                        clus
vv                       PTCH1 MUTATED PTCH1 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             5             260
[1] 2 2
[1] FALSE

Clustering(20) Variable = RBMX MUTATION ANALYSIS
D20V1, survival
                sevent
clus2              0   1
  RBMX MUTATED     3   1
  RBMX WILD-TYPE 272 141
  RBMX MUTATED RBMX WILD-TYPE 
             4            413 
  RBMX MUTATED RBMX WILD-TYPE 
             1            141 
$`RBMX MUTATED`
TCGA-AS-3778 TCGA-B0-4712 TCGA-B8-5158 TCGA-CZ-5988 
        1.41        43.96        20.91        22.78 

$`RBMX WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       38.40        31.27        28.04         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        3.16         6.64         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
      102.48        47.97        96.36        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        9.57        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5163 
       24.66        25.55        25.91        23.01        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.49        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        63.88        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 
       80.19        67.96        65.65        12.26        14.63        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  RBMX MUTATED RBMX WILD-TYPE 
          1.41           0.07 
  RBMX MUTATED RBMX WILD-TYPE 
         43.96         120.59 
  RBMX MUTATED RBMX WILD-TYPE 
        21.845         37.380 
[1] "1.4 - 44.0 (21.8)"  "0.1 - 120.6 (37.4)"
[1] "hr=" "1.4"
D20V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  RBMX MUTATED         2        0         1        1
  RBMX WILD-TYPE     195       40       112       66
D20V3, multiclass
           clus
vv          RBMX MUTATED RBMX WILD-TYPE
  STAGE I              2            195
  STAGE II             0             40
  STAGE III            1            112
  STAGE IV             1             66
[1] 4 2
[1] 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
  RBMX MUTATED     2   0   2   0
  RBMX WILD-TYPE 200  49 158   6
D20V4, multiclass
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  T1            2            200
  T2            0             49
  T3            2            158
  T4            0              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"
D20V5, binary
                cls
clus               0   1
  RBMX MUTATED     1   1
  RBMX WILD-TYPE 191  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      1    1
  RBMX WILD-TYPE  191   11
   clus
vv  RBMX MUTATED RBMX WILD-TYPE
  0            1            191
  1            1             11
[1] 2 2
[1] FALSE
D20V6, binary
                cls
clus               0   1
  RBMX MUTATED     3   1
  RBMX WILD-TYPE 347  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      3    1
  RBMX WILD-TYPE  347   66
    clus
vv   RBMX MUTATED RBMX WILD-TYPE
  M0            3            347
  M1            1             66
[1] 2 2
[1] FALSE
D20V7, binary
                cls
clus               0   1
  RBMX MUTATED     0   4
  RBMX WILD-TYPE 146 267
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0    4
  RBMX WILD-TYPE  146  267
        clus
vv       RBMX MUTATED RBMX WILD-TYPE
  FEMALE            0            146
  MALE              4            267
[1] 2 2
[1] FALSE
D20V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  RBMX MUTATED       0                         0     4
  RBMX WILD-TYPE     7                        14   386
D20V9, multiclass
                           clus
vv                          RBMX MUTATED RBMX WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             14
  WHITE                                4            386
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D20V10, binary
                cls
clus               0   1
  RBMX MUTATED     0   3
  RBMX WILD-TYPE  21 262
[1] "tbl2"
                cls
clus             [,1] [,2]
  RBMX MUTATED      0    3
  RBMX WILD-TYPE   21  262
                        clus
vv                       RBMX MUTATED RBMX WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            3            262
[1] 2 2
[1] FALSE

Clustering(21) Variable = ARAP3 MUTATION ANALYSIS
D21V1, survival
                 sevent
clus2               0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 273 141
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              3             414 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
              1             141 
$`ARAP3 MUTATED`
TCGA-A3-3323 TCGA-B0-4819 TCGA-CJ-4870 
       36.36         6.02        49.25 

$`ARAP3 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       48.59        37.38         4.50        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        35.18        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
       28.31        65.52        20.28       109.91        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       31.27        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
       16.77        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 
       15.78        46.68        56.78        60.33        84.92        90.12 
TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 
       56.94        52.77        39.55       120.59        79.36        92.98 
TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
      102.48        47.97        96.36        61.32        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        9.57        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       24.66        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.49        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       64.27        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 
       31.33        12.30        72.59        77.98         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 
       37.48        35.21        36.23        28.87        48.10         6.35 
TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 
       79.30         1.78        74.20        30.64        52.27         9.63 
TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 
       62.86        74.40        38.30        42.44        37.25        37.22 
TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 
       22.78        13.35        27.02        33.24        31.79        23.47 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
       13.41        24.62        33.47        19.82        44.55        34.95 
TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 
       31.27         0.95        59.84        46.55        63.25        73.22 
TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 
       14.17        75.88        65.69        54.61        58.95        11.05 
TCGA-CJ-4868 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       21.24        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        63.88        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
       56.94        55.33        47.01        10.85        10.22        21.76 
TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
       47.54        22.52         2.40         1.94        31.10        12.69 
TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 
       80.19        67.96        65.65        12.26        14.63        22.78 
TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 
       62.63        43.69        45.96        12.16        11.67        66.28 
TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       56.84        23.90        18.12         3.91         6.77         4.18 

  ARAP3 MUTATED ARAP3 WILD-TYPE 
           6.02            0.07 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
          49.25          120.59 
  ARAP3 MUTATED ARAP3 WILD-TYPE 
         36.360          37.315 
[1] "6.0 - 49.2 (36.4)"  "0.1 - 120.6 (37.3)"
[1] "hr=" "1.3"
D21V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  ARAP3 MUTATED         1        0         1        1
  ARAP3 WILD-TYPE     196       40       112       66
D21V3, multiclass
           clus
vv          ARAP3 MUTATED ARAP3 WILD-TYPE
  STAGE I               1             196
  STAGE II              0              40
  STAGE III             1             112
  STAGE IV              1              66
[1] 4 2
[1] 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
  ARAP3 MUTATED     1   0   2   0
  ARAP3 WILD-TYPE 201  49 158   6
D21V4, multiclass
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  T1             1             201
  T2             0              49
  T3             2             158
  T4             0               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"
D21V5, binary
                 cls
clus                0   1
  ARAP3 MUTATED     0   0
  ARAP3 WILD-TYPE 192  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      0    0
  ARAP3 WILD-TYPE  192   12
D21V6, binary
                 cls
clus                0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 348  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      2    1
  ARAP3 WILD-TYPE  348   66
    clus
vv   ARAP3 MUTATED ARAP3 WILD-TYPE
  M0             2             348
  M1             1              66
[1] 2 2
[1] FALSE
D21V7, binary
                 cls
clus                0   1
  ARAP3 MUTATED     2   1
  ARAP3 WILD-TYPE 144 270
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      2    1
  ARAP3 WILD-TYPE  144  270
        clus
vv       ARAP3 MUTATED ARAP3 WILD-TYPE
  FEMALE             2             144
  MALE               1             270
[1] 2 2
[1] FALSE
D21V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  ARAP3 MUTATED       0                         1     2
  ARAP3 WILD-TYPE     7                        13   388
D21V9, multiclass
                           clus
vv                          ARAP3 MUTATED ARAP3 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             1              13
  WHITE                                 2             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"
D21V10, binary
                 cls
clus                0   1
  ARAP3 MUTATED     0   2
  ARAP3 WILD-TYPE  21 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  ARAP3 MUTATED      0    2
  ARAP3 WILD-TYPE   21  263
                        clus
vv                       ARAP3 MUTATED ARAP3 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             2             263
[1] 2 2
[1] FALSE

Clustering(22) Variable = GPR172B MUTATION ANALYSIS
D22V1, survival
                   sevent
clus2                 0   1
  GPR172B MUTATED     3   1
  GPR172B WILD-TYPE 272 141
  GPR172B MUTATED GPR172B WILD-TYPE 
                4               413 
  GPR172B MUTATED GPR172B WILD-TYPE 
                1               141 
$`GPR172B MUTATED`
TCGA-BP-4165 TCGA-BP-4170 TCGA-BP-4761 TCGA-BP-4782 
       99.85        77.03         5.98        11.64 

$`GPR172B WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        31.27        28.04         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         0.85 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 
       33.50        16.77         6.02        36.53        14.93        54.48 
TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 
       29.10        10.09        78.44        40.70        45.30        27.42 
TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 
       53.88         6.71        56.68        11.64        10.29        65.29 
TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 
       39.45        26.07        29.03         2.27        36.85        70.52 
TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 
       20.94        43.30        11.24        11.90        25.32        18.51 
TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 
       15.09        10.95         8.05         2.24        21.86        15.95 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
       62.89        90.87        90.48        52.54        30.48        29.95 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 
       19.30        35.90        11.80        26.20        21.60         1.94 
TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 
       16.21        18.21        21.44        37.22        14.76       112.80 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
       48.89       101.13        15.78        46.68        56.78        60.33 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
       84.92        90.12        56.94        52.77        39.55       120.59 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 
       79.36        92.98       102.48        47.97        96.36        61.32 
TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 
       97.41        35.90         1.68        12.30        21.30        11.77 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 
       10.36        21.57         9.57        23.31        16.80        27.16 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
       27.55        25.05        24.66        25.55        25.91        23.01 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 
       20.91        23.74        27.02         0.85        24.23        17.16 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 
       16.60         6.38        14.27         0.49        34.39        14.30 
TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 
      111.02        85.51        94.72        90.28       101.06        93.34 
TCGA-BP-4164 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4174 
       32.61         0.43        89.36        23.05        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       64.27        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4762 TCGA-BP-4763 
       31.33        12.30        72.59        77.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       60.59        56.91        68.38        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 
       65.69        54.61        58.95        11.05        21.24        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
       24.66        27.65        39.45        59.44        50.24        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        63.88        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  GPR172B MUTATED GPR172B WILD-TYPE 
             5.98              0.07 
  GPR172B MUTATED GPR172B WILD-TYPE 
            99.85            120.59 
  GPR172B MUTATED GPR172B WILD-TYPE 
           44.335            37.250 
[1] "6.0 - 99.8 (44.3)"  "0.1 - 120.6 (37.2)"
[1] "hr=" "1.8"
D22V2, continuous
                   vv
clus                STAGE I STAGE II STAGE III STAGE IV
  GPR172B MUTATED         3        0         1        0
  GPR172B WILD-TYPE     194       40       112       67
D22V3, multiclass
           clus
vv          GPR172B MUTATED GPR172B WILD-TYPE
  STAGE I                 3               194
  STAGE II                0                40
  STAGE III               1               112
  STAGE IV                0                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
  GPR172B MUTATED     3   0   1   0
  GPR172B WILD-TYPE 199  49 159   6
D22V4, multiclass
    clus
vv   GPR172B MUTATED GPR172B WILD-TYPE
  T1               3               199
  T2               0                49
  T3               1               159
  T4               0                 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"
D22V5, binary
                   cls
clus                  0   1
  GPR172B MUTATED     2   1
  GPR172B WILD-TYPE 190  11
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR172B MUTATED      2    1
  GPR172B WILD-TYPE  190   11
   clus
vv  GPR172B MUTATED GPR172B WILD-TYPE
  0               2               190
  1               1                11
[1] 2 2
[1] FALSE
D22V6, binary
                   cls
clus                  0   1
  GPR172B MUTATED     4   0
  GPR172B WILD-TYPE 346  67
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR172B MUTATED      4    0
  GPR172B WILD-TYPE  346   67
    clus
vv   GPR172B MUTATED GPR172B WILD-TYPE
  M0               4               346
  M1               0                67
[1] 2 2
[1] FALSE
D22V7, binary
                   cls
clus                  0   1
  GPR172B MUTATED     3   1
  GPR172B WILD-TYPE 143 270
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR172B MUTATED      3    1
  GPR172B WILD-TYPE  143  270
        clus
vv       GPR172B MUTATED GPR172B WILD-TYPE
  FEMALE               3               143
  MALE                 1               270
[1] 2 2
[1] FALSE
D22V8, continuous
                   vv
clus                ASIAN BLACK OR AFRICAN AMERICAN WHITE
  GPR172B MUTATED       0                         0     4
  GPR172B WILD-TYPE     7                        14   386
D22V9, multiclass
                           clus
vv                          GPR172B MUTATED GPR172B WILD-TYPE
  ASIAN                                   0                 7
  BLACK OR AFRICAN AMERICAN               0                14
  WHITE                                   4               386
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D22V10, binary
                   cls
clus                  0   1
  GPR172B MUTATED     1   0
  GPR172B WILD-TYPE  20 265
[1] "tbl2"
                   cls
clus                [,1] [,2]
  GPR172B MUTATED      1    0
  GPR172B WILD-TYPE   20  265
                        clus
vv                       GPR172B MUTATED GPR172B WILD-TYPE
  HISPANIC OR LATINO                   1                20
  NOT HISPANIC OR LATINO               0               265
[1] 2 2
[1] FALSE

Clustering(23) Variable = EGFR MUTATION ANALYSIS
D23V1, survival
                sevent
clus2              0   1
  EGFR MUTATED     2   5
  EGFR WILD-TYPE 273 137
  EGFR MUTATED EGFR WILD-TYPE 
             7            410 
  EGFR MUTATED EGFR WILD-TYPE 
             5            137 
$`EGFR MUTATED`
TCGA-B0-4822 TCGA-B0-4849 TCGA-B0-5116 TCGA-B0-5713 TCGA-BP-4341 TCGA-BP-4354 
       36.53         2.27        21.60        61.32        52.24        33.99 
TCGA-CJ-4868 
       21.24 

$`EGFR WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        31.27        28.04         1.41         1.41         4.57 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 
        2.53         3.48        19.00        65.10         5.98         0.85 
TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 
       19.73         3.16        43.96         6.64         3.25        20.25 
TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 
       15.72        46.59         0.59         5.52        52.21        45.07 
TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       33.50        16.77         6.02        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       26.07        29.03        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       11.80        26.20         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       47.97        96.36        97.41        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 
       21.30        11.77        10.36        21.57         9.57        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        27.55        25.05        24.66        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.91        23.01        20.91        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.49 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 
       23.05        77.03        62.24        61.78        64.27        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 
       31.89        11.31        31.33        12.30        72.59        77.98 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
        5.98        44.15        41.75        71.80        48.07        13.15 
TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 
       10.82         5.33        61.97        60.59        56.91        68.38 
TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 
       11.64        15.78        48.95        36.53        36.39        10.98 
TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 
       37.25        36.95         6.71        47.97         6.94        71.41 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 
       63.62        58.68        60.30        61.22         6.74        57.40 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 
       14.24        48.89        49.38        45.50         7.23        47.11 
TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 
       53.65        14.93        36.07        33.34        46.45        31.30 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 
       25.81        36.95        27.22         3.88        46.45        16.47 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        5.82        45.07        30.64        41.62        18.51        38.70 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
       37.02        27.62        37.48        35.21        36.23        28.87 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
       48.10         6.35        79.30         1.78        74.20        30.64 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 
       52.27         9.63        62.86        74.40        38.30        42.44 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
       37.25        37.22        22.78        13.35        27.02        33.24 
TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
       31.79        23.47        13.41        24.62        33.47        19.82 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 
       44.55        34.95        31.27         0.95        59.84        46.55 
TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 
       63.25        73.22        14.17        75.88        65.69        54.61 
TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
       58.95        11.05        49.25        79.66        47.18        74.27 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
       75.06        77.36        64.27        71.87        66.21        61.91 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
       57.83        69.86        64.18        30.64        51.52        63.98 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
       68.55        26.93        50.01        24.66        27.65        39.45 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
       59.44        50.24        47.67        49.97        51.29        58.92 
TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 
       49.18        49.28        50.33        54.48        38.56        45.14 
TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 
        3.06         4.57        18.81        63.88        72.00        79.89 
TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 
       84.66        25.71        18.87        22.32        25.25        18.15 
TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 
       61.91        62.10        73.35        67.00        60.99        53.42 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
       75.58        62.66        83.77         7.36        64.57        92.02 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 
       81.83        85.78        66.31        78.18        74.66         1.35 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
       83.90       103.43        25.45        46.16         0.59        47.08 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 
       63.88        58.75        14.66        60.59        63.39         5.46 
TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 
       61.41        63.42        58.82         0.82        23.74        18.44 
TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 
       56.28        55.33        56.94        55.33        47.01        10.85 
TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 
       10.22        21.76        47.54        22.52         2.40         1.94 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 
       31.10        12.69        80.19        67.96        65.65        12.26 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 
       14.63        22.78        62.63        43.69        45.96        12.16 
TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 
       11.67        66.28        56.84        23.90        18.12         3.91 
TCGA-EU-5906 TCGA-EU-5907 
        6.77         4.18 

  EGFR MUTATED EGFR WILD-TYPE 
          2.27           0.07 
  EGFR MUTATED EGFR WILD-TYPE 
         61.32         120.59 
  EGFR MUTATED EGFR WILD-TYPE 
         33.99          37.43 
[1] "2.3 - 61.3 (34.0)"  "0.1 - 120.6 (37.4)"
[1] "hr=" "2.8"
D23V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  EGFR MUTATED         0        1         4        2
  EGFR WILD-TYPE     197       39       109       65
D23V3, multiclass
           clus
vv          EGFR MUTATED EGFR WILD-TYPE
  STAGE I              0            197
  STAGE II             1             39
  STAGE III            4            109
  STAGE IV             2             65
[1] 4 2
[1] 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
  EGFR MUTATED     0   1   5   1
  EGFR WILD-TYPE 202  48 155   5
D23V4, multiclass
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  T1            0            202
  T2            1             48
  T3            5            155
  T4            1              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"
D23V5, binary
                cls
clus               0   1
  EGFR MUTATED     3   1
  EGFR WILD-TYPE 189  11
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      3    1
  EGFR WILD-TYPE  189   11
   clus
vv  EGFR MUTATED EGFR WILD-TYPE
  0            3            189
  1            1             11
[1] 2 2
[1] FALSE
D23V6, binary
                cls
clus               0   1
  EGFR MUTATED     5   2
  EGFR WILD-TYPE 345  65
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      5    2
  EGFR WILD-TYPE  345   65
    clus
vv   EGFR MUTATED EGFR WILD-TYPE
  M0            5            345
  M1            2             65
[1] 2 2
[1] FALSE
D23V7, binary
                cls
clus               0   1
  EGFR MUTATED     1   6
  EGFR WILD-TYPE 145 265
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      1    6
  EGFR WILD-TYPE  145  265
        clus
vv       EGFR MUTATED EGFR WILD-TYPE
  FEMALE            1            145
  MALE              6            265
[1] 2 2
[1] FALSE
D23V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  EGFR MUTATED       0                         0     7
  EGFR WILD-TYPE     7                        14   383
D23V9, multiclass
                           clus
vv                          EGFR MUTATED EGFR WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             14
  WHITE                                7            383
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D23V10, binary
                cls
clus               0   1
  EGFR MUTATED     0   5
  EGFR WILD-TYPE  21 260
[1] "tbl2"
                cls
clus             [,1] [,2]
  EGFR MUTATED      0    5
  EGFR WILD-TYPE   21  260
                        clus
vv                       EGFR MUTATED EGFR WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            5            260
[1] 2 2
[1] FALSE

Clustering(24) Variable = IL1RAP MUTATION ANALYSIS
D24V1, survival
                  sevent
clus2                0   1
  IL1RAP MUTATED     1   3
  IL1RAP WILD-TYPE 274 139
  IL1RAP MUTATED IL1RAP WILD-TYPE 
               4              413 
  IL1RAP MUTATED IL1RAP WILD-TYPE 
               3              139 
$`IL1RAP MUTATED`
TCGA-B0-4693 TCGA-B0-4841 TCGA-B0-5698 TCGA-BP-4985 
        2.53         6.71        84.92        31.30 

$`IL1RAP WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 
       66.31        15.78        60.92        68.61        67.20        48.36 
TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
       42.08        58.49        48.69        28.73        22.45        37.58 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 
       38.40        31.27        28.04         1.41         1.41         4.57 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 
       29.03         2.27        36.85        70.52        20.94        43.30 
TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 
       11.24        11.90        25.32        18.51        15.09        10.95 
TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 
        8.05         2.24        21.86        15.95        62.89        90.87 
TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 
       90.48        52.54        30.48        29.95        19.30        35.90 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
       11.80        26.20        21.60         1.94        16.21        18.21 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 
       21.44        37.22        14.76       112.80        48.89       101.13 
TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5699 TCGA-B0-5701 
       15.78        46.68        56.78        60.33        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
       47.97        96.36        61.32        97.41        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       25.55        25.91        23.01        20.91        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.49        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       33.34        46.45        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 
       65.69        54.61        58.95        11.05        21.24        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
       24.66        27.65        39.45        59.44        50.24        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        63.88        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  IL1RAP MUTATED IL1RAP WILD-TYPE 
            2.53             0.07 
  IL1RAP MUTATED IL1RAP WILD-TYPE 
           84.92           120.59 
  IL1RAP MUTATED IL1RAP WILD-TYPE 
          19.005           37.380 
[1] "2.5 - 84.9 (19.0)"  "0.1 - 120.6 (37.4)"
[1] "hr=" "2.7"
D24V2, continuous
                  vv
clus               STAGE I STAGE II STAGE III STAGE IV
  IL1RAP MUTATED         1        0         2        1
  IL1RAP WILD-TYPE     196       40       111       66
D24V3, multiclass
           clus
vv          IL1RAP MUTATED IL1RAP WILD-TYPE
  STAGE I                1              196
  STAGE II               0               40
  STAGE III              2              111
  STAGE IV               1               66
[1] 4 2
[1] 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
  IL1RAP MUTATED     1   1   2   0
  IL1RAP WILD-TYPE 201  48 158   6
D24V4, multiclass
    clus
vv   IL1RAP MUTATED IL1RAP WILD-TYPE
  T1              1              201
  T2              1               48
  T3              2              158
  T4              0                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"
D24V5, binary
                  cls
clus                 0   1
  IL1RAP MUTATED     3   0
  IL1RAP WILD-TYPE 189  12
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RAP MUTATED      3    0
  IL1RAP WILD-TYPE  189   12
   clus
vv  IL1RAP MUTATED IL1RAP WILD-TYPE
  0              3              189
  1              0               12
[1] 2 2
[1] FALSE
D24V6, binary
                  cls
clus                 0   1
  IL1RAP MUTATED     3   1
  IL1RAP WILD-TYPE 347  66
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RAP MUTATED      3    1
  IL1RAP WILD-TYPE  347   66
    clus
vv   IL1RAP MUTATED IL1RAP WILD-TYPE
  M0              3              347
  M1              1               66
[1] 2 2
[1] FALSE
D24V7, binary
                  cls
clus                 0   1
  IL1RAP MUTATED     1   3
  IL1RAP WILD-TYPE 145 268
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RAP MUTATED      1    3
  IL1RAP WILD-TYPE  145  268
        clus
vv       IL1RAP MUTATED IL1RAP WILD-TYPE
  FEMALE              1              145
  MALE                3              268
[1] 2 2
[1] FALSE
D24V8, continuous
                  vv
clus               ASIAN BLACK OR AFRICAN AMERICAN WHITE
  IL1RAP MUTATED       0                         1     3
  IL1RAP WILD-TYPE     7                        13   387
D24V9, multiclass
                           clus
vv                          IL1RAP MUTATED IL1RAP WILD-TYPE
  ASIAN                                  0                7
  BLACK OR AFRICAN AMERICAN              1               13
  WHITE                                  3              387
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D24V10, binary
                  cls
clus                 0   1
  IL1RAP MUTATED     0   3
  IL1RAP WILD-TYPE  21 262
[1] "tbl2"
                  cls
clus               [,1] [,2]
  IL1RAP MUTATED      0    3
  IL1RAP WILD-TYPE   21  262
                        clus
vv                       IL1RAP MUTATED IL1RAP WILD-TYPE
  HISPANIC OR LATINO                  0               21
  NOT HISPANIC OR LATINO              3              262
[1] 2 2
[1] FALSE

Clustering(25) Variable = BCL6 MUTATION ANALYSIS
D25V1, survival
                sevent
clus2              0   1
  BCL6 MUTATED     3   2
  BCL6 WILD-TYPE 272 140
  BCL6 MUTATED BCL6 WILD-TYPE 
             5            412 
  BCL6 MUTATED BCL6 WILD-TYPE 
             2            140 
$`BCL6 MUTATED`
TCGA-A3-3387 TCGA-B0-5713 TCGA-BP-4169 TCGA-BP-5190 TCGA-CJ-4895 
       20.28        61.32        23.05        33.24        39.45 

$`BCL6 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
       18.87        28.31        65.52       109.91        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       31.27        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5812 TCGA-B2-3924 
       92.98       102.48        47.97        96.36        97.41        35.90 
TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        1.68        12.30        21.30        11.77        10.36        21.57 
TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        9.57        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       24.66        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.49        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        0.43        89.36        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       13.35        27.02        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 
       65.69        54.61        58.95        11.05        21.24        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       24.66        27.65        59.44        50.24        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4854 
       74.66         1.35        83.90       103.43        25.45        46.16 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 
        0.59        47.08        63.88        58.75        14.66        60.59 
TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
       63.39         5.46        61.41        63.42        58.82         0.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  BCL6 MUTATED BCL6 WILD-TYPE 
         20.28           0.07 
  BCL6 MUTATED BCL6 WILD-TYPE 
         61.32         120.59 
  BCL6 MUTATED BCL6 WILD-TYPE 
        33.240         37.315 
[1] "20.3 - 61.3 (33.2)" "0.1 - 120.6 (37.3)"
[1] "hr=" "1.4"
D25V2, continuous
                vv
clus             STAGE I STAGE II STAGE III STAGE IV
  BCL6 MUTATED         2        1         1        1
  BCL6 WILD-TYPE     195       39       112       66
D25V3, multiclass
           clus
vv          BCL6 MUTATED BCL6 WILD-TYPE
  STAGE I              2            195
  STAGE II             1             39
  STAGE III            1            112
  STAGE IV             1             66
[1] 4 2
[1] 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
  BCL6 MUTATED     2   1   2   0
  BCL6 WILD-TYPE 200  48 158   6
D25V4, multiclass
    clus
vv   BCL6 MUTATED BCL6 WILD-TYPE
  T1            2            200
  T2            1             48
  T3            2            158
  T4            0              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
  BCL6 MUTATED     3   0
  BCL6 WILD-TYPE 189  12
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL6 MUTATED      3    0
  BCL6 WILD-TYPE  189   12
   clus
vv  BCL6 MUTATED BCL6 WILD-TYPE
  0            3            189
  1            0             12
[1] 2 2
[1] FALSE
D25V6, binary
                cls
clus               0   1
  BCL6 MUTATED     4   1
  BCL6 WILD-TYPE 346  66
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL6 MUTATED      4    1
  BCL6 WILD-TYPE  346   66
    clus
vv   BCL6 MUTATED BCL6 WILD-TYPE
  M0            4            346
  M1            1             66
[1] 2 2
[1] FALSE
D25V7, binary
                cls
clus               0   1
  BCL6 MUTATED     2   3
  BCL6 WILD-TYPE 144 268
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL6 MUTATED      2    3
  BCL6 WILD-TYPE  144  268
        clus
vv       BCL6 MUTATED BCL6 WILD-TYPE
  FEMALE            2            144
  MALE              3            268
[1] 2 2
[1] FALSE
D25V8, continuous
                vv
clus             ASIAN BLACK OR AFRICAN AMERICAN WHITE
  BCL6 MUTATED       0                         0     5
  BCL6 WILD-TYPE     7                        14   385
D25V9, multiclass
                           clus
vv                          BCL6 MUTATED BCL6 WILD-TYPE
  ASIAN                                0              7
  BLACK OR AFRICAN AMERICAN            0             14
  WHITE                                5            385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D25V10, binary
                cls
clus               0   1
  BCL6 MUTATED     0   4
  BCL6 WILD-TYPE  21 261
[1] "tbl2"
                cls
clus             [,1] [,2]
  BCL6 MUTATED      0    4
  BCL6 WILD-TYPE   21  261
                        clus
vv                       BCL6 MUTATED BCL6 WILD-TYPE
  HISPANIC OR LATINO                0             21
  NOT HISPANIC OR LATINO            4            261
[1] 2 2
[1] FALSE

Clustering(26) Variable = NFAT5 MUTATION ANALYSIS
D26V1, survival
                 sevent
clus2               0   1
  NFAT5 MUTATED     4   2
  NFAT5 WILD-TYPE 271 140
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              6             411 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
              2             140 
$`NFAT5 MUTATED`
TCGA-AK-3431 TCGA-B0-4707 TCGA-B0-4718 TCGA-B0-5106 TCGA-B2-5633 TCGA-CW-6093 
       60.92        19.73        20.25        52.54        11.77       103.43 

$`NFAT5 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 
       18.87        28.31        65.52        20.28       109.91        73.08 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       66.31        15.78        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       31.27        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4710 
        3.48        19.00        65.10         5.98         0.85         3.16 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
       43.96         6.64         3.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
       30.48        29.95        19.30        35.90        11.80        26.20 
TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 
       21.60         1.94        16.21        18.21        21.44        37.22 
TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
       14.76       112.80        48.89       101.13        15.78        46.68 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 
       56.78        60.33        84.92        90.12        56.94        52.77 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       39.55       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       96.36        61.32        97.41        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 
       21.30        10.36        21.57         9.57        23.31        16.80 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 
       27.16        27.55        25.05        24.66        25.55        25.91 
TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
       23.01        20.91        23.74        27.02         0.85        24.23 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
       17.16        16.60         6.38        14.27         0.49        34.39 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
       14.30       111.02        85.51        94.72        90.28       101.06 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
       93.34        32.61        99.85         0.43        89.36        23.05 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 
       77.03        62.24        61.78        64.27        53.42        27.78 
TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
       62.07        80.68         0.07        93.99        18.48        52.24 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 
       74.17        62.86        49.84        49.08        44.94        12.23 
TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 
       31.89        11.31        33.99        31.33        12.30        72.59 
TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 
       77.98         5.98        44.15        41.75        71.80        48.07 
TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 
       13.15        10.82         5.33        61.97        60.59        56.91 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 
       68.38        11.64        15.78        48.95        36.53        36.39 
TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 
       10.98        37.25        36.95         6.71        47.97         6.94 
TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 
       71.41        63.62        58.68        60.30        61.22         6.74 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
       57.40        14.24        48.89        49.38        45.50         7.23 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
       47.11        53.65        14.93        36.07        33.34        46.45 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
       31.30        25.81        36.95        27.22         3.88        46.45 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 
       16.47         5.82        45.07        30.64        41.62        18.51 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 
       38.70        37.02        27.62        37.48        35.21        36.23 
TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 
       28.87        48.10         6.35        79.30         1.78        74.20 
TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5182 
       30.64        52.27         9.63        62.86        74.40        38.30 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
       42.44        37.25        37.22        22.78        13.35        27.02 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
       33.24        31.79        23.47        13.41        24.62        33.47 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
       19.82        44.55        34.95        31.27         0.95        59.84 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
       46.55        63.25        73.22        14.17        75.88        65.69 
TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 
       54.61        58.95        11.05        21.24        49.25        79.66 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
       47.18        74.27        75.06        77.36        64.27        71.87 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 
       66.21        61.91        57.83        69.86        64.18        30.64 
TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 
       51.52        63.98        68.55        26.93        50.01        24.66 
TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 
       27.65        39.45        59.44        50.24        47.67        49.97 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 
       51.29        58.92        49.18        49.28        50.33        54.48 
TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 
       38.56        45.14         3.06         4.57        18.81        63.88 
TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 
       72.00        79.89        84.66        25.71        18.87        22.32 
TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
       25.25        18.15        61.91        62.10        73.35        67.00 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
       60.99        53.42        75.58        62.66        83.77         7.36 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 TCGA-CW-5589 
       64.57        92.02        81.83        85.78        66.31        78.18 
TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 
       74.66         1.35        83.90        25.45        46.16         0.59 
TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
       47.08        63.88        58.75        14.66        60.59        63.39 
TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 
        5.46        61.41        63.42        58.82         0.82        23.74 
TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
       18.44        56.28        55.33        56.94        55.33        47.01 
TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 
       10.85        10.22        21.76        47.54        22.52         2.40 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 
        1.94        31.10        12.69        80.19        67.96        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  NFAT5 MUTATED NFAT5 WILD-TYPE 
          11.77            0.07 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
         103.43          120.59 
  NFAT5 MUTATED NFAT5 WILD-TYPE 
         36.395          37.250 
[1] "11.8 - 103.4 (36.4)" "0.1 - 120.6 (37.2)" 
[1] "hr=" "1.1"
D26V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  NFAT5 MUTATED         3        1         2        0
  NFAT5 WILD-TYPE     194       39       111       67
D26V3, multiclass
           clus
vv          NFAT5 MUTATED NFAT5 WILD-TYPE
  STAGE I               3             194
  STAGE II              1              39
  STAGE III             2             111
  STAGE IV              0              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
  NFAT5 MUTATED     3   1   2   0
  NFAT5 WILD-TYPE 199  48 158   6
D26V4, multiclass
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  T1             3             199
  T2             1              48
  T3             2             158
  T4             0               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"
D26V5, binary
                 cls
clus                0   1
  NFAT5 MUTATED     2   0
  NFAT5 WILD-TYPE 190  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      2    0
  NFAT5 WILD-TYPE  190   12
   clus
vv  NFAT5 MUTATED NFAT5 WILD-TYPE
  0             2             190
  1             0              12
[1] 2 2
[1] FALSE
D26V6, binary
                 cls
clus                0   1
  NFAT5 MUTATED     6   0
  NFAT5 WILD-TYPE 344  67
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      6    0
  NFAT5 WILD-TYPE  344   67
    clus
vv   NFAT5 MUTATED NFAT5 WILD-TYPE
  M0             6             344
  M1             0              67
[1] 2 2
[1] FALSE
D26V7, binary
                 cls
clus                0   1
  NFAT5 MUTATED     1   5
  NFAT5 WILD-TYPE 145 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      1    5
  NFAT5 WILD-TYPE  145  266
        clus
vv       NFAT5 MUTATED NFAT5 WILD-TYPE
  FEMALE             1             145
  MALE               5             266
[1] 2 2
[1] FALSE
D26V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  NFAT5 MUTATED       0                         0     6
  NFAT5 WILD-TYPE     7                        14   384
D26V9, multiclass
                           clus
vv                          NFAT5 MUTATED NFAT5 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              14
  WHITE                                 6             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"
D26V10, binary
                 cls
clus                0   1
  NFAT5 MUTATED     0   6
  NFAT5 WILD-TYPE  21 259
[1] "tbl2"
                 cls
clus              [,1] [,2]
  NFAT5 MUTATED      0    6
  NFAT5 WILD-TYPE   21  259
                        clus
vv                       NFAT5 MUTATED NFAT5 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             6             259
[1] 2 2
[1] FALSE

Clustering(27) Variable = LARP1 MUTATION ANALYSIS
D27V1, survival
                 sevent
clus2               0   1
  LARP1 MUTATED     3   2
  LARP1 WILD-TYPE 272 140
  LARP1 MUTATED LARP1 WILD-TYPE 
              5             412 
  LARP1 MUTATED LARP1 WILD-TYPE 
              2             140 
$`LARP1 MUTATED`
TCGA-A3-3346 TCGA-B2-5633 TCGA-BP-5168 TCGA-CJ-4885 TCGA-CZ-5453 
        4.50        11.77        48.10        69.86         0.82 

$`LARP1 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3357 
       48.59        36.36        37.38        52.93        45.53        88.37 
TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 
       42.97        51.25        10.49        28.70        74.63        74.76 
TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 
       24.16        53.29        35.18        20.71        18.64        18.87 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
       28.31        65.52        20.28       109.91        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       31.27        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 
        3.16        43.96         6.64         3.25        20.25        15.72 
TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 
       46.59         0.59         5.52        52.21        45.07        33.50 
TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
       16.77         6.02        36.53        14.93        54.48        29.10 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 
       10.09        78.44        40.70        45.30        27.42        53.88 
TCGA-B0-4841 TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 
        6.71        56.68        11.64        10.29        65.29        39.45 
TCGA-B0-4847 TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 
       26.07        29.03         2.27        36.85        70.52        20.94 
TCGA-B0-5077 TCGA-B0-5080 TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
       43.30        11.24        11.90        25.32        18.51        15.09 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 
       10.95         8.05         2.24        21.86        15.95        62.89 
TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 
       90.87        90.48        52.54        30.48        29.95        19.30 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 
       35.90        11.80        26.20        21.60         1.94        16.21 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 
       18.21        21.44        37.22        14.76       112.80        48.89 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
      101.13        15.78        46.68        56.78        60.33        84.92 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
       90.12        56.94        52.77        39.55       120.59        79.36 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 
       92.98       102.48        47.97        96.36        61.32        97.41 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5635 TCGA-B2-5641 
       35.90         1.68        12.30        21.30        10.36        21.57 
TCGA-B4-5377 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
        9.57        23.31        16.80        27.16        27.55        25.05 
TCGA-B8-4154 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 
       24.66        25.55        25.91        23.01        20.91        23.74 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
       27.02         0.85        24.23        17.16        16.60         6.38 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 
       14.27         0.49        34.39        14.30       111.02        85.51 
TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 
       94.72        90.28       101.06        93.34        32.61        99.85 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 
        0.43        89.36        23.05        77.03        62.24        61.78 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 
       64.27        53.42        27.78        62.07        80.68         0.07 
TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 
       93.99        18.48        52.24        74.17        62.86        49.84 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 
       49.08        44.94        12.23        31.89        11.31        33.99 
TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 
       31.33        12.30        72.59        77.98         5.98        44.15 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 
       41.75        71.80        48.07        13.15        10.82         5.33 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 
       61.97        60.59        56.91        68.38        11.64        15.78 
TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
       48.95        36.53        36.39        10.98        37.25        36.95 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 
        6.71        47.97         6.94        71.41        63.62        58.68 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 
       60.30        61.22         6.74        57.40        14.24        48.89 
TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 
       49.38        45.50         7.23        47.11        53.65        14.93 
TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 
       36.07        33.34        46.45        31.30        25.81        36.95 
TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 
       27.22         3.88        46.45        16.47         5.82        45.07 
TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
       30.64        41.62        18.51        38.70        37.02        27.62 
TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5169 TCGA-BP-5170 
       37.48        35.21        36.23        28.87         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4886 
       64.27        71.87        66.21        61.91        57.83        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
       24.66        27.65        39.45        59.44        50.24        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        63.88        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
       23.74        18.44        56.28        55.33        56.94        55.33 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 
       47.01        10.85        10.22        21.76        47.54        22.52 
TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 
        2.40         1.94        31.10        12.69        80.19        67.96 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
       65.65        12.26        14.63        22.78        62.63        43.69 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 
       45.96        12.16        11.67        66.28        56.84        23.90 
TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       18.12         3.91         6.77         4.18 

  LARP1 MUTATED LARP1 WILD-TYPE 
           0.82            0.07 
  LARP1 MUTATED LARP1 WILD-TYPE 
          69.86          120.59 
  LARP1 MUTATED LARP1 WILD-TYPE 
         11.770          37.315 
[1] "0.8 - 69.9 (11.8)"  "0.1 - 120.6 (37.3)"
[1] "hr=" "1.8"
D27V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  LARP1 MUTATED         3        1         0        1
  LARP1 WILD-TYPE     194       39       113       66
D27V3, multiclass
           clus
vv          LARP1 MUTATED LARP1 WILD-TYPE
  STAGE I               3             194
  STAGE II              1              39
  STAGE III             0             113
  STAGE IV              1              66
[1] 4 2
[1] 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
  LARP1 MUTATED     3   1   1   0
  LARP1 WILD-TYPE 199  48 159   6
D27V4, multiclass
    clus
vv   LARP1 MUTATED LARP1 WILD-TYPE
  T1             3             199
  T2             1              48
  T3             1             159
  T4             0               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"
D27V5, binary
                 cls
clus                0   1
  LARP1 MUTATED     1   0
  LARP1 WILD-TYPE 191  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      1    0
  LARP1 WILD-TYPE  191   12
   clus
vv  LARP1 MUTATED LARP1 WILD-TYPE
  0             1             191
  1             0              12
[1] 2 2
[1] FALSE
D27V6, binary
                 cls
clus                0   1
  LARP1 MUTATED     4   1
  LARP1 WILD-TYPE 346  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      4    1
  LARP1 WILD-TYPE  346   66
    clus
vv   LARP1 MUTATED LARP1 WILD-TYPE
  M0             4             346
  M1             1              66
[1] 2 2
[1] FALSE
D27V7, binary
                 cls
clus                0   1
  LARP1 MUTATED     0   5
  LARP1 WILD-TYPE 146 266
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      0    5
  LARP1 WILD-TYPE  146  266
        clus
vv       LARP1 MUTATED LARP1 WILD-TYPE
  FEMALE             0             146
  MALE               5             266
[1] 2 2
[1] FALSE
D27V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  LARP1 MUTATED       0                         0     5
  LARP1 WILD-TYPE     7                        14   385
D27V9, multiclass
                           clus
vv                          LARP1 MUTATED LARP1 WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              14
  WHITE                                 5             385
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D27V10, binary
                 cls
clus                0   1
  LARP1 MUTATED     0   2
  LARP1 WILD-TYPE  21 263
[1] "tbl2"
                 cls
clus              [,1] [,2]
  LARP1 MUTATED      0    2
  LARP1 WILD-TYPE   21  263
                        clus
vv                       LARP1 MUTATED LARP1 WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             2             263
[1] 2 2
[1] FALSE

Clustering(28) Variable = KIAA1751 MUTATION ANALYSIS
D28V1, survival
                    sevent
clus2                  0   1
  KIAA1751 MUTATED     4   2
  KIAA1751 WILD-TYPE 271 140
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 6                411 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 2                140 
$`KIAA1751 MUTATED`
TCGA-AK-3428 TCGA-AK-3430 TCGA-AK-3434 TCGA-B0-5703 TCGA-CZ-5467 TCGA-CZ-5984 
       73.08        15.78        68.61        39.55         2.40        67.96 

$`KIAA1751 WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3429 
       18.87        28.31        65.52        20.28       109.91        66.31 
TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3451 
       60.92        67.20        48.36        42.08        58.49        48.69 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
       28.73        22.45        37.58        38.40        31.27        28.04 
TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4697 
        1.41         1.41         4.57         2.53         3.48        19.00 
TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 
       65.10         5.98         0.85        19.73         3.16        43.96 
TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 
        6.64         3.25        20.25        15.72        46.59         0.59 
TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 
        5.52        52.21        45.07        33.50        16.77         6.02 
TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 
       36.53        14.93        54.48        29.10        10.09        78.44 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
       40.70        45.30        27.42        53.88         6.71        56.68 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
       11.64        10.29        65.29        39.45        26.07        29.03 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
        2.27        36.85        70.52        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        21.60         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 
       52.77       120.59        79.36        92.98       102.48        47.97 
TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
       96.36        61.32        97.41        35.90         1.68        12.30 
TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 TCGA-B8-4143 
       21.30        11.77        10.36        21.57         9.57        23.31 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4620 
       16.80        27.16        27.55        25.05        24.66        25.55 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 
       25.91        23.01        20.91        23.74        27.02         0.85 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 
       24.23        17.16        16.60         6.38        14.27         0.49 
TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 
       34.39        14.30       111.02        85.51        94.72        90.28 
TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 
      101.06        93.34        32.61        99.85         0.43        89.36 
TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4326 
       23.05        77.03        62.24        61.78        64.27        53.42 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 
       27.78        62.07        80.68         0.07        93.99        18.48 
TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
       52.24        74.17        62.86        49.84        49.08        44.94 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 
       12.23        31.89        11.31        33.99        31.33        12.30 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 
       72.59        77.98         5.98        44.15        41.75        71.80 
TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 
       48.07        13.15        10.82         5.33        61.97        60.59 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 
       56.91        68.38        11.64        15.78        48.95        36.53 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
       36.39        10.98        37.25        36.95         6.71        47.97 
TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 
        6.94        71.41        63.62        58.68        60.30        61.22 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 
        6.74        57.40        14.24        48.89        49.38        45.50 
TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 
        7.23        47.11        53.65        14.93        36.07        33.34 
TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 
       46.45        31.30        25.81        36.95        27.22         3.88 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
       46.45        16.47         5.82        45.07        30.64        41.62 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
       18.51        38.70        37.02        27.62        37.48        35.21 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
       36.23        28.87        48.10         6.35        79.30         1.78 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
       74.20        30.64        52.27         9.63        62.86        74.40 
TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 
       38.30        42.44        37.25        37.22        22.78        13.35 
TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 
       27.02        33.24        31.79        23.47        13.41        24.62 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
       33.47        19.82        44.55        34.95        31.27         0.95 
TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 
       59.84        46.55        63.25        73.22        14.17        75.88 
TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4870 
       65.69        54.61        58.95        11.05        21.24        49.25 
TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
       79.66        47.18        74.27        75.06        77.36        64.27 
TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 
       71.87        66.21        61.91        57.83        69.86        64.18 
TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 
       30.64        51.52        63.98        68.55        26.93        50.01 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4901 
       24.66        27.65        39.45        59.44        50.24        47.67 
TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
       49.97        51.29        58.92        49.18        49.28        50.33 
TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 
       54.48        38.56        45.14         3.06         4.57        18.81 
TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 
       63.88        72.00        79.89        84.66        25.71        18.87 
TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
       22.32        25.25        18.15        61.91        62.10        73.35 
TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 
       67.00        60.99        53.42        75.58        62.66        83.77 
TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5588 
        7.36        64.57        92.02        81.83        85.78        66.31 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4853 
       78.18        74.66         1.35        83.90       103.43        25.45 
TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4861 
       46.16         0.59        47.08        63.88        58.75        14.66 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 
       60.59        63.39         5.46        61.41        63.42        58.82 
TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 
        0.82        23.74        18.44        56.28        55.33        56.94 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5465 
       55.33        47.01        10.85        10.22        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5985 
       22.52         1.94        31.10        12.69        80.19        65.65 
TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
       12.26        14.63        22.78        62.63        43.69        45.96 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
       12.16        11.67        66.28        56.84        23.90        18.12 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
        3.91         6.77         4.18 

  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
              2.40               0.07 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
             73.08             120.59 
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
            53.755             37.250 
[1] "2.4 - 73.1 (53.8)"  "0.1 - 120.6 (37.2)"
[1] "hr=" "1.1"
D28V2, continuous
                    vv
clus                 STAGE I STAGE II STAGE III STAGE IV
  KIAA1751 MUTATED         3        0         3        0
  KIAA1751 WILD-TYPE     194       40       110       67
D28V3, multiclass
           clus
vv          KIAA1751 MUTATED KIAA1751 WILD-TYPE
  STAGE I                  3                194
  STAGE II                 0                 40
  STAGE III                3                110
  STAGE IV                 0                 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
  KIAA1751 MUTATED     3   0   3   0
  KIAA1751 WILD-TYPE 199  49 157   6
D28V4, multiclass
    clus
vv   KIAA1751 MUTATED KIAA1751 WILD-TYPE
  T1                3                199
  T2                0                 49
  T3                3                157
  T4                0                  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"
D28V5, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     4   1
  KIAA1751 WILD-TYPE 188  11
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      4    1
  KIAA1751 WILD-TYPE  188   11
   clus
vv  KIAA1751 MUTATED KIAA1751 WILD-TYPE
  0                4                188
  1                1                 11
[1] 2 2
[1] FALSE
D28V6, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     6   0
  KIAA1751 WILD-TYPE 344  67
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      6    0
  KIAA1751 WILD-TYPE  344   67
    clus
vv   KIAA1751 MUTATED KIAA1751 WILD-TYPE
  M0                6                344
  M1                0                 67
[1] 2 2
[1] FALSE
D28V7, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     1   5
  KIAA1751 WILD-TYPE 145 266
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      1    5
  KIAA1751 WILD-TYPE  145  266
        clus
vv       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  FEMALE                1                145
  MALE                  5                266
[1] 2 2
[1] FALSE
D28V8, continuous
[1] "Remove cluster labels:" "KIAA1751 MUTATED"      
clus
  KIAA1751 MUTATED KIAA1751 WILD-TYPE 
                 1                 22 
        TCGA-B0-4838         TCGA-B4-5377         TCGA-CZ-4854 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-4856         TCGA-CZ-4858         TCGA-CZ-4861 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-4862         TCGA-CZ-5456         TCGA-CZ-5457 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-CZ-5465         TCGA-CZ-5469         TCGA-CZ-5982 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-DV-5565         TCGA-DV-5566         TCGA-DV-5568 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-DV-5569         TCGA-DV-5574         TCGA-DV-5575 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-DV-5576         TCGA-EU-5904         TCGA-EU-5905 
"KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" "KIAA1751 WILD-TYPE" 
        TCGA-EU-5907 
"KIAA1751 WILD-TYPE" 
                    vv
clus                 ASIAN BLACK OR AFRICAN AMERICAN WHITE
  KIAA1751 MUTATED       0                         0     6
  KIAA1751 WILD-TYPE     7                        14   384
D28V9, multiclass
                           clus
vv                          KIAA1751 MUTATED KIAA1751 WILD-TYPE
  ASIAN                                    0                  7
  BLACK OR AFRICAN AMERICAN                0                 14
  WHITE                                    6                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"
D28V10, binary
                    cls
clus                   0   1
  KIAA1751 MUTATED     0   5
  KIAA1751 WILD-TYPE  21 260
[1] "tbl2"
                    cls
clus                 [,1] [,2]
  KIAA1751 MUTATED      0    5
  KIAA1751 WILD-TYPE   21  260
                        clus
vv                       KIAA1751 MUTATED KIAA1751 WILD-TYPE
  HISPANIC OR LATINO                    0                 21
  NOT HISPANIC OR LATINO                5                260
[1] 2 2
[1] FALSE

Clustering(29) Variable = INSRR MUTATION ANALYSIS
D29V1, survival
                 sevent
clus2               0   1
  INSRR MUTATED     1   3
  INSRR WILD-TYPE 274 139
  INSRR MUTATED INSRR WILD-TYPE 
              4             413 
  INSRR MUTATED INSRR WILD-TYPE 
              3             139 
$`INSRR MUTATED`
TCGA-A3-3387 TCGA-B0-4713 TCGA-B0-4945 TCGA-CZ-5462 
       20.28         6.64        70.52        10.22 

$`INSRR WILD-TYPE`
TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 
        0.53        39.16        49.08        49.02        37.15        49.58 
TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
       48.59        36.36        37.38         4.50        52.93        45.53 
TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 
       88.37        42.97        51.25        10.49        28.70        74.63 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 
       74.76        24.16        53.29        35.18        20.71        18.64 
TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3425 TCGA-AK-3428 TCGA-AK-3429 
       18.87        28.31        65.52       109.91        73.08        66.31 
TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3444 TCGA-AK-3445 
       15.78        60.92        68.61        67.20        48.36        42.08 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 
       58.49        48.69        28.73        22.45        37.58        38.40 
TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 
       31.27        28.04         1.41         1.41         4.57         2.53 
TCGA-B0-4694 TCGA-B0-4697 TCGA-B0-4700 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 
        3.48        19.00        65.10         5.98         0.85        19.73 
TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
        3.16        43.96         3.25        20.25        15.72        46.59 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
        0.59         5.52        52.21        45.07        33.50        16.77 
TCGA-B0-4819 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 
        6.02        36.53        14.93        54.48        29.10        10.09 
TCGA-B0-4833 TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 
       78.44        40.70        45.30        27.42        53.88         6.71 
TCGA-B0-4842 TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 
       56.68        11.64        10.29        65.29        39.45        26.07 
TCGA-B0-4848 TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
       29.03         2.27        36.85        20.94        43.30        11.24 
TCGA-B0-5081 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 
       11.90        25.32        18.51        15.09        10.95         8.05 
TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
        2.24        21.86        15.95        62.89        90.87        90.48 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
       52.54        30.48        29.95        19.30        35.90        11.80 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 
       26.20        21.60         1.94        16.21        18.21        21.44 
TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 
       37.22        14.76       112.80        48.89       101.13        15.78 
TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 
       46.68        56.78        60.33        84.92        90.12        56.94 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
       52.77        39.55       120.59        79.36        92.98       102.48 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4098 
       47.97        96.36        61.32        97.41        35.90         1.68 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5377 
       12.30        21.30        11.77        10.36        21.57         9.57 
TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
       23.31        16.80        27.16        27.55        25.05        24.66 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5163 
       25.55        25.91        23.01        20.91        23.74        27.02 
TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 
        0.85        24.23        17.16        16.60         6.38        14.27 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
        0.49        34.39        14.30       111.02        85.51        94.72 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
       90.28       101.06        93.34        32.61        99.85         0.43 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
       89.36        23.05        77.03        62.24        61.78        64.27 
TCGA-BP-4326 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4337 TCGA-BP-4338 
       53.42        27.78        62.07        80.68         0.07        93.99 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4345 TCGA-BP-4346 
       18.48        52.24        74.17        62.86        49.84        49.08 
TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4354 TCGA-BP-4355 
       44.94        12.23        31.89        11.31        33.99        31.33 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 
       12.30        72.59        77.98         5.98        44.15        41.75 
TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 
       71.80        48.07        13.15        10.82         5.33        61.97 
TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4787 TCGA-BP-4789 
       60.59        56.91        68.38        11.64        15.78        48.95 
TCGA-BP-4790 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 
       36.53        36.39        10.98        37.25        36.95         6.71 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
       47.97         6.94        71.41        63.62        58.68        60.30 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 
       61.22         6.74        57.40        14.24        48.89        49.38 
TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 
       45.50         7.23        47.11        53.65        14.93        36.07 
TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 
       33.34        46.45        31.30        25.81        36.95        27.22 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 
        3.88        46.45        16.47         5.82        45.07        30.64 
TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
       41.62        18.51        38.70        37.02        27.62        37.48 
TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 
       35.21        36.23        28.87        48.10         6.35        79.30 
TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 
        1.78        74.20        30.64        52.27         9.63        62.86 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
       74.40        38.30        42.44        37.25        37.22        22.78 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
       13.35        27.02        33.24        31.79        23.47        13.41 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
       24.62        33.47        19.82        44.55        34.95        31.27 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
        0.95        59.84        46.55        63.25        73.22        14.17 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 
       75.88        65.69        54.61        58.95        11.05        21.24 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
       49.25        79.66        47.18        74.27        75.06        77.36 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
       64.27        71.87        66.21        61.91        57.83        69.86 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
       64.18        30.64        51.52        63.98        68.55        26.93 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
       50.01        24.66        27.65        39.45        59.44        50.24 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 
       47.67        49.97        51.29        58.92        49.18        49.28 
TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 
       50.33        54.48        38.56        45.14         3.06         4.57 
TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 
       18.81        63.88        72.00        79.89        84.66        25.71 
TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 
       18.87        22.32        25.25        18.15        61.91        62.10 
TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 
       73.35        67.00        60.99        53.42        75.58        62.66 
TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
       83.77         7.36        64.57        92.02        81.83        85.78 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6090 TCGA-CW-6093 
       66.31        78.18        74.66         1.35        83.90       103.43 
TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 
       25.45        46.16         0.59        47.08        63.88        58.75 
TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
       14.66        60.59        63.39         5.46        61.41        63.42 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
       58.82         0.82        23.74        18.44        56.28        55.33 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 
       56.94        55.33        47.01        10.85        21.76        47.54 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
       22.52         2.40         1.94        31.10        12.69        80.19 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
       67.96        65.65        12.26        14.63        22.78        62.63 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5574 TCGA-DV-5575 
       43.69        45.96        12.16        11.67        66.28        56.84 
TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 
       23.90        18.12         3.91         6.77         4.18 

  INSRR MUTATED INSRR WILD-TYPE 
           6.64            0.07 
  INSRR MUTATED INSRR WILD-TYPE 
          70.52          120.59 
  INSRR MUTATED INSRR WILD-TYPE 
          15.25           37.38 
[1] "6.6 - 70.5 (15.2)"  "0.1 - 120.6 (37.4)"
[1] "hr=" "3.4"
D29V2, continuous
                 vv
clus              STAGE I STAGE II STAGE III STAGE IV
  INSRR MUTATED         2        0         1        1
  INSRR WILD-TYPE     195       40       112       66
D29V3, multiclass
           clus
vv          INSRR MUTATED INSRR WILD-TYPE
  STAGE I               2             195
  STAGE II              0              40
  STAGE III             1             112
  STAGE IV              1              66
[1] 4 2
[1] 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
  INSRR MUTATED     3   0   1   0
  INSRR WILD-TYPE 199  49 159   6
D29V4, multiclass
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  T1             3             199
  T2             0              49
  T3             1             159
  T4             0               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"
D29V5, binary
                 cls
clus                0   1
  INSRR MUTATED     2   0
  INSRR WILD-TYPE 190  12
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED      2    0
  INSRR WILD-TYPE  190   12
   clus
vv  INSRR MUTATED INSRR WILD-TYPE
  0             2             190
  1             0              12
[1] 2 2
[1] FALSE
D29V6, binary
                 cls
clus                0   1
  INSRR MUTATED     3   1
  INSRR WILD-TYPE 347  66
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED      3    1
  INSRR WILD-TYPE  347   66
    clus
vv   INSRR MUTATED INSRR WILD-TYPE
  M0             3             347
  M1             1              66
[1] 2 2
[1] FALSE
D29V7, binary
                 cls
clus                0   1
  INSRR MUTATED     2   2
  INSRR WILD-TYPE 144 269
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED      2    2
  INSRR WILD-TYPE  144  269
        clus
vv       INSRR MUTATED INSRR WILD-TYPE
  FEMALE             2             144
  MALE               2             269
[1] 2 2
[1] FALSE
D29V8, continuous
                 vv
clus              ASIAN BLACK OR AFRICAN AMERICAN WHITE
  INSRR MUTATED       0                         0     4
  INSRR WILD-TYPE     7                        14   386
D29V9, multiclass
                           clus
vv                          INSRR MUTATED INSRR WILD-TYPE
  ASIAN                                 0               7
  BLACK OR AFRICAN AMERICAN             0              14
  WHITE                                 4             386
[1] 3 2
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D29V10, binary
                 cls
clus                0   1
  INSRR MUTATED     0   3
  INSRR WILD-TYPE  21 262
[1] "tbl2"
                 cls
clus              [,1] [,2]
  INSRR MUTATED      0    3
  INSRR WILD-TYPE   21  262
                        clus
vv                       INSRR MUTATED INSRR WILD-TYPE
  HISPANIC OR LATINO                 0              21
  NOT HISPANIC OR LATINO             3             262
[1] 2 2
[1] FALSE
