[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"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[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_mergedClustering/KIRC-TP/11590644/KIRC-TP.mergedcluster.txt"

nPatients in clinical file=525, in cluster file=537, common to both=525
[1]  12 525
[1] "MRNA_CNMF"
[1] 3
 1  2  3 
34 24 14 
 1  2  3 
34 24 14 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
12 12  4 11 13  9 11 
 1  2  3  4  5  6  7 
12 12  4 11 13  9 11 
[1] "CN_CNMF"
[1] 3
  1   2   3 
232 131 153 
  1   2   3 
232 131 153 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
122  76 109 
  1   2   3 
122  76 109 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4   5   6 
108  62  77  81  81  45 
  1   2   3   4   5   6 
108  62  77  81  81  45 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
122 200 132 
  1   2   3 
122 200 132 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
107 218 194 
  1   2   3 
107 218 194 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
162 232 125 
  1   2   3 
162 232 125 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
121 201 182 
  1   2   3 
121 201 182 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
142 134 191  37 
  1   2   3   4 
142 134 191  37 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
30 22 49 35 
 1  2  3  4 
30 22 49 35 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
32 56 48 
 1  2  3 
32 56 48 
[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 525 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-6D-AA2E TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 
         267         1120         1436           16           NA          735 
TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 
        1493         1491         1130         1508         1478         1106 
TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3328 TCGA-A3-3329 TCGA-A3-3331 
        1186          751         1137         1385          706         1485 
TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 
         665         1043          945           NA         1610         1385 
TCGA-A3-3351 TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
         910           NA         2688         1307         2504         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
         319          873         2270         2274          735         1621 
TCGA-A3-3374 TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 
        1314         1070          630          567          574          861 
TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A6NJ TCGA-A3-A6NL TCGA-A3-A8CQ TCGA-A3-A8OX 
        1993          617           NA           NA            3           NA 
TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 
        3343           NA         2566         2223         2017          480 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
        1853         2192         2087         2044         1745         1423 
TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 
        1471         1280         1217         1779         1481         1397 
TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 
         874           NA         1143         1168          951          853 
TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 
         369         1238           43           NA           NA           NA 
TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 
          NA           NA           NA           NA           NA          110 
TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 
          NA           NA           NA           26           NA           96 
TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 
          NA           NA           NA          616           NA           NA 
TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 
          18           NA           NA           NA           NA           NA 
TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 
         183           NA           NA           NA           NA           NA 
TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 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-B0-5083 TCGA-B0-5084 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 
         665           NA           NA           NA           NA           NA 
TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 
          NA           NA          911           NA         1092          359 
TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 
         797          657          535           59          493          554 
TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 
         652         1132          449         2408         3431         1487 
TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 
        3076           NA         1420         1727         1835         2583 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 
        2741         1082         1732         1605         1203         3668 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        2414         2828         3117         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 
        1865         2963          992         1092           51          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 TCGA-B2-5639 
         648          952          358          315          919          417 
TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 
         656          507          291          175            7           38 
TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 
          16          141          166           11            7           NA 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 
         511          826          838          762          750          523 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 
         777          788          700          636          722           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 
         822           26          737          522          505          194 
TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54E 
         434           15         1046          435          830          909 
TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J TCGA-B8-A7U6 
         519           53          256          150          528          110 
TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4162 
          24         3377           NA         2881         2746         3074 
TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 
        2839           NA         3037           13         2718          701 
TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4177 TCGA-BP-4325 
          NA         1893         1879         1955         1670         2964 
TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4331 TCGA-BP-4332 
        1625           NA          845         1888           NA         1133 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 TCGA-BP-4340 TCGA-BP-4341 
         645          461           NA         2859           NA           NA 
TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4345 TCGA-BP-4346 TCGA-BP-4347 
          NA           NA         1666         1516           NA         1367 
TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 TCGA-BP-4354 TCGA-BP-4355 
         372          970           NA           NA           NA           NA 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4761 TCGA-BP-4762 
         374         2208         2372         2361          182           NA 
TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4769 TCGA-BP-4770 
          NA         2184         1462          400         1876           NA 
TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
          NA         1885         1843          411         1731         2080 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 TCGA-BP-4790 TCGA-BP-4795 
         354         1854           NA         1489           NA          620 
TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1107           NA           NA         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4963 
         211         2660         2172         1935         1785         1834 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 
        1862         1871          205         1746         1794          433 
TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 TCGA-BP-4975 TCGA-BP-4976 
        1487         1502         1384           NA         1433         1632 
TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 TCGA-BP-4985 TCGA-BP-4986 
         454           NA         1014         1413           NA          785 
TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 
        1124           NA          118         1413          501          177 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 TCGA-BP-5000 TCGA-BP-5001 
        1308         1371          932         1266          563         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5009 TCGA-BP-5010 
        1126          840         1140         1071           NA           NA 
TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 TCGA-BP-5174 TCGA-BP-5175 
          NA          193         2412           NA         2257          932 
TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5182 
          NA          293           NA         2263         1495         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 
        1291         1133         1132          693          406          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5196 
        1011          967          714          408          749         1018 
TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 
         603         1355         1063          951           29         1820 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 TCGA-CJ-4639 TCGA-CJ-4640 
        1416         1924           NA           NA         2308         1998 
TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 TCGA-CJ-4868 TCGA-CJ-4869 
          NA         1628         1793           NA          646         2554 
TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 
        1498         2423         1435         2259         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 
        1955         2186         2014         1883         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4891 
        1952           NA           NA         1946         2085           NA 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 TCGA-CJ-4897 TCGA-CJ-4899 
        1521          750          841           NA         1808         1528 
TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 
          NA         1450         1520         1560         1792         1496 
TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 TCGA-CJ-4916 TCGA-CJ-4918 
        1499         1531         1657           NA         1373           NA 
TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 TCGA-CJ-5675 TCGA-CJ-5676 
          NA           NA         1943           NA         2430         2575 
TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 TCGA-CJ-5681 TCGA-CJ-5682 
          NA           NA           NA           NA          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 TCGA-CJ-6027 TCGA-CJ-6028 
        1889         2231         2038           NA         1855           NA 
TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 TCGA-CW-5580 TCGA-CW-5581 
          NA         1906         2548           NA           NA         2799 
TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5588 TCGA-CW-5589 
        2489           NA         2609         2226         2017         2378 
TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 
          NA         2271           NA         3222         2552         3146 
TCGA-CW-6096 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 TCGA-CZ-4856 TCGA-CZ-4857 
        2701           NA          774         1404           18           NA 
TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 TCGA-CZ-4862 TCGA-CZ-4863 
        1943         1787           NA           NA         1843         1928 
TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5453 
        2830           NA         1868         1929         1789           25 
TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 
          NA           NA         1712         1683         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5465 
        1430          330           NA          662         1740         1446 
TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5982 
         685           NA           59           NA          386         2439 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5988 TCGA-CZ-5989 
        2067         1997          373           NA          693         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
        1329         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 TCGA-EU-5905 TCGA-EU-5906 
        2016         1729           NA          551          119          206 
TCGA-EU-5907 TCGA-G6-A5PC TCGA-G6-A8L6 TCGA-G6-A8L7 TCGA-GK-A6C7 TCGA-MM-A563 
         127           NA          305         1727           61          591 
TCGA-MM-A564 TCGA-MM-A84U TCGA-MW-A4EC 
         607          337          330 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=159,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=347,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=16,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=4,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 525 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=59, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
265  69 180  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
265  69 180  11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
265  69 180  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
265  69 180  11 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=8, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 30  0
  subtype2 15  2
  subtype3 13  1
subtype1 subtype2 subtype3 
      30       17       14 
subtype1 subtype2 subtype3 
       0        2        1 
$subtype1
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
        1120         1436         1508         1478         1186          751 
TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3351 
        1137          706         1485          945         1385          910 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3372 TCGA-A3-3380 TCGA-A3-3383 
        2504         1559          873          735          567          861 
TCGA-AK-3444 TCGA-AS-3778 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4102 TCGA-B8-4151 
        1471           43         1092          374          952          838 
TCGA-B8-4154 TCGA-B8-4619 TCGA-BP-4162 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 
         750          523         3074         1820         2308         1793 

$subtype2
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 
          16         1493         1491         1130         1106          665 
TCGA-A3-3347 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 TCGA-B2-4098 TCGA-B8-4620 
        1610         1314          630          574           51          777 
TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4167 TCGA-CJ-4636 TCGA-CJ-4640 
        2746         2839         2718         1924         1998 

$subtype3
TCGA-A3-3313 TCGA-A3-3328 TCGA-A3-3336 TCGA-A3-3363 TCGA-AK-3427 TCGA-AK-3440 
         735         1385         1043          319         2566         1745 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
        1423         1217         1397         1143          369         1238 
TCGA-B2-3923 TCGA-B8-4148 
         992          826 

subtype1 subtype2 subtype3 
      43       16      319 
subtype1 subtype2 subtype3 
    3074     2839     2566 
subtype1 subtype2 subtype3 
    1106     1314     1180 
[1] "43.0 - 3074.0 (1106.0)"  "16.0 - 2839.0 (1314.0)" 
[3] "319.0 - 2566.0 (1180.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      23        4         6        1
  subtype2       9        3         8        4
  subtype3       8        6         0        0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         23        9        8
  STAGE II         4        3        6
  STAGE III        6        8        0
  STAGE IV         1        4        0
[1] 4 3
[1] 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
  subtype1 23  4  7
  subtype2 10  4 10
  subtype3  8  6  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       23       10        8
  T2        4        4        6
  T3        7       10        0
[1] 3 3
[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
  subtype1 18  0
  subtype2 10  3
  subtype3  7  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18    0
  subtype2   10    3
  subtype3    7    0
   clus
vv  subtype1 subtype2 subtype3
  0       18       10        7
  1        0        3        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1
  subtype1 33  1
  subtype2 20  4
  subtype3 14  0
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       33       20       14
  M1        1        4        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus        0  1
  subtype1 15 19
  subtype2 10 14
  subtype3  4 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   19
  subtype2   10   14
  subtype3    4   10
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       10        4
  MALE         19       14       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 
       1 
character(0)
D1V9, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    32
  subtype2     0                         2    20
  subtype3     1                         3    10
D1V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        1
  BLACK OR AFRICAN AMERICAN        0        2        3
  WHITE                           32       20       10
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, binary
          cls
clus        0  1
  subtype1  5 19
  subtype2  2 11
  subtype3  0 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   19
  subtype2    2   11
  subtype3    0   12
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5        2        0
  NOT HISPANIC OR LATINO       19       11       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 11  0
  subtype2 10  0
  subtype3  2  2
  subtype4  5  1
  subtype5 10  0
  subtype6  9  0
  subtype7 11  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      11       10        4        6       10        9       11 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       0        0        2        1        0        0        0 
$subtype1
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3343 
        1120         1436         1186         1137          706          945 
TCGA-A3-3351 TCGA-A3-3383 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4102 
         910          861         1092          374          952 

$subtype2
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3374 
          16         1493         1130         1106          665         1314 
TCGA-A3-3378 TCGA-A3-3382 TCGA-B8-4620 TCGA-BP-4161 
         630          574          777         2746 

$subtype3
TCGA-A3-3313 TCGA-A3-3363 TCGA-AK-3456 TCGA-B2-4098 
         735          319         1143           51 

$subtype4
TCGA-A3-3317 TCGA-A3-3347 TCGA-BP-4163 TCGA-BP-4167 TCGA-CJ-4636 TCGA-CJ-4640 
        1491         1610         2839         2718         1924         1998 

$subtype5
TCGA-A3-3320 TCGA-A3-3331 TCGA-A3-3359 TCGA-AK-3444 TCGA-B8-4151 TCGA-B8-4154 
        1508         1485         2504         1471          838          750 
TCGA-B8-4619 TCGA-BP-4162 TCGA-CJ-4639 TCGA-CJ-4643 
         523         3074         2308         1793 

$subtype6
TCGA-A3-3322 TCGA-A3-3325 TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3372 
        1478          751         1385         1559          873          735 
TCGA-A3-3380 TCGA-AS-3778 TCGA-CJ-4634 
         567           43         1820 

$subtype7
TCGA-A3-3328 TCGA-A3-3336 TCGA-AK-3427 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 
        1385         1043         2566         1745         1423         1217 
TCGA-AK-3453 TCGA-AK-3465 TCGA-AS-3777 TCGA-B2-3923 TCGA-B8-4148 
        1397          369         1238          992          826 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
     374       16       51     1491      523       43      369 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    1436     2746     1143     2839     3074     1820     2566 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   952.0    941.5    527.0   1961.0   1496.5    873.0   1238.0 
[1] "374.0 - 1436.0 (952.0)"   "16.0 - 2746.0 (941.5)"   
[3] "51.0 - 1143.0 (527.0)"    "1491.0 - 2839.0 (1961.0)"
[5] "523.0 - 3074.0 (1496.5)"  "43.0 - 1820.0 (873.0)"   
[7] "369.0 - 2566.0 (1238.0)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1       8        2         2        0
  subtype2       8        2         2        0
  subtype3       2        2         0        0
  subtype4       0        1         6        4
  subtype5       7        2         3        1
  subtype6       8        0         1        0
  subtype7       7        4         0        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          8        8        2        0        7        8        7
  STAGE II         2        2        2        1        2        0        4
  STAGE III        2        2        0        6        3        1        0
  STAGE IV         0        0        0        4        1        0        0
[1] 4 7
[1] 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
  subtype1  8  2  2
  subtype2  8  2  2
  subtype3  2  2  0
  subtype4  1  2  8
  subtype5  7  2  4
  subtype6  8  0  1
  subtype7  7  4  0
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1        8        8        2        1        7        8        7
  T2        2        2        2        2        2        0        4
  T3        2        2        0        8        4        1        0
[1] 3 7
[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
  subtype1 6 0
  subtype2 5 0
  subtype3 3 0
  subtype4 5 3
  subtype5 9 0
  subtype6 3 0
  subtype7 4 0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    0
  subtype2    5    0
  subtype3    3    0
  subtype4    5    3
  subtype5    9    0
  subtype6    3    0
  subtype7    4    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0        6        5        3        5        9        3        4
  1        0        0        0        3        0        0        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1
  subtype1 12  0
  subtype2 12  0
  subtype3  4  0
  subtype4  7  4
  subtype5 12  1
  subtype6  9  0
  subtype7 11  0
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0       12       12        4        7       12        9       11
  M1        0        0        0        4        1        0        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1  0 12
  subtype2  3  9
  subtype3  1  3
  subtype4  6  5
  subtype5 12  1
  subtype6  3  6
  subtype7  4  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   12
  subtype2    3    9
  subtype3    1    3
  subtype4    6    5
  subtype5   12    1
  subtype6    3    6
  subtype7    4    7
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        0        3        1        6       12        3        4
  MALE         12        9        3        5        1        6        7
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype4 
       1 
character(0)
D2V9, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    11
  subtype2     0                         1    10
  subtype3     1                         3     0
  subtype4     0                         0    10
  subtype5     0                         0    13
  subtype6     0                         0     8
  subtype7     0                         1    10
D2V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        0        1        0        0
  BLACK OR AFRICAN AMERICAN        0        1        3        0        0
  WHITE                           11       10        0       10       13
                           clus
vv                          subtype6 subtype7
  ASIAN                            0        0
  BLACK OR AFRICAN AMERICAN        0        1
  WHITE                            8       10
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, binary
          cls
clus        0  1
  subtype1  1  7
  subtype2  0  4
  subtype3  0  2
  subtype4  2  6
  subtype5  3  7
  subtype6  1  5
  subtype7  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1    7
  subtype2    0    4
  subtype3    0    2
  subtype4    2    6
  subtype5    3    7
  subtype6    1    5
  subtype7    0   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        0        2        3        1
  NOT HISPANIC OR LATINO        7        4        2        6        7        5
                        clus
vv                       subtype7
  HISPANIC OR LATINO            0
  NOT HISPANIC OR LATINO       11
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 174   9
  subtype2  84   8
  subtype3  89   7
subtype1 subtype2 subtype3 
     183       92       96 
subtype1 subtype2 subtype3 
       9        8        7 
$subtype1
TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1436         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3351 TCGA-A3-3357 TCGA-A3-3358 
        1485          665          945          910         2688         1307 
TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 
        2504         1559          873         2270         2274         1621 
TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3387 TCGA-AK-3429 TCGA-AK-3431 
         630          567          861          617         2017         1853 
TCGA-AK-3444 TCGA-AK-3451 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
        1471         1481         1168          951          853           43 
TCGA-B0-4706 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5120 
          26          911         1092          797           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5696 
         554          652         2408         1487         3076         1727 
TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 
        1835         2583         2741         1203         3668         2414 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4099 
        1459         2931         1865         2963         1092          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
         648          952          358          417          507          291 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4153 
          38          141            7          511          826          762 
TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5552 TCGA-B8-5553 
         750          722          822           26         1046          435 
TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 
         830          519           53          256          528          110 
TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4165 TCGA-BP-4166 
        3377         2881         3074         2839         3037           13 
TCGA-BP-4169 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 
         701         2964          845         1888         1133          461 
TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4758 TCGA-BP-4765 TCGA-BP-4774 
        1666         1367          372         2208         2184         1885 
TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4789 TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4965 
         411         1731         1489         1124          211         1871 
TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4987 
        1794         1502         1433          454         1014         1124 
TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 
        1413          177         1371         1266         1177         1126 
TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5181 
         840         1140         1071         2257          293         1495 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        1165         1133          693          406          822         1011 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 
         714          408          749         1355         1063           29 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4868 
        1820         1924         2308         1628         1793          646 
TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4884 TCGA-CJ-4885 
        2554         1498         2283         2186         1759         2125 
TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4904 
        1952         1521          841         1528         1520         1792 
TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CW-5581 TCGA-CW-5583 
        1531         1373         1889         2231         2799         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4856 
        2609         2226         2378         3222          774           18 
TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 
        1787         2830         1929           25         1732         1683 
TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 
         662         1740         2439          373          693         1905 
TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-EU-5904 TCGA-EU-5906 
        1398          370          355         1130          551          206 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MW-A4EC 
         305           61          330 

$subtype2
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3349 TCGA-A3-3363 TCGA-A3-3374 
         267           16          735         1385          319         1314 
TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3433 TCGA-AK-3440 
        1070         1993         2566         2223         2192         1745 
TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
        1423         1217         1397         1143          369         1238 
TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5117 TCGA-B0-5400 
         110          616          183          665          535         1132 
TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5712 TCGA-B2-3923 
        3431         1420         1605         3117         2722          992 
TCGA-B2-4098 TCGA-B2-5635 TCGA-B4-5378 TCGA-B4-5838 TCGA-B8-4151 TCGA-B8-4619 
          51          315          175          166          838          523 
TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
         788          700           36          737          522          505 
TCGA-B8-5550 TCGA-B8-A54E TCGA-B8-A8YJ TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4177 
         434          909           24         2718         1893         1670 
TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4775 
        1625          645         2372         2361         1876         1843 
TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4964 
         354         1854          620         1459         1935         1862 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4976 TCGA-BP-4983 TCGA-BP-4994 
         205         1746          433         1632         1413         1308 
TCGA-BP-4998 TCGA-BP-5170 TCGA-CJ-4872 TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4889 
         932         2412         1435         2353         1883         1946 
TCGA-CJ-4890 TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-5671 
        2085         1808         1496         1499         1657         1943 
TCGA-CJ-5676 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-6093 TCGA-CZ-4862 
        2575          552         2038         1906         3146         1843 
TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5457 TCGA-CZ-5470 TCGA-DV-5567 TCGA-DV-5574 
        1928         1868         1683          386         1470         2016 
TCGA-EU-5905 TCGA-MM-A84U 
         119          337 

$subtype3
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3336 
        1120         1493         1491         1130          751         1043 
TCGA-A3-3347 TCGA-A3-3372 TCGA-A3-3382 TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3430 
        1610          735          574            3         3343          480 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-AK-3454 TCGA-B0-4710 
        2087         2044         1280         1779          874           96 
TCGA-B0-4813 TCGA-B0-5113 TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5701 TCGA-B2-5641 
          18          359          657          449         1732          656 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5843 TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5549 
           7           16           11          777          636          194 
TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4338 
          15          150         2746         1879         1955         2859 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 
         970          374          182         1462          400         2080 
TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 
        1107          204         2660         2172         1785         1834 
TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 
        1487         1384          785          118          501          563 
TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5191 
         193          932         2263         1291         1132          967 
TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4871 
        1018          603          951         1416         1998         2423 
TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4893 TCGA-CJ-4901 TCGA-CJ-4903 
        2259         1955         2014          750         1450         1560 
TCGA-CJ-5675 TCGA-CJ-5682 TCGA-CJ-6027 TCGA-CJ-6032 TCGA-CW-5588 TCGA-CW-5591 
        2430         1883         1855         2548         2017         2271 
TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5460 
        2552         1404         1943         1789         1712         1430 
TCGA-CZ-5461 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5984 TCGA-CZ-5985 
         330         1446          685           59         2067         1997 
TCGA-DV-5565 TCGA-DV-5575 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A564 
        1329         1729          127         1727          591          607 

subtype1 subtype2 subtype3 
       7       16        3 
subtype1 subtype2 subtype3 
    3668     3431     3343 
subtype1 subtype2 subtype3 
  1165.0   1416.5   1285.5 
[1] "7.0 - 3668.0 (1165.0)"  "16.0 - 3431.0 (1416.5)" "3.0 - 3343.0 (1285.5)" 
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     136       29        48       19
  subtype2      64       13        31       23
  subtype3      53       15        47       38
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        136       64       53
  STAGE II        29       13       15
  STAGE III       48       31       47
  STAGE IV        19       23       38
[1] 4 3
[1] 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
  subtype1 136  34  61   1
  subtype2  65  16  44   6
  subtype3  57  19  73   4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      136       65       57
  T2       34       16       19
  T3       61       44       73
  T4        1        6        4
[1] 4 3
[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
  subtype1 107   3
  subtype2  58   4
  subtype3  66  11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  107    3
  subtype2   58    4
  subtype3   66   11
   clus
vv  subtype1 subtype2 subtype3
  0      107       58       66
  1        3        4       11
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1 202  19  10
  subtype2 105  21   4
  subtype3 110  38   5
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      202      105      110
  M1       19       21       38
  MX       10        4        5
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1  92 140
  subtype2  55  76
  subtype3  39 114
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92  140
  subtype2   55   76
  subtype3   39  114
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       92       55       39
  MALE        140       76      114
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                        15   212
  subtype2     4                        20   106
  subtype3     2                         9   139
D3V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        4        2
  BLACK OR AFRICAN AMERICAN       15       20        9
  WHITE                          212      106      139
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
          cls
clus         0   1
  subtype1  13 145
  subtype2   7  93
  subtype3   6 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  145
  subtype2    7   93
  subtype3    6  100
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           13        7        6
  NOT HISPANIC OR LATINO      145       93      100
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = METHLYATION_CNMF
D4V1, survival
          sevent
clus2        0   1
  subtype1 101   4
  subtype2  50   3
  subtype3  55   4
subtype1 subtype2 subtype3 
     105       53       59 
subtype1 subtype2 subtype3 
       4        3        4 
$subtype1
TCGA-A3-3358 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3428 
        1307         2274         1621         1993            3         2223 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3454 
        1853         2192         1745         1779         1397          874 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-B0-4706 TCGA-B0-5110 TCGA-B0-5113 
        1168          951          853           26         1092          359 
TCGA-B0-5115 TCGA-B0-5117 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5399 TCGA-B0-5690 
         797          535           59          493          652         2408 
TCGA-B0-5691 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 
        3431         3076         1420         1082         1203         3668 
TCGA-B0-5707 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 
        2828         1459         2931         1865         2963         1092 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 
         417          507          291           38          141           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-5159 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
           7          511          722          737          522          505 
TCGA-B8-5549 TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54J 
         194         1046          435          519          256          528 
TCGA-B8-A7U6 TCGA-BP-4801 TCGA-BP-4993 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5181 
         110         1124          177         2257          293         1495 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5192 TCGA-BP-5194 
        1291         1133         1132          693          714          408 
TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 
        1355         1063           29         1808         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-6032 
        1496         1531          552         1889         2231         2548 
TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6093 
        2799         2489         2609         2378         3222         3146 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5459 
          18         1787         2830         1929           25         1683 
TCGA-CZ-5463 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 
         662         2439          373          693         1905         1329 
TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 
        1398          355         1130         1729          551          206 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MW-A4EC 
         305           61          330 

$subtype2
TCGA-6D-AA2E TCGA-A3-3376 TCGA-AK-3425 TCGA-B0-4699 TCGA-B0-4819 TCGA-B0-5108 
         267         1070         3343          110          183          911 
TCGA-B0-5400 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5702 TCGA-B0-5709 TCGA-B2-5633 
        1132         1487         1835         1605         3117          358 
TCGA-B2-5635 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5835 TCGA-B8-4621 TCGA-B8-5162 
         315          919          175           16          788           36 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54E TCGA-B8-A54G 
         822           26          434           15          909           53 
TCGA-B8-A54I TCGA-B8-A8YJ TCGA-BP-4177 TCGA-BP-4760 TCGA-BP-4782 TCGA-BP-4795 
         150           24         1670         2361          354          620 
TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5195 
        2412          932         1165          406          967          749 
TCGA-BP-5196 TCGA-CJ-4869 TCGA-CJ-4882 TCGA-CJ-4916 TCGA-CJ-5686 TCGA-CJ-6031 
        1018         2554         1883         1373         2038         1906 
TCGA-CW-5587 TCGA-CW-5588 TCGA-CZ-4863 TCGA-CZ-5452 TCGA-CZ-5458 TCGA-DV-5567 
        2226         2017         1928         1789         1732         1470 
TCGA-DV-5568 TCGA-DV-5574 TCGA-EU-5905 TCGA-G6-A8L7 TCGA-MM-A84U 
         370         2016          119         1727          337 

$subtype3
TCGA-A3-3357 TCGA-A3-3367 TCGA-A3-3387 TCGA-AK-3434 TCGA-AK-3445 TCGA-B0-4710 
        2688         2270          617         2087         1280           96 
TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5097 TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5402 
         616           18          665          657          554          449 
TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5706 TCGA-B0-5712 
        1727         2583         2741         1732         2414         2722 
TCGA-B2-4101 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5838 TCGA-B8-4153 TCGA-B8-4622 
         648          656            7          166          762          700 
TCGA-B8-5158 TCGA-B8-A54D TCGA-BP-5169 TCGA-BP-5180 TCGA-BP-5189 TCGA-BP-5190 
         636          830          193         2263          822         1011 
TCGA-BP-5198 TCGA-BP-5201 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4907 TCGA-CJ-4912 
         603          951         1450         1520         1499         1657 
TCGA-CJ-5671 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6027 TCGA-CW-5591 
        1943         2430         2575         1883         1855         2271 
TCGA-CW-6090 TCGA-CZ-4853 TCGA-CZ-4866 TCGA-CZ-5456 TCGA-CZ-5457 TCGA-CZ-5460 
        2552          774         1868         1712         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 
         330         1740         1446          685           59          386 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-EU-5907 TCGA-MM-A563 TCGA-MM-A564 
        2067         1997          127          591          607 

subtype1 subtype2 subtype3 
       3       15        7 
subtype1 subtype2 subtype3 
    3668     3343     2741 
subtype1 subtype2 subtype3 
    1124      932     1280 
[1] "3.0 - 3668.0 (1124.0)" "15.0 - 3343.0 (932.0)" "7.0 - 2741.0 (1280.0)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      82       17        13       10
  subtype2      42        2        20       12
  subtype3      22       12        41       34
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         82       42       22
  STAGE II        17        2       12
  STAGE III       13       20       41
  STAGE IV        10       12       34
[1] 4 3
[1] 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
  subtype1 82 21 19  0
  subtype2 44  3 25  4
  subtype3 23 17 65  4
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       82       44       23
  T2       21        3       17
  T3       19       25       65
  T4        0        4        4
[1] 4 3
[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
  subtype1 51  1
  subtype2 31  3
  subtype3 48  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    1
  subtype2   31    3
  subtype3   48    5
   clus
vv  subtype1 subtype2 subtype3
  0       51       31       48
  1        1        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1 102  10   9
  subtype2  58  10   7
  subtype3  73  33   3
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      102       58       73
  M1       10       10       33
  MX        9        7        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V7, binary
          cls
clus        0  1
  subtype1 59 63
  subtype2 31 45
  subtype3 21 88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   63
  subtype2   31   45
  subtype3   21   88
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       59       31       21
  MALE         63       45       88
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        13   109
  subtype2     0                        16    60
  subtype3     1                         8    97
D4V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        1
  BLACK OR AFRICAN AMERICAN       13       16        8
  WHITE                          109       60       97
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
          cls
clus        0  1
  subtype1  4 93
  subtype2  2 62
  subtype3  4 93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   93
  subtype2    2   62
  subtype3    4   93
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        4
  NOT HISPANIC OR LATINO       93       62       93
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 80  4
  subtype2 19  5
  subtype3 53  4
  subtype4 54  5
  subtype5 50  5
  subtype6 40  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      84       24       57       59       55       40 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       4        5        4        5        5        0 
$subtype1
TCGA-A3-3306 TCGA-A3-3320 TCGA-A3-3367 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 
        1120         1508         2270          567          861         1993 
TCGA-AK-3434 TCGA-B0-4706 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 
        2087           26          797           59          554          652 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 
         449         2408         1487         3076         1420         2583 
TCGA-B0-5699 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 
        2741         3668         2931         2722         1865         2963 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B4-5377 TCGA-B4-5836 TCGA-B4-5843 
         374          648          952          291          141           11 
TCGA-B4-5844 TCGA-B8-4153 TCGA-B8-5159 TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4325 
           7          762          722         3377         2746         2964 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4759 TCGA-BP-4768 TCGA-BP-4774 
         845         1888          461         2372          400         1885 
TCGA-BP-4776 TCGA-BP-4961 TCGA-BP-4975 TCGA-BP-4977 TCGA-BP-4991 TCGA-BP-4995 
         411         1935         1433          454         1413         1371 
TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5180 TCGA-BP-5181 
        1266         1177         1140         2412         2263         1495 
TCGA-BP-5192 TCGA-BP-5201 TCGA-CJ-4634 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 
         714          951         1820         1498         2423         2283 
TCGA-CJ-4878 TCGA-CJ-4893 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4916 
        2186          750         1808         1560         1792         1373 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5683 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5585 
        2430         2575         1889         2799         2489         2609 
TCGA-CW-5587 TCGA-CZ-4853 TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5465 
        2226          774         1787         2830         1929         1446 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5565 TCGA-EU-5906 
        2439         1997          373         1905         1329          206 

$subtype2
TCGA-A3-3308 TCGA-AK-3436 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5696 TCGA-B0-5709 
          16         2044          616           18         1727         3117 
TCGA-B4-5838 TCGA-B8-4622 TCGA-B8-5158 TCGA-BP-4173 TCGA-BP-4326 TCGA-BP-4761 
         166          700          636         1893         1625          182 
TCGA-BP-4983 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5175 TCGA-CJ-4869 TCGA-CJ-4875 
        1413          501          563          932         2554         2353 
TCGA-CJ-4881 TCGA-CJ-6027 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5460 TCGA-CZ-5468 
        2014         1855         1404         1943         1430           59 

$subtype3
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3336 TCGA-A3-3347 
        1491         1130         1106          665         1043         1610 
TCGA-A3-3351 TCGA-A3-3372 TCGA-A3-3387 TCGA-B0-5691 TCGA-B0-5697 TCGA-B0-5701 
         910          735          617         3431         1835         1732 
TCGA-B0-5707 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5832 
        2828          358          315          417          656            7 
TCGA-B4-5835 TCGA-B8-5164 TCGA-B8-5546 TCGA-B8-5550 TCGA-B8-5553 TCGA-BP-4351 
          16           26          505          434          435          970 
TCGA-BP-4756 TCGA-BP-4803 TCGA-BP-4963 TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-5189 
         374          204         1834         1746         1384          822 
TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5195 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4873 
        1011          967          749         1416         1998         2259 
TCGA-CJ-4876 TCGA-CJ-4884 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CW-5589 TCGA-CW-5591 
        1955         1759         1499         1657         2378         2271 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5458 
        1843         1928         1868         1789         1712         1732 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5984 
         330          662         1740          685          386         2067 
TCGA-DV-5573 TCGA-EU-5905 TCGA-EU-5907 
        1130          119          127 

$subtype4
TCGA-A3-3313 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3326 TCGA-A3-3357 TCGA-A3-3362 
         735         1478         1186         1137         2688         1559 
TCGA-A3-3363 TCGA-A3-3373 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 TCGA-AK-3427 
         319         1621         1314          630          574         2566 
TCGA-AK-3428 TCGA-AK-3444 TCGA-AK-3456 TCGA-B0-4699 TCGA-B0-5117 TCGA-B0-5400 
        2223         1471         1143          110          535         1132 
TCGA-B0-5700 TCGA-B0-5702 TCGA-B0-5703 TCGA-B2-3923 TCGA-B2-3924 TCGA-B2-4098 
        1082         1605         1203          992         1092           51 
TCGA-B8-4146 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5549 TCGA-B8-5551 TCGA-BP-4165 
         511          777          788          194           15         3037 
TCGA-BP-4174 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4766 TCGA-BP-4777 
        1879         1133          645         2859         1462         1731 
TCGA-BP-4801 TCGA-BP-4959 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4972 
        1124         2660         1862          205         1794         1502 
TCGA-BP-4989 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5185 
         118          177         1308         1126          193         1132 
TCGA-BP-5187 TCGA-BP-5194 TCGA-BP-5198 TCGA-CJ-4885 TCGA-CJ-4901 TCGA-CJ-5681 
         406          408          603         2125         1450          552 
TCGA-CJ-6031 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-DV-5575 
        1906           25         1683         1683         1729 

$subtype5
TCGA-A3-3316 TCGA-A3-3349 TCGA-A3-3365 TCGA-A3-3376 TCGA-AK-3451 TCGA-B0-4819 
        1493         1385          873         1070         1481          183 
TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5706 TCGA-B0-5710 TCGA-B2-5636 TCGA-B4-5378 
         665          911         2414         1459          919          175 
TCGA-B4-5834 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5545 TCGA-BP-4169 TCGA-BP-4345 
          38           36          822          522          701         1516 
TCGA-BP-4349 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4784 TCGA-BP-4804 TCGA-BP-4960 
         372         2184         1876         1854         1459         2172 
TCGA-BP-4962 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4998 TCGA-BP-5177 TCGA-BP-5196 
        1785          433         1487          932          293         1018 
TCGA-BP-5199 TCGA-BP-5200 TCGA-CJ-4868 TCGA-CJ-4872 TCGA-CJ-4882 TCGA-CJ-4886 
        1355         1063          646         1435         1883         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 
        1946         2085         1521          841         1528         1520 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 
        1496         1531         1943         1883         2231         2038 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4856 TCGA-CZ-5988 TCGA-DV-5567 TCGA-DV-5574 
        3222         2552           18          693         1470         2016 
TCGA-EU-5904 
         551 

$subtype6
TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3370 TCGA-B0-4710 TCGA-B0-5110 TCGA-B0-5113 
         706         1485         2274           96         1092          359 
TCGA-B0-5116 TCGA-B0-5120 TCGA-B8-5165 TCGA-B8-5552 TCGA-BP-4344 TCGA-BP-4347 
         657          493          737         1046         1666         1367 
TCGA-BP-4758 TCGA-BP-4760 TCGA-BP-4775 TCGA-BP-4781 TCGA-BP-4789 TCGA-BP-4797 
        2208         2361         1843         2080         1489         1107 
TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4986 TCGA-BP-4987 
         211         1871         1632         1014          785         1124 
TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5174 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 
         840         1071         2257         1165         1291         1133 
TCGA-BP-5186 TCGA-BP-5202 TCGA-CJ-4642 TCGA-CJ-6032 TCGA-CW-5588 TCGA-CW-6093 
         693           29         1628         2548         2017         3146 
TCGA-CW-6096 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
        2701         1398          370          355 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       7       16        7       15       18       29 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    3668     3117     3431     3037     3222     3146 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  1503.0   1408.5   1106.0   1133.0   1459.0   1149.0 
[1] "7.0 - 3668.0 (1503.0)"  "16.0 - 3117.0 (1408.5)" "7.0 - 3431.0 (1106.0)" 
[4] "15.0 - 3037.0 (1133.0)" "18.0 - 3222.0 (1459.0)" "29.0 - 3146.0 (1149.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      58       12        24       14
  subtype2       8        4        26       24
  subtype3      33       10        23       11
  subtype4      47        7        18        9
  subtype5      38        9        16       18
  subtype6      35        2         8        0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         58        8       33       47       38       35
  STAGE II        12        4       10        7        9        2
  STAGE III       24       26       23       18       16        8
  STAGE IV        14       24       11        9       18        0
[1] 4 6
[1] 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
  subtype1 58 16 33  1
  subtype2  9  9 40  4
  subtype3 35 10 32  0
  subtype4 48  7 25  1
  subtype5 39 10 27  5
  subtype6 35  2  8  0
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       58        9       35       48       39       35
  T2       16        9       10        7       10        2
  T3       33       40       32       25       27        8
  T4        1        4        0        1        5        0
[1] 4 6
[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
  subtype1 51  1
  subtype2 26  8
  subtype3 40  2
  subtype4 38  3
  subtype5 39  2
  subtype6 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    1
  subtype2   26    8
  subtype3   40    2
  subtype4   38    3
  subtype5   39    2
  subtype6   14    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       51       26       40       38       39       14
  1        1        8        2        3        2        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1
  subtype1 94 14
  subtype2 38 24
  subtype3 66 11
  subtype4 72  9
  subtype5 64 17
  subtype6 45  0
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       94       38       66       72       64       45
  M1       14       24       11        9       17        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 46 62
  subtype2 16 46
  subtype3 23 54
  subtype4 22 59
  subtype5 25 56
  subtype6 19 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46   62
  subtype2   16   46
  subtype3   23   54
  subtype4   22   59
  subtype5   25   56
  subtype6   19   26
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       46       16       23       22       25       19
  MALE         62       46       54       59       56       26
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"              
clus
subtype2 subtype3 subtype4 
       1        1        1 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         5   101
  subtype2     2                         0    60
  subtype3     1                         1    71
  subtype4     1                         7    73
  subtype5     3                         5    73
  subtype6     1                         2    42
D5V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        1        1        3
  BLACK OR AFRICAN AMERICAN        5        0        1        7        5
  WHITE                          101       60       71       73       73
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        2
  WHITE                           42
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, binary
          cls
clus        0  1
  subtype1  6 72
  subtype2  3 45
  subtype3  5 53
  subtype4  1 45
  subtype5  1 55
  subtype6  3 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   72
  subtype2    3   45
  subtype3    5   53
  subtype4    1   45
  subtype5    1   55
  subtype6    3   25
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        3        5        1        1        3
  NOT HISPANIC OR LATINO       72       45       53       45       55       25
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  90   3
  subtype2 153   7
  subtype3  53  13
subtype1 subtype2 subtype3 
      93      160       66 
subtype1 subtype2 subtype3 
       3        7       13 
$subtype1
TCGA-A3-3306 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3326 TCGA-A3-3336 
        1120         1491         1130         1106         1137         1043 
TCGA-A3-3351 TCGA-A3-3367 TCGA-A3-3372 TCGA-A3-3383 TCGA-A3-3385 TCGA-B0-5116 
         910         2270          735          861         1993          657 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5698 
         652          449         2408         1487         1835         2583 
TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5705 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-4101 
        2741         1732         3668         1865         2963          648 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-5641 TCGA-B4-5377 TCGA-B4-5835 
         952          315          417          656          291           16 
TCGA-B4-5843 TCGA-B8-4153 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5546 TCGA-B8-5550 
          11          762          722           26          505          434 
TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4347 
        3377         2746         1893         2964         1888         1367 
TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4768 TCGA-BP-4959 TCGA-BP-4963 TCGA-BP-4965 
         970          374          400         2660         1834         1871 
TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-5000 
        1746         1384          454         1413          501          563 
TCGA-BP-5174 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        2257         1291         1132          822         1011          967 
TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4884 
        1416         1998         2554         2259         1955         1759 
TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CW-5581 
        1808         1499         1657         1373         2430         2799 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5591 TCGA-CW-6096 TCGA-CZ-4853 TCGA-CZ-4862 
        2609         2226         2271         2701          774         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5458 
        1928         2830         1868         1929         1789         1732 
TCGA-CZ-5459 TCGA-CZ-5466 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5989 
        1683          685         2067         1997          373         1905 
TCGA-DV-5565 TCGA-EU-5906 TCGA-EU-5907 
        1329          206          127 

$subtype2
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3329 
          16         1493         1508         1478         1186          706 
TCGA-A3-3331 TCGA-A3-3349 TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3370 
        1485         1385         2688         1559          873         2274 
TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3444 
        1621         1070          567          574          617         1471 
TCGA-AK-3451 TCGA-B0-4710 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 
        1481           96          665          911         1092          359 
TCGA-B0-5115 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5693 TCGA-B0-5700 TCGA-B0-5702 
         797          493          554         3076         1082         1605 
TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-4098 
        2414         1459         2931         2722         1092           51 
TCGA-B2-4099 TCGA-B2-5633 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5834 TCGA-B8-4146 
         374          358          919          175           38          511 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5552 
          36          822          737          522          194         1046 
TCGA-B8-5553 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4174 TCGA-BP-4326 TCGA-BP-4332 
         435         3037          701         1879         1625         1133 
TCGA-BP-4344 TCGA-BP-4349 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 
        1666          372         2208         2372         2361         2184 
TCGA-BP-4769 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4781 
        1876         1885         1843          411         1731         2080 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 
        1854         1489         1107         1124          204         1459 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 
         211         1935         1785         1862          205         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 
         433         1487         1502         1433         1632         1014 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         785         1124          177         1371          932         1266 
TCGA-BP-5001 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5177 TCGA-BP-5181 
        1177          840         1140         1071          293         1495 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5192 TCGA-BP-5194 
        1165         1133          693          406          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4870 TCGA-CJ-4871 
          29         1820         1628          646         1498         2423 
TCGA-CJ-4872 TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
        1435         2283         2186         1952         1946         2085 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
         750          841         1528         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 
        1792         1496         1531         1943         2575         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5588 
        1889         2231         2038         2548         2489         2017 
TCGA-CW-5589 TCGA-CW-6088 TCGA-CW-6090 TCGA-CW-6093 TCGA-CZ-4856 TCGA-CZ-4859 
        2378         3222         2552         3146           18         1787 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 
          25         1683          330          662         1446         2439 
TCGA-CZ-5988 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 
         693         1398         1470          370          355         1130 
TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
        2016         1729          551          119 

$subtype3
TCGA-A3-3313 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3378 
         735          665         1610          319         1314          630 
TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3456 TCGA-B0-4699 
        2566         2223         2087         2044         1143          110 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5117 TCGA-B0-5119 
          26          616           18          183          535           59 
TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5703 TCGA-B0-5707 
        1132         3431         1420         1727         1203         2828 
TCGA-B0-5709 TCGA-B2-3923 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5838 TCGA-B4-5844 
        3117          992            7          141          166            7 
TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 TCGA-B8-5551 TCGA-BP-4329 
         777          788          700          636           15          845 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 TCGA-BP-4345 TCGA-BP-4761 TCGA-BP-4766 
         645          461         2859         1516          182         1462 
TCGA-BP-4960 TCGA-BP-4983 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5169 
        2172         1413          118         1308         1126          193 
TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5180 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 
        2412          932         2263         2353         2014         1883 
TCGA-CJ-4885 TCGA-CJ-4892 TCGA-CJ-5681 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CZ-4854 
        2125         1521          552         1855         1906         1404 
TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5470 
        1943         1712         1430         1740           59          386 

subtype1 subtype2 subtype3 
      11       16        7 
subtype1 subtype2 subtype3 
    3668     3222     3431 
subtype1 subtype2 subtype3 
  1487.0   1378.0   1137.5 
[1] "11.0 - 3668.0 (1487.0)" "16.0 - 3222.0 (1378.0)" "7.0 - 3431.0 (1137.5)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      54       15        39       14
  subtype2     130       16        37       17
  subtype3      35       13        39       45
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         54      130       35
  STAGE II        15       16       13
  STAGE III       39       37       39
  STAGE IV        14       17       45
[1] 4 3
[1] 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
  subtype1  55  17  49   1
  subtype2 132  19  48   1
  subtype3  37  18  68   9
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       55      132       37
  T2       17       19       18
  T3       49       48       68
  T4        1        1        9
[1] 4 3
[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
  subtype1 63  2
  subtype2 78  4
  subtype3 67 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63    2
  subtype2   78    4
  subtype3   67   10
   clus
vv  subtype1 subtype2 subtype3
  0       63       78       67
  1        2        4       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1
  subtype1 109  13
  subtype2 182  18
  subtype3  88  44
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      109      182       88
  M1       13       18       44
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  34  88
  subtype2  77 123
  subtype3  40  92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   88
  subtype2   77  123
  subtype3   40   92
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       34       77       40
  MALE         88      123       92
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype3 
       1        2 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         4   115
  subtype2     4                         9   184
  subtype3     3                         7   121
D6V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        4        3
  BLACK OR AFRICAN AMERICAN        4        9        7
  WHITE                          115      184      121
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
          cls
clus         0   1
  subtype1   9  82
  subtype2   8 117
  subtype3   2  96
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   82
  subtype2    8  117
  subtype3    2   96
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            9        8        2
  NOT HISPANIC OR LATINO       82      117       96
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1  76   8
  subtype2 170   4
  subtype3 104  11
subtype1 subtype2 subtype3 
      84      174      115 
subtype1 subtype2 subtype3 
       8        4       11 
$subtype1
TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3328 TCGA-A3-3349 TCGA-A3-3362 
         267          735         1491         1385         1385         1559 
TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3374 TCGA-A3-3376 TCGA-AK-3427 TCGA-AK-3428 
         319          873         1314         1070         2566         2223 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3453 
        1853         2192         1745         1423         1217         1397 
TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4706 
        1143          853          369         1238          110           26 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5691 TCGA-B0-5697 TCGA-B0-5702 TCGA-B0-5707 
         535          493         3431         1835         1605         2828 
TCGA-B0-5709 TCGA-B0-5812 TCGA-B2-3923 TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5838 
        3117         2963          992          919          175          166 
TCGA-B8-4619 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5552 TCGA-B8-A54E 
         523          737          522          505         1046          909 
TCGA-B8-A54F TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4329 
         519         2839           13          701         1670          845 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4344 TCGA-BP-4345 TCGA-BP-4759 TCGA-BP-4760 
        1133          645         1666         1516         2372         2361 
TCGA-BP-4769 TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4970 
        1876         1854         1489          620         1124          433 
TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5008 TCGA-BP-5177 TCGA-BP-5182 
        1308         1371          932         1071          293         1165 
TCGA-BP-5187 TCGA-BP-5199 TCGA-CJ-4642 TCGA-CJ-4889 TCGA-CJ-4899 TCGA-CJ-4905 
         406         1355         1628         1946         1528         1496 
TCGA-CJ-4907 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CW-5583 TCGA-CW-5589 
        1499          552         1883         1889         2489         2378 
TCGA-CW-5591 TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
        2271         1329         1470          355         1130         2016 

$subtype2
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
        1120         1436         1508         1478         1186          751 
TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3351 TCGA-A3-3358 
        1137          706         1485          945          910         1307 
TCGA-A3-3359 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3380 
        2504         2270         2274          735         1621          567 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3429 TCGA-AK-3434 TCGA-AK-3444 
         861         1993            3         2017         2087         1471 
TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4710 
        1779          874         1168          951           43           96 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 
        1092          359          797           59          554          652 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
         449         2408         1487         3076         1420         1727 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 
        2583         2741         1082         1203         3668         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 
        2931         2722         1865         1092          374          648 
TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 
         952          315          417          507          291           38 
TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
         141           11            7          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5549 
         762          750          700          722           26          194 
TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 
         435          256          528          110         3377         2881 
TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4347 
        3074         3037         2964         1888          461         1367 
TCGA-BP-4349 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
         372          374         2208         2184         1462          400 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4807 
        1885         1843          411         1731          354          211 
TCGA-BP-4961 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4972 
        1935         1862         1871         1746         1794         1502 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 
        1384         1433         1632         1014         1124         1413 
TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 
         177         1266         1177         1126          840         1140 
TCGA-BP-5174 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        2257         1495         1291         1133         1132          693 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 
        1011          714          408         1063          951           29 
TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4875 
        1820         2308         1793         1498         2283         2353 
TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 
        1955         2186         2125         1952         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4916 
         841         1808         1560         1792         1531         1373 
TCGA-CJ-5675 TCGA-CJ-5684 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5587 
        2430         2231         2548         2799         2609         2226 
TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4863 
        3222         3146          774           18         1787         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 
        2830         1929           25         1683         1732         1430 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 
         662         1446         2439          373         1905         1398 
TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MW-A4EC 
        1729          551          206          305           61          330 

$subtype3
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3347 
          16         1493         1130         1106          665         1610 
TCGA-A3-3357 TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3436 
        2688          630          574          617         3343         2044 
TCGA-AK-3445 TCGA-AK-3451 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
        1280         1481          616           18          183          665 
TCGA-B0-5108 TCGA-B0-5116 TCGA-B0-5400 TCGA-B0-5701 TCGA-B0-5706 TCGA-B2-4098 
         911          657         1132         1732         2414           51 
TCGA-B2-5633 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4620 TCGA-B8-4621 
         358          656            7           16          777          788 
TCGA-B8-5158 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54D 
         636           36          822          434           15          830 
TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 
          53          150         2746         2718         1893         1879 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4781 
        1955         1625         2859          970          182         2080 
TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 
        1107          204         1459         2660         2172         1785 
TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4971 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4986 
        1834          205         1487          454         1413          785 
TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 
         118          501          563          193         2412          932 
TCGA-BP-5180 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 
        2263          822          967          749         1018          603 
TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4640 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 
        1416         1924         1998          646         2554         2423 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4890 
        1435         2259         2014         1883         1759         2085 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5686 
        1450         1520         1657         1943         2575         2038 
TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 
        1855         1906         2017         2552         1404         1943 
TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5459 TCGA-CZ-5461 
        1843         1868         1789         1712         1683          330 
TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 
        1740          685           59          386         2067         1997 
TCGA-CZ-5988 TCGA-DV-5568 TCGA-EU-5905 TCGA-EU-5907 TCGA-G6-A8L7 TCGA-MM-A564 
         693          370          119          127         1727          607 
TCGA-MM-A84U 
         337 

subtype1 subtype2 subtype3 
      13        3        7 
subtype1 subtype2 subtype3 
    3431     3668     3343 
subtype1 subtype2 subtype3 
    1311     1299     1280 
[1] "13.0 - 3431.0 (1311.0)" "3.0 - 3668.0 (1299.0)"  "7.0 - 3343.0 (1280.0)" 
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      66       12        19       10
  subtype2     129       23        41       25
  subtype3      61       22        65       46
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         66      129       61
  STAGE II        12       23       22
  STAGE III       19       41       65
  STAGE IV        10       25       46
[1] 4 3
[1] 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
  subtype1  67  13  24   3
  subtype2 129  27  60   2
  subtype3  66  29  93   6
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       67      129       66
  T2       13       27       29
  T3       24       60       93
  T4        3        2        6
[1] 4 3
[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
  subtype1  48   3
  subtype2 100   2
  subtype3  89  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48    3
  subtype2  100    2
  subtype3   89   12
   clus
vv  subtype1 subtype2 subtype3
  0       48      100       89
  1        3        2       12
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1  94   9   4
  subtype2 185  24   8
  subtype3 142  46   6
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       94      185      142
  M1        9       24       46
  MX        4        8        6
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  36  71
  subtype2 101 117
  subtype3  47 147
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36   71
  subtype2  101  117
  subtype3   47  147
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       36      101       47
  MALE         71      117      147
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 
       2        3        5 
[1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype2" "subtype3" "subtype3"
[8] "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        15    87
  subtype2     2                        14   199
  subtype3     2                        13   176
D7V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4        2        2
  BLACK OR AFRICAN AMERICAN       15       14       13
  WHITE                           87      199      176
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, binary
          cls
clus         0   1
  subtype1   3  75
  subtype2  16 137
  subtype3   7 130
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   75
  subtype2   16  137
  subtype3    7  130
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3       16        7
  NOT HISPANIC OR LATINO       75      137      130
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 119   7
  subtype2 176   7
  subtype3  55   9
subtype1 subtype2 subtype3 
     126      183       64 
subtype1 subtype2 subtype3 
       7        7        9 
$subtype1
TCGA-6D-AA2E TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3323 TCGA-A3-3328 TCGA-A3-3351 
         267          735         1491         1106         1385          910 
TCGA-A3-3357 TCGA-A3-3362 TCGA-A3-3363 TCGA-A3-3365 TCGA-A3-3374 TCGA-AK-3427 
        2688         1559          319          873         1314         2566 
TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3451 
        1853         2192         1745         1423         1217         1481 
TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 
        1397         1143          853          369         1238          110 
TCGA-B0-5117 TCGA-B0-5120 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5697 
         535          493         3431         1420         1727         1835 
TCGA-B0-5700 TCGA-B0-5701 TCGA-B0-5702 TCGA-B0-5707 TCGA-B0-5709 TCGA-B0-5812 
        1082         1732         1605         2828         3117         2963 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 TCGA-B2-5639 
         992           51          358          315          919          417 
TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4619 TCGA-B8-4621 
         656          175           16          166          523          788 
TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5552 
         737          522          505          194          434         1046 
TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G TCGA-BP-4160 TCGA-BP-4163 
         830          909          519           53         2881         2839 
TCGA-BP-4166 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4334 TCGA-BP-4351 TCGA-BP-4756 
          13         1893         1670          645          970          374 
TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 
        2361         1876         1731         2080          354         1854 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4959 
         620         1107         1124          204          211         2660 
TCGA-BP-4962 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4977 
        1785          205         1746          433         1487          454 
TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5000 
         118          501         1308         1371          932          563 
TCGA-BP-5008 TCGA-BP-5174 TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5195 
        1071         2257         1165          406          822          749 
TCGA-CJ-4636 TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4884 TCGA-CJ-4889 
        1924         1998         2554         2423         1759         1946 
TCGA-CJ-4907 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CW-5581 
        1499         2430          552         1889         2231         2799 
TCGA-CW-5589 TCGA-CW-5591 TCGA-CZ-4862 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5458 
        2378         2271         1843         1868         1789         1732 
TCGA-CZ-5459 TCGA-CZ-5985 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 
        1683         1997          693         1329         1398         1470 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-MM-A564 TCGA-MM-A84U 
         370          355         1130         2016          607          337 

$subtype2
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 
        1120         1436         1508         1478         1186          751 
TCGA-A3-3326 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3335 TCGA-A3-3343 TCGA-A3-3349 
        1137          706         1485          665          945         1385 
TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 
        1307         2504         2270         2274          735         1621 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-3387 TCGA-A3-A8CQ 
        1070          567          861         1993          617            3 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3454 
        2223         2017         2087         1471         1779          874 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-4718 
        1168          951           43           26           96          616 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5119 TCGA-B0-5121 
        1092          359          797          657           59          554 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5698 
         652          449         2408         1487         3076         2583 
TCGA-B0-5699 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        2741         1203         3668         1459         2931         2722 
TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-A4SR 
        1865         1092          374          648          952          507 
TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 
         291           38          141           11            7          511 
TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 
         826          838          762          750          700          722 
TCGA-B8-5164 TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 
          26          435          256          528          110         3377 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4329 
        2746         3074         3037         1879         2964          845 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 
        1888         1133          461         1666         1367          372 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4774 
        2208         2372         2184         1462          400         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4789 TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4964 
        1843          411         1489         1935         1834         1862 
TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 
        1871         1794         1502         1384         1433         1632 
TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5001 
        1014         1124         1413          177         1266         1177 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 
        1126          840         1140          293         2263         1495 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5190 TCGA-BP-5192 
        1291         1133         1132          693         1011          714 
TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 
         408         1063          951           29         1820         2308 
TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 
        1628         1793         1498         2283         2353         1955 
TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 
        2186         2125         1952         1521          750          841 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4908 
        1808         1528         1560         1792         1496         1531 
TCGA-CJ-4916 TCGA-CJ-5682 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5585 
        1373         1883         2038         2548         2489         2609 
TCGA-CW-5587 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 
        2226         3222         3146          774           18         1787 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5460 
        1928         2830         1929           25         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5982 
         330          662         1446          685          386         2439 
TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 
         373         1905         1729          551          206          127 
TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MW-A4EC 
         305           61          330 

$subtype3
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3347 TCGA-A3-3378 TCGA-A3-3382 
          16         1493         1130         1610          630          574 
TCGA-AK-3425 TCGA-AK-3436 TCGA-AK-3445 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
        3343         2044         1280           18          183          665 
TCGA-B0-5108 TCGA-B0-5400 TCGA-B0-5706 TCGA-B4-5832 TCGA-B8-4620 TCGA-B8-5158 
         911         1132         2414            7          777          636 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4167 TCGA-BP-4169 
          36          822           15          150         2718          701 
TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4345 TCGA-BP-4761 TCGA-BP-4804 
        1955         1625         2859         1516          182         1459 
TCGA-BP-4960 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 
        2172         1413          785          193         2412          932 
TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4635 TCGA-CJ-4868 
         967         1018          603         1355         1416          646 
TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4890 TCGA-CJ-4901 
        1435         2259         2014         1883         2085         1450 
TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-6027 TCGA-CJ-6031 
        1520         1657         1943         2575         1855         1906 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5464 
        2017         2552         1404         1943         1712         1740 
TCGA-CZ-5468 TCGA-CZ-5984 TCGA-EU-5905 TCGA-G6-A8L7 
          59         2067          119         1727 

subtype1 subtype2 subtype3 
      13        3        7 
subtype1 subtype2 subtype3 
    3431     3668     3343 
subtype1 subtype2 subtype3 
  1154.0   1291.0   1425.5 
[1] "13.0 - 3431.0 (1154.0)" "3.0 - 3668.0 (1291.0)"  "7.0 - 3343.0 (1425.5)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      92       19        35       16
  subtype2     131       26        44       31
  subtype3      33       12        46       34
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         92      131       33
  STAGE II        19       26       12
  STAGE III       35       44       46
  STAGE IV        16       31       34
[1] 4 3
[1] 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
  subtype1  96  22  42   2
  subtype2 132  33  65   2
  subtype3  34  14  70   7
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       96      132       34
  T2       22       33       14
  T3       42       65       70
  T4        2        2        7
[1] 4 3
[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
  subtype1  72   6
  subtype2 103   1
  subtype3  62  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   72    6
  subtype2  103    1
  subtype3   62   10
   clus
vv  subtype1 subtype2 subtype3
  0       72      103       62
  1        6        1       10
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1 138  16   8
  subtype2 193  30   8
  subtype3  90  33   2
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      138      193       90
  M1       16       30       33
  MX        8        8        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  50 112
  subtype2 104 128
  subtype3  30  95
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50  112
  subtype2  104  128
  subtype3   30   95
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       50      104       30
  MALE        112      128       95
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       5        3        2 
[1] "subtype2" "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype1"
[8] "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        21   136
  subtype2     2                        16   208
  subtype3     2                         5   118
D8V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4        2        2
  BLACK OR AFRICAN AMERICAN       21       16        5
  WHITE                          136      208      118
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
          cls
clus         0   1
  subtype1   8 113
  subtype2  13 144
  subtype3   5  85
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  113
  subtype2   13  144
  subtype3    5   85
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8       13        5
  NOT HISPANIC OR LATINO      113      144       85
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1  89   4
  subtype2 151   7
  subtype3  97  12
subtype1 subtype2 subtype3 
      93      158      109 
subtype1 subtype2 subtype3 
       4        7       12 
$subtype1
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3347 
         267           16          735         1493         1491         1610 
TCGA-A3-3349 TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3387 
        1385         1559          873         1621         1070          617 
TCGA-A3-A8CQ TCGA-AK-3425 TCGA-AK-3431 TCGA-AK-3461 TCGA-B0-5108 TCGA-B0-5119 
           3         3343         1853          853          911           59 
TCGA-B0-5120 TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5812 
         493         3431         1605         3117         1459         2963 
TCGA-B2-5636 TCGA-B4-5836 TCGA-B4-5838 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5545 
         919          141          166           36          822          522 
TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-A54H TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 
         434         1046          256          110           24         2881 
TCGA-BP-4166 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4332 
          13         2718          701         1893         1670         1133 
TCGA-BP-4345 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4789 TCGA-BP-4795 
        1516         2361         2184         1876         1489          620 
TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4969 
        1124         1459          211         1935         1871         1794 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4982 TCGA-BP-5170 TCGA-BP-5177 
         433         1487         1502         1014         2412          293 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 
        1165         1133          693         1018          603         1355 
TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4872 TCGA-CJ-4882 
        1063         1820         1924         1628         1435         1883 
TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 
        1952         1946         2085         1520         1496         1499 
TCGA-CJ-4908 TCGA-CJ-5671 TCGA-CJ-6031 TCGA-CW-5583 TCGA-CW-5588 TCGA-CW-6088 
        1531         1943         1906         2489         2017         3222 
TCGA-CW-6090 TCGA-CZ-5988 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 
        2552          693          370         1130         2016         1729 
TCGA-EU-5905 TCGA-G6-A8L7 TCGA-MM-A563 
         119         1727          591 

$subtype2
TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 TCGA-A3-3326 
        1436         1508         1478         1106         1186         1137 
TCGA-A3-3331 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 
        1485          910         1307         2270         2274          735 
TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3434 
         567          861         1993         2223         2017         2087 
TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3460 TCGA-B0-4706 TCGA-B0-4710 
        1471         1779          874          951           26           96 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5399 
        1092          359          797          657          554          652 
TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 
         449         2408         1487         3076         1420         1727 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5711 
        2583         2741         1082         1203         3668         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 
        2722         1865         1092          374          648          952 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5843 TCGA-B4-5844 
         417          507          291           38           11            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 
         511          826          838          762          750          700 
TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5553 
         722           26          737          505          194          435 
TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4174 TCGA-BP-4325 
         528         3377         3074         3037         1879         2964 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4756 
         845         1888          461         1666         1367          374 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4776 
        2208         2372         1462          400         1843          411 
TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4992 
        1384         1433         1632         1124         1413          501 
TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 TCGA-BP-5174 
         177         1371         1177         1126         1140         2257 
TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 
        1495         1291         1132          406         1011          714 
TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5201 TCGA-BP-5202 TCGA-CJ-4639 TCGA-CJ-4643 
         408          749          951           29         2308         1793 
TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4892 TCGA-CJ-4893 
        1498         2353         2186         2125         1521          750 
TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4916 
         841         1808         1528         1560         1792         1373 
TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 
        2430          552         1883         1889         2231         2038 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6093 
        2548         2799         2609         2226         2378         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 
         774           18         1787         1843         1928         2830 
TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 
        1929           25         1683         1732         1683         1430 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5565 
         662         1446         2439          373         1905         1329 
TCGA-DV-5566 TCGA-DV-5569 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 
        1398          355          551          206          127          305 
TCGA-GK-A6C7 TCGA-MW-A4EC 
          61          330 

$subtype3
TCGA-A3-3319 TCGA-A3-3357 TCGA-A3-3363 TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3382 
        1130         2688          319         1314          630          574 
TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 
        2566          480         2192         2044         1745         1423 
TCGA-AK-3445 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3458 
        1280         1217         1481         1397         1143         1168 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 
         369         1238          110          616           18          183 
TCGA-B0-5097 TCGA-B0-5117 TCGA-B0-5400 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5706 
         665          535         1132         1835         1732         2414 
TCGA-B0-5707 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 
        2828          992           51          358          315          656 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 
         175            7           16          523          777          788 
TCGA-B8-5158 TCGA-B8-5551 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54F TCGA-B8-A54G 
         636           15          830          909          519           53 
TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4176 TCGA-BP-4326 TCGA-BP-4334 
         150         2746         2839         1955         1625          645 
TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 
        2859          970          182         1731         2080          354 
TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 
        1107          204         2660         2172         1785         1834 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4989 
         205         1746          454         1413          785          118 
TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5175 
        1308          932          563         1071          193          932 
TCGA-BP-5180 TCGA-BP-5189 TCGA-BP-5191 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4869 
        2263          822          967         1416         1998         2554 
TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4901 
        2423         2259         1955         2014         1759         1450 
TCGA-CJ-4912 TCGA-CJ-5676 TCGA-CJ-6027 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 
        1657         2575         1855         2271         1404         1943 
TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 
        1868         1789         1712          330         1740          685 
TCGA-CZ-5468 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-DV-5567 TCGA-MM-A564 
          59          386         2067         1997         1470          607 
TCGA-MM-A84U 
         337 

subtype1 subtype2 subtype3 
       3        7        7 
subtype1 subtype2 subtype3 
    3431     3668     2859 
subtype1 subtype2 subtype3 
    1459     1318     1143 
[1] "3.0 - 3431.0 (1459.0)" "7.0 - 3668.0 (1318.0)" "7.0 - 2859.0 (1143.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      72       11        28       10
  subtype2     108       20        45       28
  subtype3      64       24        52       42
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         72      108       64
  STAGE II        11       20       24
  STAGE III       28       45       52
  STAGE IV        10       28       42
[1] 4 3
[1] 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
  subtype1  73  11  33   4
  subtype2 109  26  64   2
  subtype3  67  30  80   5
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       73      109       67
  T2       11       26       30
  T3       33       64       80
  T4        4        2        5
[1] 4 3
[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
  subtype1 55  3
  subtype2 87  2
  subtype3 83 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    3
  subtype2   87    2
  subtype3   83   13
   clus
vv  subtype1 subtype2 subtype3
  0       55       87       83
  1        3        2       13
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1 104   9   6
  subtype2 168  27   6
  subtype3 133  42   7
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      104      168      133
  M1        9       27       42
  MX        6        6        7
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus         0   1
  subtype1  43  78
  subtype2  87 114
  subtype3  48 134
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   78
  subtype2   87  114
  subtype3   48  134
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       43       87       48
  MALE         78      114      134
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype1 subtype2 subtype3 
       4        2        6 
 [1] "subtype1" "subtype3" "subtype3" "subtype3" "subtype3" "subtype3"
 [7] "subtype1" "subtype3" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                        15   104
  subtype2     3                        12   182
  subtype3     4                        17   159
D9V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        3        4
  BLACK OR AFRICAN AMERICAN       15       12       17
  WHITE                          104      182      159
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
          cls
clus         0   1
  subtype1   2  78
  subtype2  12 130
  subtype3  10 125
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   78
  subtype2   12  130
  subtype3   10  125
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2       12       10
  NOT HISPANIC OR LATINO       78      130      125
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  92   7
  subtype2  85  10
  subtype3 147   5
  subtype4  13   1
subtype1 subtype2 subtype3 subtype4 
      99       95      152       14 
subtype1 subtype2 subtype3 subtype4 
       7       10        5        1 
$subtype1
TCGA-6D-AA2E TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3362 
         267           16         1493         1610         1385         1559 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3436 
        2274         1621         1070          574         3343         2044 
TCGA-AK-3445 TCGA-AK-3454 TCGA-AK-3461 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5108 
        1280          874          853           18          183          911 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 
          59          493         1132         3431         1605         3117 
TCGA-B0-5710 TCGA-B0-5812 TCGA-B2-5636 TCGA-B2-5641 TCGA-B4-5378 TCGA-B8-4620 
        1459         2963          919          656          175          777 
TCGA-B8-5162 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54F 
          36          522          434           15         1046          519 
TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4160 TCGA-BP-4169 
         256          150          110           24         2881          701 
TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4345 TCGA-BP-4760 TCGA-BP-4765 
        1893         1670         1625         1516         2361         2184 
TCGA-BP-4769 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 
        1876         2080          354         1489          620         1124 
TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4965 TCGA-BP-4967 
        1459          211         2660         2172         1871          205 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4972 TCGA-BP-4983 TCGA-BP-4989 TCGA-BP-4998 
        1746          433         1502         1413          118          932 
TCGA-BP-5008 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5187 TCGA-BP-5196 
        1071          193         2412          293          406         1018 
TCGA-BP-5198 TCGA-BP-5200 TCGA-CJ-4634 TCGA-CJ-4882 TCGA-CJ-4889 TCGA-CJ-4901 
         603         1063         1820         1883         1946         1450 
TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-5671 TCGA-CJ-6031 
        1520         1496         1499         1531         1943         1906 
TCGA-CW-5583 TCGA-CW-5588 TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5464 TCGA-CZ-5988 
        2489         2017         1943         1712         1740          693 
TCGA-DV-5565 TCGA-DV-5567 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 
        1329         1470         1130         2016         1729          551 
TCGA-EU-5905 TCGA-G6-A8L7 TCGA-MM-A563 
         119         1727          591 

$subtype2
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3331 TCGA-A3-3357 TCGA-A3-3363 TCGA-A3-3372 
        1491         1130         1485         2688          319          735 
TCGA-A3-3374 TCGA-A3-3378 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3430 TCGA-AK-3433 
        1314          630          617         2566          480         2192 
TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3456 TCGA-AK-3458 
        1745         1423         1217         1481         1143         1168 
TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-5116 TCGA-B0-5117 
         369         1238          110          616          657          535 
TCGA-B0-5402 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5703 TCGA-B0-5706 
         449         1727         1835         1732         1203         2414 
TCGA-B0-5707 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5832 TCGA-B4-5835 
        2828          992           51          417            7           16 
TCGA-B4-5838 TCGA-B4-5844 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
         166            7          523          788          700          636 
TCGA-B8-5546 TCGA-B8-A54D TCGA-B8-A54E TCGA-B8-A54G TCGA-BP-4161 TCGA-BP-4163 
         505          830          909           53         2746         2839 
TCGA-BP-4176 TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4338 
        1955          845         1133          645          461         2859 
TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4777 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4962 
         374          182         1731         1107          204         1785 
TCGA-BP-4963 TCGA-BP-4971 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4993 TCGA-BP-4994 
        1834         1487         1384          454          177         1308 
TCGA-BP-5000 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5189 TCGA-BP-5190 
         563          932         2263         1165          822         1011 
TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5201 TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4873 
         967          749          951         1998         2554         2259 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4884 TCGA-CJ-4904 TCGA-CJ-5681 TCGA-CW-5581 
        2353         2014         1759         1792          552         2799 
TCGA-CW-5591 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5458 TCGA-CZ-5466 TCGA-CZ-5468 
        2271         1868         1789         1732          685           59 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-DV-5568 TCGA-MM-A84U 
         386         2067         1997          370          337 

$subtype3
TCGA-A3-3307 TCGA-A3-3313 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
        1436          735         1508         1478         1106         1186 
TCGA-A3-3326 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3380 
        1137          910         1307          873         2270          567 
TCGA-A3-3383 TCGA-A3-3385 TCGA-A3-A8CQ TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3434 
         861         1993            3         2223         2017         2087 
TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3453 TCGA-AK-3460 TCGA-B0-4706 TCGA-B0-4710 
        1471         1779         1397          951           26           96 
TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5690 
        1092          359          797          554          652         2408 
TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 
        1487         3076         1420         2583         2741         1082 
TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-4099 
        3668         2931         2722         1865         1092          374 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-A4SR TCGA-B4-5377 
         648          952          358          315          507          291 
TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
          38          141           11          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5549 
         762          750          722           26          737          194 
TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 
         435          528         3377         3074         3037           13 
TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 
        1879         2964         1888         1666         1367          970 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4775 TCGA-BP-4776 
        2208         2372         1462          400         1843          411 
TCGA-BP-4961 TCGA-BP-4969 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4987 
        1935         1794         1433         1632         1014         1124 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4995 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
        1413          501         1371         1177         1126         1140 
TCGA-BP-5174 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        2257         1495         1291         1133         1132          693 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5199 TCGA-BP-5202 TCGA-CJ-4639 TCGA-CJ-4643 
         714          408         1355           29         2308         1793 
TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 
        1498         1955         2186         2125         1952         1521 
TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 TCGA-CJ-4912 
         750          841         1808         1528         1560         1657 
TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        1373         2430         2575         1883         1889         2231 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6088 
        2038         2548         2609         2226         2378         3222 
TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 
        3146          774           18         1787         1843         1928 
TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 
        2830         1929           25         1683         1683         1430 
TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 
         330          662         1446         2439          373         1905 
TCGA-DV-5566 TCGA-DV-5569 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A8L6 TCGA-GK-A6C7 
        1398          355          206          127          305           61 
TCGA-MM-A564 TCGA-MW-A4EC 
         607          330 

$subtype4
TCGA-AK-3431 TCGA-B0-5097 TCGA-B8-5163 TCGA-BP-4167 TCGA-BP-4986 TCGA-CJ-4635 
        1853          665          822         2718          785         1416 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4890 TCGA-CJ-6027 
        1924         1628         2423         1435         2085         1855 
TCGA-CW-6090 TCGA-CZ-4854 
        2552         1404 

subtype1 subtype2 subtype3 subtype4 
      15        7        3      665 
subtype1 subtype2 subtype3 subtype4 
    3431     2859     3668     2718 
subtype1 subtype2 subtype3 subtype4 
  1385.0   1107.0   1372.0   1740.5 
[1] "15.0 - 3431.0 (1385.0)"  "7.0 - 2859.0 (1107.0)"  
[3] "3.0 - 3668.0 (1372.0)"   "665.0 - 2718.0 (1740.5)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      79       10        36       17
  subtype2      49       17        35       33
  subtype3     107       24        42       18
  subtype4       9        4        12       12
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         79       49      107        9
  STAGE II        10       17       24        4
  STAGE III       36       35       42       12
  STAGE IV        17       33       18       12
[1] 4 4
[1] 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
  subtype1  80  11  46   5
  subtype2  51  23  57   3
  subtype3 109  28  53   1
  subtype4   9   5  21   2
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       80       51      109        9
  T2       11       23       28        5
  T3       46       57       53       21
  T4        5        3        1        2
[1] 4 4
[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
  subtype1 60  8
  subtype2 65  8
  subtype3 84  1
  subtype4 16  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    8
  subtype2   65    8
  subtype3   84    1
  subtype4   16    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       60       65       84       16
  1        8        8        1        1
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1  MX
  subtype1 118  15   7
  subtype2  98  32   4
  subtype3 165  18   8
  subtype4  24  13   0
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0      118       98      165       24
  M1       15       32       18       13
  MX        7        4        8        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  54  88
  subtype2  36  98
  subtype3  82 109
  subtype4   6  31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54   88
  subtype2   36   98
  subtype3   82  109
  subtype4    6   31
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       54       36       82        6
  MALE         88       98      109       31
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
      14       10       16        1 
 [1] "subtype3" "subtype3" "subtype3" "subtype1" "subtype2" "subtype2"
 [7] "subtype2" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
[13] "subtype3" "subtype2" "subtype3" "subtype2" "subtype3" "subtype1"
[19] "subtype1" "subtype2" "subtype3" "subtype1" "subtype3" "subtype3"
[25] "subtype2" "subtype3" "subtype1" "subtype3" "subtype1" "subtype2"
[31] "subtype3" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[37] "subtype1" "subtype3" "subtype3" "subtype1"
D10V9, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                        18   120
  subtype2     2                        12   117
  subtype3     2                        14   171
  subtype4     0                         0    37
D10V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            4        2        2        0
  BLACK OR AFRICAN AMERICAN       18       12       14        0
  WHITE                          120      117      171       37
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, binary
          cls
clus         0   1
  subtype1   2  91
  subtype2   4  96
  subtype3  14 120
  subtype4   4  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   91
  subtype2    4   96
  subtype3   14  120
  subtype4    4   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4       14        4
  NOT HISPANIC OR LATINO       91       96      120       26
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 21  1
  subtype2 18  0
  subtype3 37  4
  subtype4 17  1
subtype1 subtype2 subtype3 subtype4 
      22       18       41       18 
subtype1 subtype2 subtype3 subtype4 
       1        0        4        1 
$subtype1
TCGA-6D-AA2E TCGA-A3-A8CQ TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 TCGA-B2-3924 
         267            3         1745          369          992         1092 
TCGA-B2-5635 TCGA-B8-A54H TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4173 TCGA-BP-4961 
         315          256          528          110         1893         1935 
TCGA-BP-4982 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CZ-4854 TCGA-G6-A8L6 
        1014         1498         2353         2014         1404          305 
TCGA-GK-A6C7 TCGA-MM-A563 TCGA-MM-A564 TCGA-MM-A84U 
          61          591          607          337 

$subtype2
TCGA-A3-3317 TCGA-A3-3387 TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 TCGA-B2-5636 
        1491          617         3431         1605         3117          919 
TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5552 TCGA-B8-A8YJ TCGA-BP-4789 TCGA-BP-4804 
         522          434         1046           24         1489         1459 
TCGA-BP-4807 TCGA-BP-4970 TCGA-BP-5008 TCGA-CJ-4889 TCGA-CJ-5671 TCGA-CJ-6031 
         211          433         1071         1946         1943         1906 

$subtype3
TCGA-A3-3358 TCGA-AK-3458 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5399 TCGA-B0-5692 
        1307         1168           26           96          652         1487 
TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 
        3076         1420         1727         2741         1082         3668 
TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 TCGA-B8-5553 TCGA-BP-4969 TCGA-BP-4976 
         417          291          141          435         1794         1632 
TCGA-BP-4995 TCGA-BP-5001 TCGA-CJ-4878 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5681 
        1371         1177         2186         2430         2575          552 
TCGA-CJ-5683 TCGA-CJ-6032 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4864 
        1889         2548         2609         2378         3222         2830 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5989 
          25         1683         1683          662          685         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5573 TCGA-EU-5904 
        1329         1398          355         1130          551 

$subtype4
TCGA-B2-5633 TCGA-B8-4621 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4761 TCGA-BP-4959 
         358          788           15          150          182         2660 
TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-4998 TCGA-CJ-4876 
         205         1746          118          501          932         1955 
TCGA-CJ-4890 TCGA-CJ-5686 TCGA-CZ-4858 TCGA-CZ-5464 TCGA-CZ-5470 TCGA-G6-A8L7 
        2085         2038         1943         1740          386         1727 

subtype1 subtype2 subtype3 subtype4 
       3       24       25       15 
subtype1 subtype2 subtype3 subtype4 
    2353     3431     3668     2660 
subtype1 subtype2 subtype3 subtype4 
     599     1265     1398      860 
[1] "3.0 - 2353.0 (599.0)"   "24.0 - 3431.0 (1265.0)" "25.0 - 3668.0 (1398.0)"
[4] "15.0 - 2660.0 (860.0)" 
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      17        5         3        5
  subtype2      15        1         4        2
  subtype3      22        7        12        8
  subtype4      14        4         6       11
D11V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         17       15       22       14
  STAGE II         5        1        7        4
  STAGE III        3        4       12        6
  STAGE IV         5        2        8       11
[1] 4 4
[1] 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
  subtype1 17  6  6  1
  subtype2 16  1  4  1
  subtype3 22  8 19  0
  subtype4 15  4 13  3
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       17       16       22       15
  T2        6        1        8        4
  T3        6        4       19       13
  T4        1        1        0        3
[1] 4 4
[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
  subtype1  6  1
  subtype2  9  1
  subtype3 23  0
  subtype4 17  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6    1
  subtype2    9    1
  subtype3   23    0
  subtype4   17    3
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0        6        9       23       17
  1        1        1        0        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 13  4 12
  subtype2 20  1  0
  subtype3 41  8  0
  subtype4 23 10  2
D11V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       13       20       41       23
  M1        4        1        8       10
  MX       12        0        0        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V7, binary
          cls
clus        0  1
  subtype1 15 15
  subtype2  6 16
  subtype3 20 29
  subtype4  6 29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   15
  subtype2    6   16
  subtype3   20   29
  subtype4    6   29
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       15        6       20        6
  MALE         15       16       29       29
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V8, continuous
D11V9, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype4"              
clus
subtype1 subtype2 subtype4 
       3        1        2 
[1] "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        16    14
  subtype2     1                         2    18
  subtype3     0                         0    48
  subtype4     2                         4    28
D11V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        0        2
  BLACK OR AFRICAN AMERICAN       16        2        0        4
  WHITE                           14       18       48       28
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V11, binary
          cls
clus        0  1
  subtype1  0 24
  subtype2  1 13
  subtype3  4 37
  subtype4  1 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   24
  subtype2    1   13
  subtype3    4   37
  subtype4    1   22
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        1        4        1
  NOT HISPANIC OR LATINO       24       13       37       22
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 23  1
  subtype2 35  1
  subtype3 35  4
subtype1 subtype2 subtype3 
      24       36       39 
subtype1 subtype2 subtype3 
       1        1        4 
$subtype1
TCGA-6D-AA2E TCGA-A3-A8CQ TCGA-AK-3440 TCGA-AK-3465 TCGA-B2-3923 TCGA-B2-3924 
         267            3         1745          369          992         1092 
TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5636 TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A54J 
         358          315          919          256          150          528 
TCGA-B8-A7U6 TCGA-BP-4173 TCGA-BP-4804 TCGA-BP-4961 TCGA-BP-4982 TCGA-CJ-4870 
         110         1893         1459         1935         1014         1498 
TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CZ-4854 TCGA-G6-A8L6 TCGA-GK-A6C7 TCGA-MM-A84U 
        2353         2014         1404          305           61          337 

$subtype2
TCGA-A3-3317 TCGA-A3-3387 TCGA-AK-3458 TCGA-B0-5399 TCGA-B0-5691 TCGA-B0-5696 
        1491          617         1168          652         3431         1727 
TCGA-B0-5702 TCGA-B0-5709 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
        1605         3117          522          434           15         1046 
TCGA-B8-A8YJ TCGA-BP-4761 TCGA-BP-4789 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4967 
          24          182         1489          211         2660          205 
TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4989 TCGA-BP-4998 TCGA-BP-5008 TCGA-CJ-4889 
        1746          433          118          932         1071         1946 
TCGA-CJ-4890 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-6031 TCGA-CW-5589 TCGA-CW-6088 
        2085         1943         2575         1906         2378         3222 
TCGA-CZ-4858 TCGA-CZ-5464 TCGA-DV-5573 TCGA-G6-A8L7 TCGA-MM-A563 TCGA-MM-A564 
        1943         1740         1130         1727          591          607 

$subtype3
TCGA-A3-3358 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
        1307           26           96         1487         3076         1420 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5705 TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5836 
        2741         1082         3668          417          291          141 
TCGA-B8-4621 TCGA-B8-5553 TCGA-BP-4969 TCGA-BP-4976 TCGA-BP-4992 TCGA-BP-4995 
         788          435         1794         1632          501         1371 
TCGA-BP-5001 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5683 
        1177         1955         2186         2430          552         1889 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5585 TCGA-CZ-4864 TCGA-CZ-5453 TCGA-CZ-5457 
        2038         2548         2609         2830           25         1683 
TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5989 TCGA-DV-5565 
        1683          662          685          386         1905         1329 
TCGA-DV-5566 TCGA-DV-5569 TCGA-EU-5904 
        1398          355          551 

subtype1 subtype2 subtype3 
       3       15       25 
subtype1 subtype2 subtype3 
    2353     3431     3668 
subtype1 subtype2 subtype3 
   723.5   1328.5   1371.0 
[1] "3.0 - 2353.0 (723.5)"   "15.0 - 3431.0 (1328.5)" "25.0 - 3668.0 (1371.0)"
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      20        4         3        5
  subtype2      27        4        12       13
  subtype3      21        9        10        8
D12V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         20       27       21
  STAGE II         4        4        9
  STAGE III        3       12       10
  STAGE IV         5       13        8
[1] 4 3
[1] 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
  subtype1 21  5  5  1
  subtype2 27  4 21  4
  subtype3 22 10 16  0
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       21       27       22
  T2        5        4       10
  T3        5       21       16
  T4        1        4        0
[1] 4 3
[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
  subtype1  7  1
  subtype2 26  4
  subtype3 22  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7    1
  subtype2   26    4
  subtype3   22    0
   clus
vv  subtype1 subtype2 subtype3
  0        7       26       22
  1        1        4        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 16  4 11
  subtype2 41 11  3
  subtype3 40  8  0
D12V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       16       41       40
  M1        4       11        8
  MX       11        3        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V7, binary
          cls
clus        0  1
  subtype1 15 17
  subtype2 10 46
  subtype3 22 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   17
  subtype2   10   46
  subtype3   22   26
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       10       22
  MALE         17       46       26
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, continuous
D12V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       2        3        1 
[1] "subtype2" "subtype2" "subtype2"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        15    17
  subtype2     3                         6    46
  subtype3     0                         1    45
D12V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        3        0
  BLACK OR AFRICAN AMERICAN       15        6        1
  WHITE                           17       46       45
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, binary
          cls
clus        0  1
  subtype1  0 26
  subtype2  3 35
  subtype3  3 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   26
  subtype2    3   35
  subtype3    3   35
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        3        3
  NOT HISPANIC OR LATINO       26       35       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
