[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/10005959/KIRC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRC-TP/10668118/KIRC-TP.mergedcluster.txt"

nPatients in clinical file=515, in cluster file=537, common to both=515
[1]  12 515
[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 
202 145 158 
  1   2   3 
202 145 158 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
118  72 107 
  1   2   3 
118  72 107 
[1] "RPPA_CNMF"
[1] 3
  1   2   3   4   5   6 
101  90  86  76  44  57 
  1   2   3   4   5   6 
101  90  86  76  44  57 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
 95 203 156 
  1   2   3 
 95 203 156 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
212 109 186 
  1   2   3 
212 109 186 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
118 173 126  29  32  29 
  1   2   3   4   5   6 
118 173 126  29  32  29 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
119 203 170 
  1   2   3 
119 203 170 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
156 233 103 
  1   2   3 
156 233 103 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
52 91 87 
 1  2  3 
52 91 87 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3 
90 96 44 
 1  2  3 
90 96 44 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 515 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A3-3306 TCGA-A3-3307 TCGA-A3-3308 TCGA-A3-3311 TCGA-A3-3313 TCGA-A3-3316 
        1120         1436           16           NA          735         1493 
TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3323 TCGA-A3-3324 
        1491         1130         1508         1478         1106         1186 
TCGA-A3-3325 TCGA-A3-3326 TCGA-A3-3328 TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3335 
         751         1137         1385          706         1485          665 
TCGA-A3-3336 TCGA-A3-3343 TCGA-A3-3346 TCGA-A3-3347 TCGA-A3-3349 TCGA-A3-3351 
        1043          945           NA         1610         1385          910 
TCGA-A3-3352 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 TCGA-A3-3363 
          NA         2688         1307         2504         1559          319 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3374 
         873         2270         2274          735         1621         1314 
TCGA-A3-3376 TCGA-A3-3378 TCGA-A3-3380 TCGA-A3-3382 TCGA-A3-3383 TCGA-A3-3385 
        1070          630          567          574          861         1993 
TCGA-A3-3387 TCGA-A3-A8CQ TCGA-A3-A8OX TCGA-AK-3425 TCGA-AK-3426 TCGA-AK-3427 
         617            3           NA         3343           NA         2566 
TCGA-AK-3428 TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3431 TCGA-AK-3433 TCGA-AK-3434 
        2223         2017          480         1853         2192         2087 
TCGA-AK-3436 TCGA-AK-3440 TCGA-AK-3443 TCGA-AK-3444 TCGA-AK-3445 TCGA-AK-3447 
        2044         1745         1423         1471         1280         1217 
TCGA-AK-3450 TCGA-AK-3451 TCGA-AK-3453 TCGA-AK-3454 TCGA-AK-3455 TCGA-AK-3456 
        1779         1481         1397          874           NA         1143 
TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AK-3465 TCGA-AS-3777 TCGA-AS-3778 
        1168          951          853          369         1238           43 
TCGA-B0-4688 TCGA-B0-4690 TCGA-B0-4691 TCGA-B0-4693 TCGA-B0-4694 TCGA-B0-4696 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4697 TCGA-B0-4698 TCGA-B0-4699 TCGA-B0-4700 TCGA-B0-4701 TCGA-B0-4703 
          NA           NA          110           NA           NA           NA 
TCGA-B0-4706 TCGA-B0-4707 TCGA-B0-4710 TCGA-B0-4712 TCGA-B0-4713 TCGA-B0-4714 
          26           NA           96           NA           NA           NA 
TCGA-B0-4718 TCGA-B0-4810 TCGA-B0-4811 TCGA-B0-4813 TCGA-B0-4814 TCGA-B0-4815 
         616           NA           NA           18           NA           NA 
TCGA-B0-4816 TCGA-B0-4817 TCGA-B0-4818 TCGA-B0-4819 TCGA-B0-4821 TCGA-B0-4822 
          NA           NA           NA          183           NA           NA 
TCGA-B0-4823 TCGA-B0-4824 TCGA-B0-4827 TCGA-B0-4828 TCGA-B0-4833 TCGA-B0-4834 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4836 TCGA-B0-4837 TCGA-B0-4838 TCGA-B0-4839 TCGA-B0-4841 TCGA-B0-4842 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4843 TCGA-B0-4844 TCGA-B0-4845 TCGA-B0-4846 TCGA-B0-4847 TCGA-B0-4848 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-4849 TCGA-B0-4852 TCGA-B0-4945 TCGA-B0-5075 TCGA-B0-5077 TCGA-B0-5080 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5081 TCGA-B0-5083 TCGA-B0-5084 TCGA-B0-5085 TCGA-B0-5088 TCGA-B0-5092 
          NA           NA           NA           NA           NA           NA 
TCGA-B0-5094 TCGA-B0-5095 TCGA-B0-5096 TCGA-B0-5097 TCGA-B0-5098 TCGA-B0-5099 
          NA           NA           NA          665           NA           NA 
TCGA-B0-5100 TCGA-B0-5102 TCGA-B0-5104 TCGA-B0-5106 TCGA-B0-5107 TCGA-B0-5108 
          NA           NA           NA           NA           NA          911 
TCGA-B0-5109 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5117 
          NA         1092          359          797          657          535 
TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5400 TCGA-B0-5402 
          59          493          554          652         1132          449 
TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5694 TCGA-B0-5695 
        2408         3431         1487         3076           NA         1420 
TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5701 
        1727         1835         2583         2741         1082         1732 
TCGA-B0-5702 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 
        1605         1203         3668         2414         2828         3117 
TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3923 
        1459         2931         2722         1865         2963          992 
TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1092           51          374          648          952          358 
TCGA-B2-5635 TCGA-B2-5636 TCGA-B2-5639 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B4-5377 
         315          919          417          656          507          291 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5834 TCGA-B4-5835 TCGA-B4-5836 TCGA-B4-5838 
         175            7           38           16          141          166 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4143 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 
          11            7           NA          511          826          838 
TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 
         762          750          523          777          788          700 
TCGA-B8-5158 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5165 
         636          722           36          822           26          737 
TCGA-B8-5545 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 
         522          505          194          434           15         1046 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H TCGA-B8-A54I 
         435          830          519           53          256          150 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-B8-A8YJ TCGA-BP-4158 TCGA-BP-4159 TCGA-BP-4160 
          66          110           24         3377           NA         2881 
TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4163 TCGA-BP-4164 TCGA-BP-4165 TCGA-BP-4166 
        2746         3074         2839           NA         3037           13 
TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4170 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
        2718          701           NA         1893         1879         1955 
TCGA-BP-4177 TCGA-BP-4325 TCGA-BP-4326 TCGA-BP-4327 TCGA-BP-4329 TCGA-BP-4330 
        1670         2964         1625           NA          845         1888 
TCGA-BP-4331 TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4337 TCGA-BP-4338 
          NA         1133          645          461           NA         2859 
TCGA-BP-4340 TCGA-BP-4341 TCGA-BP-4342 TCGA-BP-4343 TCGA-BP-4344 TCGA-BP-4345 
          NA           NA           NA           NA         1666         1516 
TCGA-BP-4346 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 TCGA-BP-4352 TCGA-BP-4353 
          NA         1367          372          970           NA           NA 
TCGA-BP-4354 TCGA-BP-4355 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 
          NA           NA          374         2208         2372         2361 
TCGA-BP-4761 TCGA-BP-4762 TCGA-BP-4763 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
         182           NA           NA         2184         1462          400 
TCGA-BP-4769 TCGA-BP-4770 TCGA-BP-4771 TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 
        1876           NA           NA         1885         1843          411 
TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4787 TCGA-BP-4789 
        1731         2080          354         1854           NA         1489 
TCGA-BP-4790 TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4798 TCGA-BP-4799 TCGA-BP-4801 
          NA          620         1107           NA           NA         1124 
TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4961 
         204         1459          211         2660         2172         1935 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
        1785         1834         1862         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4974 
        1794          433         1487         1502         1384           NA 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4981 TCGA-BP-4982 TCGA-BP-4983 
        1433         1632          454           NA         1014         1413 
TCGA-BP-4985 TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-4988 TCGA-BP-4989 TCGA-BP-4991 
          NA          785         1124           NA          118         1413 
TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
         501          177         1308         1371          932         1266 
TCGA-BP-5000 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 
         563         1177         1126          840         1140         1071 
TCGA-BP-5009 TCGA-BP-5010 TCGA-BP-5168 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5173 
          NA           NA           NA          193         2412           NA 
TCGA-BP-5174 TCGA-BP-5175 TCGA-BP-5176 TCGA-BP-5177 TCGA-BP-5178 TCGA-BP-5180 
        2257          932           NA          293           NA         2263 
TCGA-BP-5181 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 
        1495         1165         1291         1133         1132          693 
TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 TCGA-BP-5192 TCGA-BP-5194 
         406          822         1011          967          714          408 
TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5201 
         749         1018          603         1355         1063          951 
TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4635 TCGA-CJ-4636 TCGA-CJ-4637 TCGA-CJ-4638 
          29         1820         1416         1924           NA           NA 
TCGA-CJ-4639 TCGA-CJ-4640 TCGA-CJ-4641 TCGA-CJ-4642 TCGA-CJ-4643 TCGA-CJ-4644 
        2308         1998           NA         1628         1793           NA 
TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
         646         2554         1498         2423         1435         2259 
TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4881 TCGA-CJ-4882 
        2283         2353         1955         2186         2014         1883 
TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4887 TCGA-CJ-4888 TCGA-CJ-4889 
        1759         2125         1952           NA           NA         1946 
TCGA-CJ-4890 TCGA-CJ-4891 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4895 
        2085           NA         1521          750          841           NA 
TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4900 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 
        1808         1528           NA         1450         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-4912 TCGA-CJ-4913 
        1792         1496         1499         1531         1657           NA 
TCGA-CJ-4916 TCGA-CJ-4918 TCGA-CJ-4920 TCGA-CJ-4923 TCGA-CJ-5671 TCGA-CJ-5672 
        1373           NA           NA           NA         1943           NA 
TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5677 TCGA-CJ-5678 TCGA-CJ-5679 TCGA-CJ-5680 
        2430         2575           NA           NA           NA           NA 
TCGA-CJ-5681 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-5689 
         552         1883         1889         2231         2038           NA 
TCGA-CJ-6027 TCGA-CJ-6028 TCGA-CJ-6030 TCGA-CJ-6031 TCGA-CJ-6032 TCGA-CJ-6033 
        1855           NA           NA         1906         2548           NA 
TCGA-CW-5580 TCGA-CW-5581 TCGA-CW-5583 TCGA-CW-5584 TCGA-CW-5585 TCGA-CW-5587 
          NA         2799         2489           NA         2609         2226 
TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-5590 TCGA-CW-5591 TCGA-CW-6087 TCGA-CW-6088 
        2017         2378           NA         2271           NA         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6096 TCGA-CW-6097 TCGA-CZ-4853 TCGA-CZ-4854 
        2552         3146         2701           NA          774         1404 
TCGA-CZ-4856 TCGA-CZ-4857 TCGA-CZ-4858 TCGA-CZ-4859 TCGA-CZ-4860 TCGA-CZ-4861 
          18           NA         1943         1787           NA           NA 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4865 TCGA-CZ-4866 TCGA-CZ-5451 
        1843         1928         2830           NA         1868         1929 
TCGA-CZ-5452 TCGA-CZ-5453 TCGA-CZ-5454 TCGA-CZ-5455 TCGA-CZ-5456 TCGA-CZ-5457 
        1789           25           NA           NA         1712         1683 
TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5462 TCGA-CZ-5463 
        1732         1683         1430          330           NA          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5467 TCGA-CZ-5468 TCGA-CZ-5469 
        1740         1446          685           NA           59          946 
TCGA-CZ-5470 TCGA-CZ-5982 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 
         386         2439         2067         1997          373          435 
TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
         693         1905         1329         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-DV-5576 TCGA-EU-5904 
         355         1130          723         1729           NA          551 
TCGA-EU-5905 TCGA-EU-5906 TCGA-EU-5907 TCGA-G6-A5PC TCGA-GK-A6C7 
         119          206          127           NA           61 
Variable 1:'AGE':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=159,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=342,	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=58,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=5,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=2,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 20:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=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 515 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 
258  67 179  11 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
258  67 179  11 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
258  67 179  11 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
258  67 179  11 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=5, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=6, binary=FALSE, numeric=TRUE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = 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 155   7
  subtype2  96   9
  subtype3  87  10
subtype1 subtype2 subtype3 
     162      105       97 
subtype1 subtype2 subtype3 
       7        9       10 
$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-A3-3351 TCGA-A3-3357 TCGA-A3-3358 TCGA-A3-3359 TCGA-A3-3362 
        1485          910         2688         1307         2504         1559 
TCGA-A3-3365 TCGA-A3-3367 TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3378 TCGA-A3-3380 
         873         2270         2274         1621          630          567 
TCGA-A3-3383 TCGA-A3-3387 TCGA-A3-A8CQ TCGA-AK-3429 TCGA-AK-3431 TCGA-AK-3433 
         861          617            3         2017         1853         2192 
TCGA-AK-3451 TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AK-3461 TCGA-AS-3778 
        1481          874         1168          951          853           43 
TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5120 
          26          616         1092          797           59          493 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5697 TCGA-B0-5699 
         554          652         1487         3076         1835         2741 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5706 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        1203         3668         2414         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 
        1865         2963         1092          648          952          358 
TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5844 
         417          507          291           38          141            7 
TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5164 
         511          826          722           36          822           26 
TCGA-B8-5552 TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54H 
        1046          435          830          519           53          256 
TCGA-B8-A54J TCGA-B8-A7U6 TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4163 TCGA-BP-4165 
          66          110         3377         2881         2839         3037 
TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4344 
          13          701          845         1888         1133         1666 
TCGA-BP-4347 TCGA-BP-4758 TCGA-BP-4774 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4789 
        1367         2208         1885          411         1731         1489 
TCGA-BP-4801 TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4972 TCGA-BP-4975 
        1124          211         1935         1871         1502         1433 
TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4999 
         454         1014         1413          177         1371         1266 
TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5008 TCGA-BP-5174 TCGA-BP-5181 
        1126          840         1140         1071         2257         1495 
TCGA-BP-5182 TCGA-BP-5184 TCGA-BP-5187 TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 
        1165         1133          406         1011          714          408 
TCGA-BP-5195 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4636 
         749         1355         1063           29         1820         1924 
TCGA-CJ-4639 TCGA-CJ-4642 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4870 TCGA-CJ-4874 
        2308         1628          646         2554         1498         2283 
TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4903 
        1952         1521          841         1528         1520         1560 
TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CW-5581 
        1792         1531         1373         1889         2231         2799 
TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5589 TCGA-CW-6088 TCGA-CZ-4853 TCGA-CZ-4856 
        2489         2609         2378         3222          774           18 
TCGA-CZ-4859 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 
        1787         2830         1929           25         1683         1732 
TCGA-CZ-5459 TCGA-CZ-5463 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-CZ-5989 TCGA-DV-5566 
        1683          662          373          693         1905         1398 
TCGA-DV-5568 TCGA-DV-5569 TCGA-DV-5573 TCGA-EU-5904 TCGA-EU-5906 TCGA-GK-A6C7 
         370          355         1130          551          206           61 

$subtype2
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3363 TCGA-A3-3374 
          16          735          945         1385          319         1314 
TCGA-A3-3376 TCGA-A3-3385 TCGA-AK-3427 TCGA-AK-3428 TCGA-AK-3440 TCGA-AK-3443 
        1070         1993         2566         2223         1745         1423 
TCGA-AK-3444 TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3456 TCGA-AK-3465 TCGA-AS-3777 
        1471         1217         1397         1143          369         1238 
TCGA-B0-4699 TCGA-B0-4710 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5117 
         110           96          183          665          911          535 
TCGA-B0-5400 TCGA-B0-5690 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 
        1132         2408         3431         1420         1727         2583 
TCGA-B0-5702 TCGA-B0-5709 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5635 
        1605         3117          992           51          374          315 
TCGA-B4-5378 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
         175           16          166          838          762          750 
TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5546 
         523          788          700          737          522          505 
TCGA-B8-5550 TCGA-BP-4162 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4326 
         434         3074         2718         1893         1670         1625 
TCGA-BP-4334 TCGA-BP-4335 TCGA-BP-4349 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 
         645          461          372         2372         2361         2184 
TCGA-BP-4769 TCGA-BP-4775 TCGA-BP-4782 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4804 
        1876         1843          354         1854          620         1459 
TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
        1862          205         1746         1794          433         1487 
TCGA-BP-4973 TCGA-BP-4976 TCGA-BP-4983 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5001 
        1384         1632         1413         1308          932         1177 
TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5186 TCGA-BP-5196 TCGA-CJ-4643 TCGA-CJ-4872 
        2412          293          693         1018         1793         1435 
TCGA-CJ-4875 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4885 TCGA-CJ-4889 TCGA-CJ-4890 
        2353         1883         1759         2125         1946         2085 
TCGA-CJ-4897 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CJ-6031 
        1808         1496         1499          552         2038         1906 
TCGA-CW-5588 TCGA-CW-6093 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-5470 TCGA-CZ-5982 
        2017         3146         1843         1928          386         2439 
TCGA-DV-5567 TCGA-DV-5574 TCGA-EU-5905 
        1470          723          119 

$subtype3
TCGA-A3-3306 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3319 TCGA-A3-3325 TCGA-A3-3335 
        1120         1493         1491         1130          751          665 
TCGA-A3-3336 TCGA-A3-3347 TCGA-A3-3372 TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3430 
        1043         1610          735          574         3343          480 
TCGA-AK-3434 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3450 TCGA-B0-4813 TCGA-B0-5113 
        2087         2044         1280         1779           18          359 
TCGA-B0-5116 TCGA-B0-5402 TCGA-B0-5701 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5843 
         657          449         1732          656            7           11 
TCGA-B8-4620 TCGA-B8-5158 TCGA-B8-5549 TCGA-B8-5551 TCGA-B8-A54I TCGA-BP-4161 
         777          636          194           15          150         2746 
TCGA-BP-4174 TCGA-BP-4176 TCGA-BP-4325 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4756 
        1879         1955         2964         2859          970          374 
TCGA-BP-4761 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 
         182         1462          400         2080         1107          204 
TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4986 TCGA-BP-4987 
        2660         2172         1785         1834          785         1124 
TCGA-BP-4989 TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5175 TCGA-BP-5180 
         118          501          563          193          932         2263 
TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5191 TCGA-BP-5198 TCGA-BP-5201 
        1291         1132          822          967          603          951 
TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4878 
        1416         1998         2423         2259         1955         2186 
TCGA-CJ-4881 TCGA-CJ-4893 TCGA-CJ-4901 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5675 
        2014          750         1450         1657         1943         2430 
TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-6027 TCGA-CJ-6032 TCGA-CW-5587 TCGA-CW-5591 
        2575         1883         1855         2548         2226         2271 
TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5456 
        2552         1404         1943         1868         1789         1712 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5466 TCGA-CZ-5468 
        1430          330         1740         1446          685           59 
TCGA-CZ-5469 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5565 TCGA-DV-5575 
         946         2067         1997          435         1329         1729 
TCGA-EU-5907 
         127 

subtype1 subtype2 subtype3 
       3       16        7 
subtype1 subtype2 subtype3 
    3668     3431     3343 
subtype1 subtype2 subtype3 
  1152.5   1385.0   1404.0 
[1] "3.0 - 3668.0 (1152.5)"  "16.0 - 3431.0 (1385.0)" "7.0 - 3343.0 (1404.0)" 
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     119       26        44       13
  subtype2      75       13        32       25
  subtype3      50       17        50       41
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        119       75       50
  STAGE II        26       13       17
  STAGE III       44       32       50
  STAGE IV        13       25       41
[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 119  30  53   0
  subtype2  76  16  46   7
  subtype3  55  21  78   4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      119       76       55
  T2       30       16       21
  T3       53       46       78
  T4        0        7        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 93  3
  subtype2 69  4
  subtype3 68 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93    3
  subtype2   69    4
  subtype3   68   11
   clus
vv  subtype1 subtype2 subtype3
  0       93       69       68
  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 180  14   7
  subtype2 121  23   1
  subtype3 116  41   1
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      180      121      116
  M1       14       23       41
  MX        7        1        1
[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  76 126
  subtype2  61  84
  subtype3  41 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   76  126
  subtype2   61   84
  subtype3   41  117
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       76       61       41
  MALE        126       84      117
[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
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype1 subtype2 subtype3 
       5        1        2 
[1] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                        12   186
  subtype2     4                        16   124
  subtype3     3                         5   147
D3V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        4        3
  BLACK OR AFRICAN AMERICAN       12       16        5
  WHITE                          186      124      147
[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   9 132
  subtype2   6  96
  subtype3   9 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  132
  subtype2    6   96
  subtype3    9  102
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            9        6        9
  NOT HISPANIC OR LATINO      132       96      102
[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 99  4
  subtype2 46  3
  subtype3 53  6
subtype1 subtype2 subtype3 
     103       49       59 
subtype1 subtype2 subtype3 
       4        3        6 
$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           66 
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-GK-A6C7 
          61 

$subtype2
TCGA-A3-3376 TCGA-AK-3425 TCGA-B0-4699 TCGA-B0-4819 TCGA-B0-5108 TCGA-B0-5400 
        1070         3343          110          183          911         1132 
TCGA-B0-5692 TCGA-B0-5697 TCGA-B0-5702 TCGA-B0-5709 TCGA-B2-5633 TCGA-B2-5635 
        1487         1835         1605         3117          358          315 
TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5835 TCGA-B8-4621 TCGA-B8-5162 TCGA-B8-5163 
         919          175           16          788           36          822 
TCGA-B8-5164 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54G TCGA-B8-A54I TCGA-B8-A8YJ 
          26          434           15           53          150           24 
TCGA-BP-4177 TCGA-BP-4760 TCGA-BP-4782 TCGA-BP-4795 TCGA-BP-5170 TCGA-BP-5175 
        1670         2361          354          620         2412          932 
TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5196 TCGA-CJ-4869 
        1165          406          967          749         1018         2554 
TCGA-CJ-4882 TCGA-CJ-4916 TCGA-CJ-5686 TCGA-CJ-6031 TCGA-CW-5587 TCGA-CW-5588 
        1883         1373         2038         1906         2226         2017 
TCGA-CZ-4863 TCGA-CZ-5452 TCGA-CZ-5458 TCGA-DV-5567 TCGA-DV-5568 TCGA-DV-5574 
        1928         1789         1732         1470          370          723 
TCGA-EU-5905 
         119 

$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-5469 
         330         1740         1446          685           59          946 
TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-EU-5907 
         386         2067         1997          435          127 

subtype1 subtype2 subtype3 
       3       15        7 
subtype1 subtype2 subtype3 
    3668     3343     2741 
subtype1 subtype2 subtype3 
    1130      932     1280 
[1] "3.0 - 3668.0 (1130.0)" "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      79       17        13        9
  subtype2      38        2        20       12
  subtype3      21       11        41       34
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         79       38       21
  STAGE II        17        2       11
  STAGE III       13       20       41
  STAGE IV         9       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 79 20 19  0
  subtype2 40  3 25  4
  subtype3 23 16 64  4
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       79       40       23
  T2       20        3       16
  T3       19       25       64
  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 30  3
  subtype3 48  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   51    1
  subtype2   30    3
  subtype3   48    5
   clus
vv  subtype1 subtype2 subtype3
  0       51       30       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   5
  subtype2  58  10   3
  subtype3  73  33   1
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      102       58       73
  M1       10       10       33
  MX        5        3        1
[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 56 62
  subtype2 27 45
  subtype3 21 86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   56   62
  subtype2   27   45
  subtype3   21   86
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       56       27       21
  MALE         62       45       86
[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
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 
       3        4        2 
[1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2" "subtype2"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         9   109
  subtype2     0                        12    60
  subtype3     1                         6    97
D4V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        1
  BLACK OR AFRICAN AMERICAN        9       12        6
  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  3 90
  subtype2  1 59
  subtype3  4 91
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   90
  subtype2    1   59
  subtype3    4   91
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        4
  NOT HISPANIC OR LATINO       90       59       91
[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 74  3
  subtype2 54  5
  subtype3 62  6
  subtype4 52  5
  subtype5 36  0
  subtype6 18  6
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      77       59       68       57       36       24 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       3        5        6        5        0        6 
$subtype1
TCGA-A3-3306 TCGA-A3-3320 TCGA-A3-3329 TCGA-A3-3367 TCGA-A3-3380 TCGA-A3-3383 
        1120         1508          706         2270          567          861 
TCGA-A3-3385 TCGA-AK-3434 TCGA-B0-4706 TCGA-B0-5110 TCGA-B0-5115 TCGA-B0-5119 
        1993         2087           26         1092          797           59 
TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5693 TCGA-B0-5695 
         554          652          449         2408         3076         1420 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        2583         2741         3668         2931         2722         1865 
TCGA-B0-5812 TCGA-B2-4099 TCGA-B2-4101 TCGA-B4-5377 TCGA-B4-5843 TCGA-B4-5844 
        2963          374          648          291           11            7 
TCGA-B8-4153 TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 
         762         3377         2746         2964          845         1888 
TCGA-BP-4335 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4768 TCGA-BP-4774 TCGA-BP-4776 
         461         2208         2372          400         1885          411 
TCGA-BP-4961 TCGA-BP-4975 TCGA-BP-4991 TCGA-BP-4995 TCGA-BP-4999 TCGA-BP-5001 
        1935         1433         1413         1371         1266         1177 
TCGA-BP-5007 TCGA-BP-5170 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5192 TCGA-BP-5201 
        1140         2412         2263         1495          714          951 
TCGA-CJ-4634 TCGA-CJ-4870 TCGA-CJ-4871 TCGA-CJ-4874 TCGA-CJ-4878 TCGA-CJ-4897 
        1820         1498         2423         2283         2186         1808 
TCGA-CJ-4904 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5683 TCGA-CW-5583 
        1792         1373         2430         2575         1889         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CZ-4859 TCGA-CZ-5451 TCGA-CZ-5465 TCGA-CZ-5982 
        2609         2226         1787         1929         1446         2439 
TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5575 TCGA-EU-5906 
         373         1905         1329         1729          206 

$subtype2
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3349 TCGA-A3-3365 TCGA-A3-3376 TCGA-AK-3451 
          16         1493         1385          873         1070         1481 
TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5120 TCGA-B0-5706 TCGA-B0-5710 
         183          665          911          493         2414         1459 
TCGA-B2-5636 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5836 TCGA-B8-5162 TCGA-B8-5163 
         919          175           38          141           36          822 
TCGA-B8-5545 TCGA-B8-5551 TCGA-BP-4169 TCGA-BP-4345 TCGA-BP-4349 TCGA-BP-4765 
         522           15          701         1516          372         2184 
TCGA-BP-4769 TCGA-BP-4784 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4970 
        1876         1854         1459         2172         1785          433 
TCGA-BP-4971 TCGA-BP-4998 TCGA-BP-5177 TCGA-BP-5196 TCGA-BP-5199 TCGA-BP-5200 
        1487          932          293         1018         1355         1063 
TCGA-CJ-4868 TCGA-CJ-4872 TCGA-CJ-4882 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 
         646         1435         1883         1952         1946         2085 
TCGA-CJ-4892 TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4908 
        1521          841         1528         1520         1496         1531 
TCGA-CJ-5671 TCGA-CJ-5682 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CW-6088 TCGA-CW-6090 
        1943         1883         2231         2038         3222         2552 
TCGA-CZ-4856 TCGA-CZ-5988 TCGA-DV-5567 TCGA-DV-5574 TCGA-EU-5904 
          18          693         1470          723          551 

$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-B0-5692 TCGA-B0-5697 
         910          735          617         3431         1487         1835 
TCGA-B0-5701 TCGA-B0-5707 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5639 
        1732         2828          952          358          315          417 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5546 
         656            7           16          722           26          505 
TCGA-B8-5550 TCGA-B8-5553 TCGA-BP-4351 TCGA-BP-4756 TCGA-BP-4803 TCGA-BP-4963 
         434          435          970          374          204         1834 
TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1746         1384          454          822         1011          967 
TCGA-BP-5195 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4884 
         749         1416         1998         2259         1955         1759 
TCGA-CJ-4893 TCGA-CJ-4903 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CW-5581 TCGA-CW-5588 
         750         1560         1499         1657         2799         2017 
TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 
        2271          774         1843         1928         2830         1868 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5458 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5464 
        1789         1712         1732          330          662         1740 
TCGA-CZ-5466 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-DV-5573 
         685          946          386         2067         1997         1130 
TCGA-EU-5905 TCGA-EU-5907 
         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-BP-4165 TCGA-BP-4174 
         511          777          788          194         3037         1879 
TCGA-BP-4332 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4766 TCGA-BP-4777 TCGA-BP-4801 
        1133          645         2859         1462         1731         1124 
TCGA-BP-4959 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4989 
        2660         1862          205         1794         1502          118 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5004 TCGA-BP-5169 TCGA-BP-5185 TCGA-BP-5187 
         177         1308         1126          193         1132          406 
TCGA-BP-5194 TCGA-BP-5198 TCGA-CJ-4885 TCGA-CJ-4901 TCGA-CJ-5681 TCGA-CJ-6031 
         408          603         2125         1450          552         1906 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 
          25         1683         1683 

$subtype5
TCGA-A3-3331 TCGA-A3-3370 TCGA-B0-4710 TCGA-B0-5113 TCGA-B0-5116 TCGA-B8-5165 
        1485         2274           96          359          657          737 
TCGA-B8-5552 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4760 TCGA-BP-4775 TCGA-BP-4781 
        1046         1666         1367         2361         1843         2080 
TCGA-BP-4789 TCGA-BP-4797 TCGA-BP-4807 TCGA-BP-4965 TCGA-BP-4976 TCGA-BP-4982 
        1489         1107          211         1871         1632         1014 
TCGA-BP-4986 TCGA-BP-4987 TCGA-BP-5006 TCGA-BP-5008 TCGA-BP-5174 TCGA-BP-5182 
         785         1124          840         1071         2257         1165 
TCGA-BP-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5202 TCGA-CJ-4642 TCGA-CJ-6032 
        1291         1133          693           29         1628         2548 
TCGA-CW-5589 TCGA-CW-6093 TCGA-CW-6096 TCGA-DV-5566 TCGA-DV-5568 TCGA-DV-5569 
        2378         3146         2701         1398          370          355 

$subtype6
TCGA-AK-3436 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-5696 TCGA-B0-5709 TCGA-B4-5838 
        2044          616           18         1727         3117          166 
TCGA-B8-4622 TCGA-B8-5158 TCGA-BP-4173 TCGA-BP-4326 TCGA-BP-4761 TCGA-BP-4983 
         700          636         1893         1625          182         1413 
TCGA-BP-4992 TCGA-BP-5000 TCGA-BP-5175 TCGA-CJ-4869 TCGA-CJ-4875 TCGA-CJ-4881 
         501          563          932         2554         2353         2014 
TCGA-CJ-6027 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5460 TCGA-CZ-5468 TCGA-CZ-5987 
        1855         1404         1943         1430           59          435 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       7       15        7       25       29       18 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    3668     3222     3431     3037     3146     3117 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  1729.0   1385.0   1074.5   1133.0   1228.0   1408.5 
[1] "7.0 - 3668.0 (1729.0)"  "15.0 - 3222.0 (1385.0)" "7.0 - 3431.0 (1074.5)" 
[4] "25.0 - 3037.0 (1133.0)" "29.0 - 3146.0 (1228.0)" "18.0 - 3117.0 (1408.5)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      54       11        22       14
  subtype2      42        9        19       20
  subtype3      39       12        24       11
  subtype4      44        7        17        8
  subtype5      33        2         9        0
  subtype6       7        3        24       23
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         54       42       39       44       33        7
  STAGE II        11        9       12        7        2        3
  STAGE III       22       19       24       17        9       24
  STAGE IV        14       20       11        8        0       23
[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 54 15 31  1
  subtype2 43 10 32  5
  subtype3 41 12 33  0
  subtype4 45  7 23  1
  subtype5 33  2  9  0
  subtype6  8  8 37  4
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       54       43       41       45       33        8
  T2       15       10       12        7        2        8
  T3       31       32       33       23        9       37
  T4        1        5        0        1        0        4
[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 48  1
  subtype2 46  2
  subtype3 43  2
  subtype4 35  3
  subtype5 13  0
  subtype6 23  8
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48    1
  subtype2   46    2
  subtype3   43    2
  subtype4   35    3
  subtype5   13    0
  subtype6   23    8
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       48       46       43       35       13       23
  1        1        2        2        3        0        8
[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 87 14
  subtype2 71 19
  subtype3 75 11
  subtype4 68  8
  subtype5 44  0
  subtype6 34 23
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       87       71       75       68       44       34
  M1       14       19       11        8        0       23
[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 44 57
  subtype2 29 61
  subtype3 27 59
  subtype4 18 58
  subtype5 18 26
  subtype6 15 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   57
  subtype2   29   61
  subtype3   27   59
  subtype4   18   58
  subtype5   18   26
  subtype6   15   42
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       44       29       27       18       18       15
  MALE         57       61       59       58       26       42
[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
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       7        8       10        2        4        3 
 [1] "subtype3" "subtype3" "subtype1" "subtype2" "subtype3" "subtype2"
 [7] "subtype3" "subtype2" "subtype6" "subtype1" "subtype1" "subtype6"
[13] "subtype2" "subtype6" "subtype2" "subtype3" "subtype3" "subtype1"
[19] "subtype3" "subtype1" "subtype1" "subtype5" "subtype2" "subtype5"
[25] "subtype5" "subtype3" "subtype2" "subtype1" "subtype5" "subtype2"
[31] "subtype3" "subtype3"
D5V9, continuous
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
[4] "subtype6"              
clus
subtype3 subtype4 subtype6 
       1        1        1 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         5    94
  subtype2     3                         6    81
  subtype3     1                         1    80
  subtype4     1                         6    69
  subtype5     1                         2    41
  subtype6     2                         0    55
D5V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        3        1        1        1
  BLACK OR AFRICAN AMERICAN        5        6        1        6        2
  WHITE                           94       81       80       69       41
                           clus
vv                          subtype6
  ASIAN                            2
  BLACK OR AFRICAN AMERICAN        0
  WHITE                           55
[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 65
  subtype2  2 63
  subtype3  5 60
  subtype4  1 40
  subtype5  3 24
  subtype6  2 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   65
  subtype2    2   63
  subtype3    5   60
  subtype4    1   40
  subtype5    3   24
  subtype6    2   43
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            6        2        5        1        3        2
  NOT HISPANIC OR LATINO       65       63       60       40       24       43
[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  69   3
  subtype2 161   7
  subtype3  66  15
subtype1 subtype2 subtype3 
      72      168       81 
subtype1 subtype2 subtype3 
       3        7       15 
$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-A3-3387 
         910         2270          735          861         1993          617 
TCGA-B0-5116 TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5697 
         657          652          449         2408         1487         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5705 TCGA-B0-5713 TCGA-B0-5812 
        2583         2741         1732         3668         1865         2963 
TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5635 TCGA-B2-5639 TCGA-B4-5377 TCGA-B4-5835 
         648          952          315          417          291           16 
TCGA-B8-5163 TCGA-B8-5164 TCGA-B8-5550 TCGA-BP-4173 TCGA-BP-4325 TCGA-BP-4963 
         822           26          434         1893         2964         1834 
TCGA-BP-4968 TCGA-BP-4973 TCGA-BP-4977 TCGA-BP-4986 TCGA-BP-4992 TCGA-BP-5000 
        1746         1384          454          785          501          563 
TCGA-BP-5185 TCGA-BP-5189 TCGA-BP-5190 TCGA-CJ-4635 TCGA-CJ-4640 TCGA-CJ-4876 
        1132          822         1011         1416         1998         1955 
TCGA-CJ-4884 TCGA-CJ-4897 TCGA-CJ-4907 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 
        1759         1808         1499         1657         1373         2430 
TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5591 TCGA-CZ-4853 TCGA-CZ-4862 
        2799         2609         2226         2271          774         1843 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5452 TCGA-CZ-5458 TCGA-CZ-5466 
        1928         2830         1929         1789         1732          685 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5989 TCGA-DV-5565 TCGA-EU-5906 TCGA-EU-5907 
        2067         1997         1905         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-AK-3444 TCGA-AK-3451 
        1621         1070          567          574         1471         1481 
TCGA-B0-4710 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 
          96          665          911         1092          359          797 
TCGA-B0-5120 TCGA-B0-5693 TCGA-B0-5700 TCGA-B0-5702 TCGA-B0-5706 TCGA-B0-5710 
         493         3076         1082         1605         2414         1459 
TCGA-B0-5711 TCGA-B0-5712 TCGA-B2-3924 TCGA-B2-4098 TCGA-B2-4099 TCGA-B2-5633 
        2931         2722         1092           51          374          358 
TCGA-B2-5636 TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5843 TCGA-B8-4146 
         919          656          175           38           11          511 
TCGA-B8-5159 TCGA-B8-5162 TCGA-B8-5165 TCGA-B8-5545 TCGA-B8-5549 TCGA-B8-5552 
         722           36          737          522          194         1046 
TCGA-B8-5553 TCGA-BP-4158 TCGA-BP-4165 TCGA-BP-4169 TCGA-BP-4174 TCGA-BP-4326 
         435         3377         3037          701         1879         1625 
TCGA-BP-4330 TCGA-BP-4332 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
        1888         1133         1666         1367          372          970 
TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4765 TCGA-BP-4768 TCGA-BP-4769 
        2208         2372         2361         2184          400         1876 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4777 TCGA-BP-4781 TCGA-BP-4784 TCGA-BP-4789 
        1885         1843         1731         2080         1854         1489 
TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4804 TCGA-BP-4807 TCGA-BP-4959 
        1107         1124          204         1459          211         2660 
TCGA-BP-4961 TCGA-BP-4962 TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4969 
        1935         1785         1862         1871          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-4987 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-4999 
        1124         1413          177         1371          932         1266 
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-5183 TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5187 TCGA-BP-5191 
        1165         1291         1133          693          406          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
         714          408         1018          603         1355         1063 
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-4878 TCGA-CJ-4886 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4893 
        1435         2186         1952         1946         2085          750 
TCGA-CJ-4894 TCGA-CJ-4899 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4903 TCGA-CJ-4904 
         841         1528         1450         1520         1560         1792 
TCGA-CJ-4905 TCGA-CJ-4908 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5684 
        1496         1531         1943         2575         1883         2231 
TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5588 TCGA-CW-5589 TCGA-CW-6088 
        2038         2548         2489         2017         2378         3222 
TCGA-CW-6090 TCGA-CW-6093 TCGA-CW-6096 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4866 
        2552         3146         2701           18         1787         1868 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 
          25         1683         1683          330          662         1446 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5988 TCGA-DV-5566 TCGA-DV-5567 TCGA-DV-5568 
        2439          373          693         1398         1470          370 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5905 
         355         1130          723         1729          551          119 

$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-B0-5121 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5703 
         554         1132         3431         1420         1727         1203 
TCGA-B0-5707 TCGA-B0-5709 TCGA-B2-3923 TCGA-B4-5832 TCGA-B4-5836 TCGA-B4-5838 
        2828         3117          992            7          141          166 
TCGA-B4-5844 TCGA-B8-4153 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-4622 TCGA-B8-5158 
           7          762          777          788          700          636 
TCGA-B8-5546 TCGA-B8-5551 TCGA-BP-4161 TCGA-BP-4329 TCGA-BP-4334 TCGA-BP-4335 
         505           15         2746          845          645          461 
TCGA-BP-4338 TCGA-BP-4345 TCGA-BP-4756 TCGA-BP-4761 TCGA-BP-4766 TCGA-BP-4776 
        2859         1516          374          182         1462          411 
TCGA-BP-4960 TCGA-BP-4983 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5001 TCGA-BP-5004 
        2172         1413          118         1308         1177         1126 
TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5195 TCGA-BP-5201 
         193         2412          932         2263          749          951 
TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4881 TCGA-CJ-4882 
        2554         2259         2283         2353         2014         1883 
TCGA-CJ-4885 TCGA-CJ-4892 TCGA-CJ-5681 TCGA-CJ-5683 TCGA-CJ-6027 TCGA-CJ-6031 
        2125         1521          552         1889         1855         1906 
TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5460 TCGA-CZ-5464 TCGA-CZ-5468 
        1404         1943         1712         1430         1740           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5987 
         946          386          435 

subtype1 subtype2 subtype3 
      16       11        7 
subtype1 subtype2 subtype3 
    3668     3377     3431 
subtype1 subtype2 subtype3 
  1451.5   1405.5   1126.0 
[1] "16.0 - 3668.0 (1451.5)" "11.0 - 3377.0 (1405.5)" "7.0 - 3431.0 (1126.0)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      39       13        31       12
  subtype2     132       16        39       16
  subtype3      48       15        45       48
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         39      132       48
  STAGE II        13       16       15
  STAGE III       31       39       45
  STAGE IV        12       16       48
[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  40  14  40   1
  subtype2 134  19  49   1
  subtype3  50  21  76   9
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       40      134       50
  T2       14       19       21
  T3       40       49       76
  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 48  1
  subtype2 80  4
  subtype3 80 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48    1
  subtype2   80    4
  subtype3   80   11
   clus
vv  subtype1 subtype2 subtype3
  0       48       80       80
  1        1        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
  subtype1  84  11
  subtype2 186  17
  subtype3 109  47
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       84      186      109
  M1       11       17       47
[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  24  71
  subtype2  76 127
  subtype3  51 105
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   71
  subtype2   76  127
  subtype3   51  105
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       24       76       51
  MALE         71      127      105
[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     0                         2    90
  subtype2     4                        10   187
  subtype3     4                         8   143
D6V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        4        4
  BLACK OR AFRICAN AMERICAN        2       10        8
  WHITE                           90      187      143
[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   7  65
  subtype2   8 118
  subtype3   4 112
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   65
  subtype2    8  118
  subtype3    4  112
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        8        4
  NOT HISPANIC OR LATINO       65      118      112
[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 166   4
  subtype2  76   8
  subtype3  99  13
subtype1 subtype2 subtype3 
     170       84      112 
subtype1 subtype2 subtype3 
       4        8       13 
$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-A3-3351 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-AK-3429 TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3450 
         861         1993         2017         2087         1471         1779 
TCGA-AK-3454 TCGA-AK-3458 TCGA-AK-3460 TCGA-AS-3778 TCGA-B0-4710 TCGA-B0-5110 
         874         1168          951           43           96         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 
         359          797           59          554          652          449 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 
        2408         1487         3076         1420         1727         2583 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 
        2741         1082         1203         3668         1459         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-B2-5635 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 
         315          417          507          291           38          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5549 TCGA-B8-5553 
         750          700          722           26          194          435 
TCGA-B8-A54H TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4160 TCGA-BP-4162 TCGA-BP-4165 
         256           66         3377         2881         3074         3037 
TCGA-BP-4325 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4351 
        2964         1888          461         1367          372          970 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 TCGA-BP-4774 
         374         2208         2184         1462          400         1885 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4961 
        1843          411         1731          354          211         1935 
TCGA-BP-4964 TCGA-BP-4965 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4973 TCGA-BP-4975 
        1862         1871         1746         1794         1384         1433 
TCGA-BP-4976 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 TCGA-BP-4993 TCGA-BP-4999 
        1632         1014         1124         1413          177         1266 
TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 TCGA-BP-5007 TCGA-BP-5174 TCGA-BP-5181 
        1177         1126          840         1140         2257         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-4643 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4878 
        1793         1498         2283         2353         1955         2186 
TCGA-CJ-4885 TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 
        2125         1952         1521          750          841         1808 
TCGA-CJ-4903 TCGA-CJ-4904 TCGA-CJ-4908 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5684 
        1560         1792         1531         1373         2430         2231 
TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-6088 TCGA-CW-6093 
        2548         2799         2609         2226         3222         3146 
TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
         774           18         1787         1928         2830         1929 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5465 
          25         1683         1732         1430          662         1446 
TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 TCGA-DV-5575 TCGA-EU-5904 
        2439          373         1905         1398         1729          551 
TCGA-EU-5906 TCGA-GK-A6C7 
         206           61 

$subtype2
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3317 TCGA-A3-3328 TCGA-A3-3349 TCGA-A3-3362 
          16          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-A54F 
         523          737          522          505         1046          519 
TCGA-BP-4163 TCGA-BP-4166 TCGA-BP-4169 TCGA-BP-4177 TCGA-BP-4329 TCGA-BP-4332 
        2839           13          701         1670          845         1133 
TCGA-BP-4334 TCGA-BP-4344 TCGA-BP-4345 TCGA-BP-4759 TCGA-BP-4760 TCGA-BP-4769 
         645         1666         1516         2372         2361         1876 
TCGA-BP-4784 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4970 TCGA-BP-4972 
        1854         1489          620         1124          433         1502 
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          723 

$subtype3
TCGA-A3-3316 TCGA-A3-3319 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3347 TCGA-A3-3357 
        1493         1130         1106          665         1610         2688 
TCGA-A3-3378 TCGA-A3-3382 TCGA-A3-3387 TCGA-AK-3425 TCGA-AK-3436 TCGA-AK-3445 
         630          574          617         3343         2044         1280 
TCGA-AK-3451 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 
        1481          616           18          183          665          911 
TCGA-B0-5116 TCGA-B0-5400 TCGA-B0-5701 TCGA-B0-5706 TCGA-B2-4098 TCGA-B2-5633 
         657         1132         1732         2414           51          358 
TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5158 
         656            7           16          777          788          636 
TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-A54D TCGA-B8-A54G 
          36          822          434           15          830           53 
TCGA-B8-A54I TCGA-BP-4161 TCGA-BP-4167 TCGA-BP-4173 TCGA-BP-4174 TCGA-BP-4176 
         150         2746         2718         1893         1879         1955 
TCGA-BP-4326 TCGA-BP-4338 TCGA-BP-4761 TCGA-BP-4781 TCGA-BP-4797 TCGA-BP-4803 
        1625         2859          182         2080         1107          204 
TCGA-BP-4804 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 
        1459         2660         2172         1785         1834          205 
TCGA-BP-4971 TCGA-BP-4977 TCGA-BP-4983 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4992 
        1487          454         1413          785          118          501 
TCGA-BP-5000 TCGA-BP-5169 TCGA-BP-5170 TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5189 
         563          193         2412          932         2263          822 
TCGA-BP-5191 TCGA-BP-5195 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 TCGA-CJ-4636 
         967          749         1018          603         1416         1924 
TCGA-CJ-4640 TCGA-CJ-4868 TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4873 
        1998          646         2554         2423         1435         2259 
TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4884 TCGA-CJ-4890 TCGA-CJ-4901 TCGA-CJ-4902 
        2014         1883         1759         2085         1450         1520 
TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-5686 TCGA-CJ-6027 TCGA-CJ-6031 
        1657         1943         2575         2038         1855         1906 
TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-4862 TCGA-CZ-4866 
        2017         2552         1404         1943         1843         1868 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5459 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 
        1789         1712         1683          330         1740          685 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
          59          946          386         2067         1997          435 
TCGA-CZ-5988 TCGA-DV-5568 TCGA-EU-5905 TCGA-EU-5907 
         693          370          119          127 

subtype1 subtype2 subtype3 
       7       13        7 
subtype1 subtype2 subtype3 
    3668     3431     3343 
subtype1 subtype2 subtype3 
    1337     1311     1342 
[1] "7.0 - 3668.0 (1337.0)"  "13.0 - 3431.0 (1311.0)" "7.0 - 3343.0 (1342.0)" 
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1     125       23        41       23
  subtype2      63       12        22       12
  subtype3      58       21        62       45
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I        125       63       58
  STAGE II        23       12       21
  STAGE III       41       22       62
  STAGE IV        23       12       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 125  26  59   2
  subtype2  64  13  29   3
  subtype3  63  28  89   6
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1      125       64       63
  T2       26       13       28
  T3       59       29       89
  T4        2        3        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 101   2
  subtype2  51   3
  subtype3  84  12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  101    2
  subtype2   51    3
  subtype3   84   12
   clus
vv  subtype1 subtype2 subtype3
  0      101       51       84
  1        2        3       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 186  23   3
  subtype2  97  11   1
  subtype3 138  45   3
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      186       97      138
  M1       23       11       45
  MX        3        1        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"
D7V7, binary
          cls
clus         0   1
  subtype1  95 117
  subtype2  36  73
  subtype3  43 143
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   95  117
  subtype2   36   73
  subtype3   43  143
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       95       36       43
  MALE        117       73      143
[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"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       2        1        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         8   198
  subtype2     4                        12    92
  subtype3     2                        10   172
D7V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        4        2
  BLACK OR AFRICAN AMERICAN        8       12       10
  WHITE                          198       92      172
[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  15 131
  subtype2   2  76
  subtype3   7 125
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15  131
  subtype2    2   76
  subtype3    7  125
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           15        2        7
  NOT HISPANIC OR LATINO      131       76      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(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  83   6
  subtype2 138   3
  subtype3  55  10
  subtype4  23   4
  subtype5  19   0
  subtype6  23   2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      89      141       65       27       19       25 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       6        3       10        4        0        2 
$subtype1
TCGA-A3-3306 TCGA-A3-3323 TCGA-A3-3335 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3365 
        1120         1106          665          910         1307          873 
TCGA-A3-3376 TCGA-A3-3380 TCGA-A3-3387 TCGA-AK-3428 TCGA-AK-3431 TCGA-AK-3458 
        1070          567          617         2223         1853         1168 
TCGA-AK-3461 TCGA-AS-3778 TCGA-B0-4706 TCGA-B0-4718 TCGA-B0-5116 TCGA-B0-5120 
         853           43           26          616          657          493 
TCGA-B0-5402 TCGA-B0-5698 TCGA-B0-5701 TCGA-B0-5812 TCGA-B2-4101 TCGA-B2-5633 
         449         2583         1732         2963          648          358 
TCGA-B2-5635 TCGA-B2-5641 TCGA-B2-A4SR TCGA-B8-4622 TCGA-B8-5545 TCGA-B8-5549 
         315          656          507          700          522          194 
TCGA-B8-5552 TCGA-B8-A54F TCGA-BP-4160 TCGA-BP-4161 TCGA-BP-4166 TCGA-BP-4173 
        1046          519         2881         2746           13         1893 
TCGA-BP-4329 TCGA-BP-4332 TCGA-BP-4344 TCGA-BP-4351 TCGA-BP-4759 TCGA-BP-4768 
         845         1133         1666          970         2372          400 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4801 TCGA-BP-4803 TCGA-BP-4807 TCGA-BP-4961 
        2080          354         1124          204          211         1935 
TCGA-BP-4963 TCGA-BP-4964 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4970 TCGA-BP-4977 
        1834         1862          205         1746          433          454 
TCGA-BP-4989 TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4998 TCGA-BP-5007 TCGA-BP-5008 
         118         1413          501          932         1140         1071 
TCGA-BP-5180 TCGA-BP-5182 TCGA-BP-5183 TCGA-BP-5187 TCGA-BP-5189 TCGA-BP-5190 
        2263         1165         1291          406          822         1011 
TCGA-BP-5195 TCGA-BP-5201 TCGA-CJ-4642 TCGA-CJ-4871 TCGA-CJ-4875 TCGA-CJ-4889 
         749          951         1628         2423         2353         1946 
TCGA-CJ-4899 TCGA-CJ-4907 TCGA-CJ-4908 TCGA-CJ-5682 TCGA-CZ-4862 TCGA-CZ-5458 
        1528         1499         1531         1883         1843         1732 
TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5985 
        1683         1430          330          685          386         1997 
TCGA-CZ-5987 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5568 TCGA-EU-5907 
         435          693         1329          370          127 

$subtype2
TCGA-A3-3307 TCGA-A3-3320 TCGA-A3-3322 TCGA-A3-3324 TCGA-A3-3325 TCGA-A3-3326 
        1436         1508         1478         1186          751         1137 
TCGA-A3-3329 TCGA-A3-3331 TCGA-A3-3343 TCGA-A3-3349 TCGA-A3-3359 TCGA-A3-3367 
         706         1485          945         1385         2504         2270 
TCGA-A3-3370 TCGA-A3-3372 TCGA-A3-3373 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3429 
        2274          735         1621          861         1993         2017 
TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3454 TCGA-AK-3460 TCGA-AS-3777 
        2087         1471         1779          874          951         1238 
TCGA-B0-4710 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5119 TCGA-B0-5121 
          96         1092          359          797           59          554 
TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5696 TCGA-B0-5699 
         652         2408         1487         3076         1727         2741 
TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 
        1203         3668         1459         2931         2722         1865 
TCGA-B2-3924 TCGA-B2-4099 TCGA-B2-4102 TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 
        1092          374          952          291           38          141 
TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 
          11            7          511          826          838          762 
TCGA-B8-4154 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5553 TCGA-B8-A54H TCGA-B8-A54J 
         750          722           26          435          256           66 
TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4330 
        3377         3074         3037         1879         2964         1888 
TCGA-BP-4335 TCGA-BP-4347 TCGA-BP-4349 TCGA-BP-4758 TCGA-BP-4765 TCGA-BP-4766 
         461         1367          372         2208         2184         1462 
TCGA-BP-4774 TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4777 TCGA-BP-4789 TCGA-BP-4965 
        1885         1843          411         1731         1489         1871 
TCGA-BP-4969 TCGA-BP-4972 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4982 
        1794         1502         1384         1433         1632         1014 
TCGA-BP-4987 TCGA-BP-4993 TCGA-BP-4999 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5006 
        1124          177         1266         1177         1126          840 
TCGA-BP-5177 TCGA-BP-5181 TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5192 
         293         1495         1133         1132          693          714 
TCGA-BP-5194 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 TCGA-CJ-4639 TCGA-CJ-4640 
         408         1063           29         1820         2308         1998 
TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4874 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 
        1793         1498         2283         1955         2186         2125 
TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4903 
        1952         1521          750          841         1808         1560 
TCGA-CJ-4904 TCGA-CJ-4905 TCGA-CJ-4916 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 
        1792         1496         1373         2038         2548         2489 
TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 
        2609         2226         3222         3146          774           18 
TCGA-CZ-4859 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 
        1787         1928         2830         1929           25         1683 
TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5575 
         662         1446         2439          373         1905         1729 
TCGA-EU-5904 TCGA-EU-5906 TCGA-GK-A6C7 
         551          206           61 

$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-5000 TCGA-BP-5169 TCGA-BP-5170 
        2172         1413          785          563          193         2412 
TCGA-BP-5175 TCGA-BP-5191 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-CJ-4635 
         932          967         1018          603         1355         1416 
TCGA-CJ-4868 TCGA-CJ-4872 TCGA-CJ-4873 TCGA-CJ-4881 TCGA-CJ-4882 TCGA-CJ-4890 
         646         1435         2259         2014         1883         2085 
TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4912 TCGA-CJ-5671 TCGA-CJ-5676 TCGA-CJ-6027 
        1450         1520         1657         1943         2575         1855 
TCGA-CJ-6031 TCGA-CW-5588 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5456 
        1906         2017         2552         1404         1943         1712 
TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5984 TCGA-EU-5905 
        1740           59          946         2067          119 

$subtype4
TCGA-A3-3313 TCGA-A3-3362 TCGA-A3-3363 TCGA-AK-3456 TCGA-B0-5691 TCGA-B0-5695 
         735         1559          319         1143         3431         1420 
TCGA-B0-5697 TCGA-B0-5700 TCGA-B0-5707 TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5835 
        1835         1082         2828           51          417           16 
TCGA-B8-4621 TCGA-B8-5165 TCGA-B8-5546 TCGA-BP-4756 TCGA-CJ-5675 TCGA-CJ-5681 
         788          737          505          374         2430          552 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CW-5581 TCGA-CW-5589 TCGA-CW-5591 TCGA-DV-5566 
        1889         2231         2799         2378         2271         1398 
TCGA-DV-5569 TCGA-DV-5573 TCGA-DV-5574 
         355         1130          723 

$subtype5
TCGA-A3-3317 TCGA-A3-3357 TCGA-AK-3451 TCGA-B0-5709 TCGA-B4-5838 TCGA-B8-5550 
        1491         2688         1481         3117          166          434 
TCGA-B8-A54D TCGA-B8-A54G TCGA-BP-4163 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4962 
         830           53         2839         1107         2660         1785 
TCGA-BP-4971 TCGA-BP-5174 TCGA-CJ-4636 TCGA-CJ-4869 TCGA-CJ-4884 TCGA-CZ-4866 
        1487         2257         1924         2554         1759         1868 
TCGA-CZ-5452 
        1789 

$subtype6
TCGA-A3-3328 TCGA-A3-3374 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 
        1385         1314         2566         2192         1745         1423 
TCGA-AK-3447 TCGA-AK-3453 TCGA-AK-3465 TCGA-B0-4699 TCGA-B0-5117 TCGA-B0-5702 
        1217         1397          369          110          535         1605 
TCGA-B2-3923 TCGA-B2-5636 TCGA-B4-5378 TCGA-B8-4619 TCGA-BP-4177 TCGA-BP-4334 
         992          919          175          523         1670          645 
TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4784 TCGA-BP-4795 TCGA-BP-4994 TCGA-BP-4995 
        2361         1876         1854          620         1308         1371 
TCGA-DV-5567 
        1470 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      13        7        7       16       53      110 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    2963     3668     3343     3431     3117     2566 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
     970     1446     1413     1130     1785     1371 
[1] "13.0 - 2963.0 (970.0)"   "7.0 - 3668.0 (1446.0)"  
[3] "7.0 - 3343.0 (1413.0)"   "16.0 - 3431.0 (1130.0)" 
[5] "53.0 - 3117.0 (1785.0)"  "110.0 - 2566.0 (1371.0)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      61       12        25       20
  subtype2     106       19        36       12
  subtype3      33       12        45       36
  subtype4      21        3         2        3
  subtype5       4        5        15        8
  subtype6      21        5         2        1
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I         61      106       33       21        4       21
  STAGE II        12       19       12        3        5        5
  STAGE III       25       36       45        2       15        2
  STAGE IV        20       12       36        3        8        1
[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  64  16  36   2
  subtype2 106  21  46   0
  subtype3  34  15  70   7
  subtype4  21   3   5   0
  subtype5   6   7  18   1
  subtype6  21   5   2   1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       64      106       34       21        6       21
  T2       16       21       15        3        7        5
  T3       36       46       70        5       18        2
  T4        2        0        7        0        1        1
[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"
D8V5, binary
          cls
clus        0  1
  subtype1 47  1
  subtype2 82  1
  subtype3 62 10
  subtype4 15  1
  subtype5 16  4
  subtype6 14  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47    1
  subtype2   82    1
  subtype3   62   10
  subtype4   15    1
  subtype5   16    4
  subtype6   14    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       47       82       62       15       16       14
  1        1        1       10        1        4        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  MX
  subtype1  98  19   1
  subtype2 157  13   3
  subtype3  90  35   1
  subtype4  26   3   0
  subtype5  22   8   2
  subtype6  28   1   0
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       98      157       90       26       22       28
  M1       19       13       35        3        8        1
  MX        1        3        1        0        2        0
[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"
D8V7, binary
          cls
clus        0  1
  subtype1 19 99
  subtype2 91 82
  subtype3 30 96
  subtype4 11 18
  subtype5 15 17
  subtype6  8 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   99
  subtype2   91   82
  subtype3   30   96
  subtype4   11   18
  subtype5   15   17
  subtype6    8   21
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       19       91       30       11       15        8
  MALE         99       82       96       18       17       21
[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"
D8V8, continuous
[1] "Remove cluster labels:" "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       5       12        8        6        1        3 
 [1] "subtype3" "subtype2" "subtype4" "subtype2" "subtype6" "subtype3"
 [7] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype3"
[13] "subtype2" "subtype3" "subtype3" "subtype1" "subtype1" "subtype3"
[19] "subtype2" "subtype2" "subtype3" "subtype2" "subtype1" "subtype4"
[25] "subtype6" "subtype1" "subtype4" "subtype4" "subtype4" "subtype2"
[31] "subtype6" "subtype2" "subtype3" "subtype1"
D8V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype3"               "subtype4"               "subtype5"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       2        1        1        1        2 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         6   105
  subtype2     1                         6   164
  subtype3     2                         4   120
  subtype4     2                         5    22
  subtype5     0                         3    28
  subtype6     0                         6    23
D8V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        1        2        2        0
  BLACK OR AFRICAN AMERICAN        6        6        4        5        3
  WHITE                          105      164      120       22       28
                           clus
vv                          subtype6
  ASIAN                            0
  BLACK OR AFRICAN AMERICAN        6
  WHITE                           23
[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"
D8V11, binary
          cls
clus         0   1
  subtype1   5  73
  subtype2  12 101
  subtype3   5  85
  subtype4   1  25
  subtype5   1  23
  subtype6   0  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   73
  subtype2   12  101
  subtype3    5   85
  subtype4    1   25
  subtype5    1   23
  subtype6    0   25
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            5       12        5        1        1        0
  NOT HISPANIC OR LATINO       73      101       85       25       23       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(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2        0   1
  subtype1  86   4
  subtype2 154   7
  subtype3  87  14
subtype1 subtype2 subtype3 
      90      161      101 
subtype1 subtype2 subtype3 
       4        7       14 
$subtype1
TCGA-A3-3308 TCGA-A3-3313 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3347 TCGA-A3-3349 
          16          735         1493         1491         1610         1385 
TCGA-A3-3362 TCGA-A3-3365 TCGA-A3-3373 TCGA-A3-3376 TCGA-A3-3387 TCGA-AK-3425 
        1559          873         1621         1070          617         3343 
TCGA-AK-3431 TCGA-AK-3461 TCGA-B0-5108 TCGA-B0-5119 TCGA-B0-5120 TCGA-B0-5691 
        1853          853          911           59          493         3431 
TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5812 TCGA-B2-5636 TCGA-B4-5836 
        1605         3117         1459         2963          919          141 
TCGA-B4-5838 TCGA-B8-5162 TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5552 
         166           36          822          522          434         1046 
TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A7U6 TCGA-BP-4160 TCGA-BP-4166 TCGA-BP-4167 
         519          256          110         2881           13         2718 
TCGA-BP-4169 TCGA-BP-4173 TCGA-BP-4177 TCGA-BP-4332 TCGA-BP-4345 TCGA-BP-4760 
         701         1893         1670         1133         1516         2361 
TCGA-BP-4765 TCGA-BP-4769 TCGA-BP-4789 TCGA-BP-4795 TCGA-BP-4801 TCGA-BP-4804 
        2184         1876         1489          620         1124         1459 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4969 TCGA-BP-4970 TCGA-BP-4971 
         211         1935         1871         1794          433         1487 
TCGA-BP-4972 TCGA-BP-4982 TCGA-BP-5008 TCGA-BP-5170 TCGA-BP-5177 TCGA-BP-5182 
        1502         1014         1071         2412          293         1165 
TCGA-BP-5184 TCGA-BP-5186 TCGA-BP-5196 TCGA-BP-5198 TCGA-BP-5199 TCGA-BP-5200 
        1133          693         1018          603         1355         1063 
TCGA-CJ-4634 TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4872 TCGA-CJ-4882 TCGA-CJ-4886 
        1820         1924         1628         1435         1883         1952 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 TCGA-CJ-4908 
        1946         2085         1520         1496         1499         1531 
TCGA-CJ-5671 TCGA-CJ-6031 TCGA-CW-5583 TCGA-CW-5588 TCGA-CW-6088 TCGA-CW-6090 
        1943         1906         2489         2017         3222         2552 
TCGA-CZ-5988 TCGA-DV-5568 TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5905 
         693          370         1130          723         1729          119 

$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-3456 TCGA-AK-3460 TCGA-B0-4706 
        1471         1779          874         1143          951           26 
TCGA-B0-4710 TCGA-B0-5110 TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5121 
          96         1092          359          797          657          554 
TCGA-B0-5399 TCGA-B0-5402 TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 
         652          449         2408         1487         3076         1420 
TCGA-B0-5696 TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 
        1727         2583         2741         1082         1203         3668 
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-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5843 
         952          417          507          291           38           11 
TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4148 TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 
           7          511          826          838          762          750 
TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5549 
         700          722           26          737          505          194 
TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4158 TCGA-BP-4161 TCGA-BP-4162 TCGA-BP-4165 
         435           66         3377         2746         3074         3037 
TCGA-BP-4174 TCGA-BP-4325 TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4344 
        1879         2964          845         1888          461         1666 
TCGA-BP-4347 TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4766 TCGA-BP-4768 
        1367          374         2208         2372         1462          400 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4987 
        1843          411         1384         1433         1632         1124 
TCGA-BP-4991 TCGA-BP-4992 TCGA-BP-4993 TCGA-BP-4995 TCGA-BP-5001 TCGA-BP-5004 
        1413          501          177         1371         1177         1126 
TCGA-BP-5007 TCGA-BP-5174 TCGA-BP-5181 TCGA-BP-5183 TCGA-BP-5185 TCGA-BP-5187 
        1140         2257         1495         1291         1132          406 
TCGA-BP-5190 TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5195 TCGA-BP-5201 TCGA-BP-5202 
        1011          714          408          749          951           29 
TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4875 TCGA-CJ-4878 TCGA-CJ-4885 
        2308         1793         1498         2353         2186         2125 
TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 TCGA-CJ-4903 
        1521          750          841         1808         1528         1560 
TCGA-CJ-4904 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5682 
        1792         1657         1373         2430          552         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5581 TCGA-CW-5585 
        1889         2231         2038         2548         2799         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6093 TCGA-CZ-4853 TCGA-CZ-4856 TCGA-CZ-4859 
        2226         2378         3146          774           18         1787 
TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 
        1843         1928         2830         1868         1929           25 
TCGA-CZ-5457 TCGA-CZ-5458 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5465 
        1683         1732         1683         1430          662         1446 
TCGA-CZ-5982 TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5565 TCGA-DV-5566 
        2439         1997          373         1905         1329         1398 
TCGA-DV-5569 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         355          551          206          127           61 

$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-3458 TCGA-AK-3465 
        1280         1217         1481         1397         1168          369 
TCGA-AS-3777 TCGA-B0-4699 TCGA-B0-4718 TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 
        1238          110          616           18          183          665 
TCGA-B0-5117 TCGA-B0-5400 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5706 TCGA-B0-5707 
         535         1132         1835         1732         2414         2828 
TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5378 
         992           51          358          315          656          175 
TCGA-B4-5832 TCGA-B4-5835 TCGA-B8-4619 TCGA-B8-4620 TCGA-B8-4621 TCGA-B8-5158 
           7           16          523          777          788          636 
TCGA-B8-5551 TCGA-B8-A54D TCGA-B8-A54G TCGA-B8-A54I TCGA-BP-4163 TCGA-BP-4176 
          15          830           53          150         2839         1955 
TCGA-BP-4326 TCGA-BP-4334 TCGA-BP-4338 TCGA-BP-4351 TCGA-BP-4761 TCGA-BP-4777 
        1625          645         2859          970          182         1731 
TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4797 TCGA-BP-4803 TCGA-BP-4959 TCGA-BP-4960 
        2080          354         1107          204         2660         2172 
TCGA-BP-4962 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4977 TCGA-BP-4983 
        1785         1834          205         1746          454         1413 
TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5169 
         785          118         1308          932          563          193 
TCGA-BP-5175 TCGA-BP-5180 TCGA-BP-5189 TCGA-BP-5191 TCGA-CJ-4635 TCGA-CJ-4640 
         932         2263          822          967         1416         1998 
TCGA-CJ-4869 TCGA-CJ-4871 TCGA-CJ-4873 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-4884 
        2554         2423         2259         1955         2014         1759 
TCGA-CJ-4901 TCGA-CJ-5676 TCGA-CJ-6027 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 
        1450         2575         1855         2271         1404         1943 
TCGA-CZ-5452 TCGA-CZ-5456 TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 
        1789         1712          330         1740          685           59 
TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5987 TCGA-DV-5567 
         946          386         2067          435         1470 

subtype1 subtype2 subtype3 
      13        7        7 
subtype1 subtype2 subtype3 
    3431     3668     2859 
subtype1 subtype2 subtype3 
    1459     1371     1132 
[1] "13.0 - 3431.0 (1459.0)" "7.0 - 3668.0 (1371.0)"  "7.0 - 2859.0 (1132.0)" 
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      69       11        29       10
  subtype2     107       23        45       28
  subtype3      58       20        51       41
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         69      107       58
  STAGE II        11       23       20
  STAGE III       29       45       51
  STAGE IV        10       28       41
[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  71  11  33   4
  subtype2 108  29  64   2
  subtype3  61  25  79   5
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       71      108       61
  T2       11       29       25
  T3       33       64       79
  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 90  2
  subtype3 79 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    3
  subtype2   90    2
  subtype3   79   13
   clus
vv  subtype1 subtype2 subtype3
  0       55       90       79
  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 106   9   3
  subtype2 173  28   2
  subtype3 126  41   3
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      106      173      126
  M1        9       28       41
  MX        3        2        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"
D9V7, binary
          cls
clus         0   1
  subtype1  40  79
  subtype2  85 118
  subtype3  44 126
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40   79
  subtype2   85  118
  subtype3   44  126
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       40       85       44
  MALE         79      118      126
[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:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       1        2        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                        11   106
  subtype2     3                        10   186
  subtype3     4                        11   153
D9V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        3        4
  BLACK OR AFRICAN AMERICAN       11       10       11
  WHITE                          106      186      153
[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  75
  subtype2  12 131
  subtype3   8 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   75
  subtype2   12  131
  subtype3    8  118
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2       12        8
  NOT HISPANIC OR LATINO       75      131      118
[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  86   8
  subtype2 176   9
  subtype3  65   8
subtype1 subtype2 subtype3 
      94      185       73 
subtype1 subtype2 subtype3 
       8        9        8 
$subtype1
TCGA-A3-3308 TCGA-A3-3316 TCGA-A3-3317 TCGA-A3-3347 TCGA-A3-3362 TCGA-A3-3376 
          16         1493         1491         1610         1559         1070 
TCGA-A3-3382 TCGA-AK-3425 TCGA-AK-3431 TCGA-AK-3436 TCGA-AK-3445 TCGA-AK-3461 
         574         3343         1853         2044         1280          853 
TCGA-B0-4813 TCGA-B0-4819 TCGA-B0-5097 TCGA-B0-5108 TCGA-B0-5119 TCGA-B0-5120 
          18          183          665          911           59          493 
TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 TCGA-B0-5710 TCGA-B0-5812 
        1132         3431         1605         3117         1459         2963 
TCGA-B2-5636 TCGA-B2-5641 TCGA-B4-5378 TCGA-B4-5838 TCGA-B8-4620 TCGA-B8-5162 
         919          656          175          166          777           36 
TCGA-B8-5163 TCGA-B8-5545 TCGA-B8-5550 TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54F 
         822          522          434           15         1046          519 
TCGA-B8-A54H TCGA-B8-A54I TCGA-BP-4160 TCGA-BP-4167 TCGA-BP-4169 TCGA-BP-4173 
         256          150         2881         2718          701         1893 
TCGA-BP-4177 TCGA-BP-4326 TCGA-BP-4345 TCGA-BP-4760 TCGA-BP-4769 TCGA-BP-4789 
        1670         1625         1516         2361         1876         1489 
TCGA-BP-4795 TCGA-BP-4797 TCGA-BP-4801 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4965 
         620         1107         1124         1459         2172         1871 
TCGA-BP-4970 TCGA-BP-4971 TCGA-BP-4972 TCGA-BP-4983 TCGA-BP-4989 TCGA-BP-5169 
         433         1487         1502         1413          118          193 
TCGA-BP-5170 TCGA-BP-5182 TCGA-BP-5187 TCGA-BP-5196 TCGA-BP-5198 TCGA-CJ-4635 
        2412         1165          406         1018          603         1416 
TCGA-CJ-4636 TCGA-CJ-4642 TCGA-CJ-4871 TCGA-CJ-4872 TCGA-CJ-4881 TCGA-CJ-4882 
        1924         1628         2423         1435         2014         1883 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-4901 TCGA-CJ-4902 TCGA-CJ-4905 TCGA-CJ-4907 
        1946         2085         1450         1520         1496         1499 
TCGA-CJ-4908 TCGA-CJ-5671 TCGA-CJ-6027 TCGA-CJ-6031 TCGA-CW-5588 TCGA-CW-6090 
        1531         1943         1855         1906         2017         2552 
TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5456 TCGA-CZ-5988 TCGA-DV-5565 TCGA-DV-5567 
        1404         1943         1712          693         1329         1470 
TCGA-DV-5573 TCGA-DV-5574 TCGA-DV-5575 TCGA-EU-5905 
        1130          723         1729          119 

$subtype2
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-A3-3349 TCGA-A3-3351 TCGA-A3-3358 TCGA-A3-3365 TCGA-A3-3367 
        1137         1385          910         1307          873         2270 
TCGA-A3-3370 TCGA-A3-3373 TCGA-A3-3380 TCGA-A3-3383 TCGA-A3-3385 TCGA-AK-3428 
        2274         1621          567          861         1993         2223 
TCGA-AK-3429 TCGA-AK-3430 TCGA-AK-3434 TCGA-AK-3444 TCGA-AK-3450 TCGA-AK-3453 
        2017          480         2087         1471         1779         1397 
TCGA-AK-3454 TCGA-AK-3456 TCGA-AK-3460 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5110 
         874         1143          951           26           96         1092 
TCGA-B0-5113 TCGA-B0-5115 TCGA-B0-5116 TCGA-B0-5121 TCGA-B0-5399 TCGA-B0-5402 
         359          797          657          554          652          449 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5698 TCGA-B0-5699 
        2408         1487         3076         1420         2583         2741 
TCGA-B0-5700 TCGA-B0-5705 TCGA-B0-5711 TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 
        1082         3668         2931         2722         1865         1092 
TCGA-B2-4099 TCGA-B2-4101 TCGA-B2-4102 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-A4SR 
         374          648          952          358          315          507 
TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5836 TCGA-B4-5843 TCGA-B8-4146 TCGA-B8-4148 
         291           38          141           11          511          826 
TCGA-B8-4151 TCGA-B8-4153 TCGA-B8-4154 TCGA-B8-4622 TCGA-B8-5159 TCGA-B8-5164 
         838          762          750          700          722           26 
TCGA-B8-5165 TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54J TCGA-B8-A7U6 
         737          505          194          435           66          110 
TCGA-BP-4158 TCGA-BP-4162 TCGA-BP-4165 TCGA-BP-4166 TCGA-BP-4174 TCGA-BP-4325 
        3377         3074         3037           13         1879         2964 
TCGA-BP-4329 TCGA-BP-4330 TCGA-BP-4335 TCGA-BP-4344 TCGA-BP-4347 TCGA-BP-4351 
         845         1888          461         1666         1367          970 
TCGA-BP-4756 TCGA-BP-4758 TCGA-BP-4759 TCGA-BP-4765 TCGA-BP-4766 TCGA-BP-4768 
         374         2208         2372         2184         1462          400 
TCGA-BP-4775 TCGA-BP-4776 TCGA-BP-4781 TCGA-BP-4782 TCGA-BP-4807 TCGA-BP-4959 
        1843          411         2080          354          211         2660 
TCGA-BP-4961 TCGA-BP-4963 TCGA-BP-4967 TCGA-BP-4968 TCGA-BP-4969 TCGA-BP-4973 
        1935         1834          205         1746         1794         1384 
TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4987 TCGA-BP-4991 
        1433         1632          454         1014         1124         1413 
TCGA-BP-4992 TCGA-BP-4995 TCGA-BP-4998 TCGA-BP-5001 TCGA-BP-5004 TCGA-BP-5007 
         501         1371          932         1177         1126         1140 
TCGA-BP-5008 TCGA-BP-5174 TCGA-BP-5177 TCGA-BP-5180 TCGA-BP-5181 TCGA-BP-5183 
        1071         2257          293         2263         1495         1291 
TCGA-BP-5184 TCGA-BP-5185 TCGA-BP-5186 TCGA-BP-5189 TCGA-BP-5190 TCGA-BP-5191 
        1133         1132          693          822         1011          967 
TCGA-BP-5192 TCGA-BP-5194 TCGA-BP-5199 TCGA-BP-5200 TCGA-BP-5202 TCGA-CJ-4634 
         714          408         1355         1063           29         1820 
TCGA-CJ-4639 TCGA-CJ-4643 TCGA-CJ-4870 TCGA-CJ-4876 TCGA-CJ-4878 TCGA-CJ-4885 
        2308         1793         1498         1955         2186         2125 
TCGA-CJ-4886 TCGA-CJ-4892 TCGA-CJ-4893 TCGA-CJ-4894 TCGA-CJ-4897 TCGA-CJ-4899 
        1952         1521          750          841         1808         1528 
TCGA-CJ-4903 TCGA-CJ-4912 TCGA-CJ-4916 TCGA-CJ-5675 TCGA-CJ-5676 TCGA-CJ-5682 
        1560         1657         1373         2430         2575         1883 
TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5585 
        1889         2231         2038         2548         2489         2609 
TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-5591 TCGA-CW-6088 TCGA-CW-6093 TCGA-CZ-4853 
        2226         2378         2271         3222         3146          774 
TCGA-CZ-4856 TCGA-CZ-4859 TCGA-CZ-4862 TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 
          18         1787         1843         1928         2830         1929 
TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 
          25         1683         1683         1430          330          662 
TCGA-CZ-5464 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 TCGA-DV-5566 
        1740         1446         2439          373         1905         1398 
TCGA-DV-5569 TCGA-EU-5904 TCGA-EU-5906 TCGA-EU-5907 TCGA-GK-A6C7 
         355          551          206          127           61 

$subtype3
TCGA-A3-3319 TCGA-A3-3331 TCGA-A3-3357 TCGA-A3-3363 TCGA-A3-3372 TCGA-A3-3374 
        1130         1485         2688          319          735         1314 
TCGA-A3-3378 TCGA-A3-3387 TCGA-AK-3427 TCGA-AK-3433 TCGA-AK-3440 TCGA-AK-3443 
         630          617         2566         2192         1745         1423 
TCGA-AK-3447 TCGA-AK-3451 TCGA-AK-3458 TCGA-AK-3465 TCGA-AS-3777 TCGA-B0-4699 
        1217         1481         1168          369         1238          110 
TCGA-B0-4718 TCGA-B0-5117 TCGA-B0-5696 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5703 
         616          535         1727         1835         1732         1203 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B2-3923 TCGA-B2-4098 TCGA-B2-5639 TCGA-B4-5832 
        2414         2828          992           51          417            7 
TCGA-B4-5835 TCGA-B4-5844 TCGA-B8-4619 TCGA-B8-4621 TCGA-B8-5158 TCGA-B8-A54D 
          16            7          523          788          636          830 
TCGA-B8-A54G TCGA-BP-4161 TCGA-BP-4163 TCGA-BP-4176 TCGA-BP-4332 TCGA-BP-4334 
          53         2746         2839         1955         1133          645 
TCGA-BP-4338 TCGA-BP-4761 TCGA-BP-4777 TCGA-BP-4803 TCGA-BP-4962 TCGA-BP-4986 
        2859          182         1731          204         1785          785 
TCGA-BP-4993 TCGA-BP-4994 TCGA-BP-5000 TCGA-BP-5175 TCGA-BP-5195 TCGA-BP-5201 
         177         1308          563          932          749          951 
TCGA-CJ-4640 TCGA-CJ-4869 TCGA-CJ-4873 TCGA-CJ-4875 TCGA-CJ-4884 TCGA-CJ-4904 
        1998         2554         2259         2353         1759         1792 
TCGA-CJ-5681 TCGA-CW-5581 TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5458 TCGA-CZ-5466 
         552         2799         1868         1789         1732          685 
TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 
          59          946          386         2067         1997          435 
TCGA-DV-5568 
         370 

subtype1 subtype2 subtype3 
      15       11        7 
subtype1 subtype2 subtype3 
    3431     3668     2859 
subtype1 subtype2 subtype3 
  1454.5   1355.0   1133.0 
[1] "15.0 - 3431.0 (1454.5)" "11.0 - 3668.0 (1355.0)" "7.0 - 2859.0 (1133.0)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      65       14        49       28
  subtype2     130       25        51       27
  subtype3      39       15        25       24
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         65      130       39
  STAGE II        14       25       15
  STAGE III       49       51       25
  STAGE IV        28       27       24
[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  17  65   7
  subtype2 132  30  69   2
  subtype3  41  18  42   2
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       67      132       41
  T2       17       30       18
  T3       65       69       42
  T4        7        2        2
[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"
D10V5, binary
          cls
clus         0   1
  subtype1  71   9
  subtype2 102   3
  subtype3  51   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71    9
  subtype2  102    3
  subtype3   51    6
   clus
vv  subtype1 subtype2 subtype3
  0       71      102       51
  1        9        3        6
[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 125  27   4
  subtype2 203  27   2
  subtype3  77  24   2
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0      125      203       77
  M1       27       27       24
  MX        4        2        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"
D10V7, binary
          cls
clus         0   1
  subtype1  47 109
  subtype2  92 141
  subtype3  30  73
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47  109
  subtype2   92  141
  subtype3   30   73
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       47       92       30
  MALE        109      141       73
[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"
D10V8, continuous
D10V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
clus
subtype1 subtype2 subtype3 
       1        2        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                        13   139
  subtype2     4                        12   213
  subtype3     1                         7    93
D10V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        4        1
  BLACK OR AFRICAN AMERICAN       13       12        7
  WHITE                          139      213       93
[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"
D10V11, binary
          cls
clus         0   1
  subtype1   5 107
  subtype2  13 142
  subtype3   4  75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  107
  subtype2   13  142
  subtype3    4   75
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            5       13        4
  NOT HISPANIC OR LATINO      107      142       75
[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(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2       0  1
  subtype1 38  0
  subtype2 75  3
  subtype3 47  7
subtype1 subtype2 subtype3 
      38       78       54 
subtype1 subtype2 subtype3 
       0        3        7 
$subtype1
TCGA-A3-3317 TCGA-A3-3387 TCGA-AK-3465 TCGA-B0-5691 TCGA-B0-5702 TCGA-B0-5709 
        1491          617          369         3431         1605         3117 
TCGA-B0-5812 TCGA-B2-5636 TCGA-B4-5836 TCGA-B4-5838 TCGA-B8-5545 TCGA-B8-5550 
        2963          919          141          166          522          434 
TCGA-B8-5552 TCGA-B8-A54H TCGA-B8-A7U6 TCGA-BP-4173 TCGA-BP-4789 TCGA-BP-4804 
        1046          256          110         1893         1489         1459 
TCGA-BP-4807 TCGA-BP-4961 TCGA-BP-4970 TCGA-BP-4982 TCGA-BP-4998 TCGA-BP-5008 
         211         1935          433         1014          932         1071 
TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-5671 TCGA-CJ-6031 TCGA-CW-5583 TCGA-CW-5588 
        1946         2085         1943         1906         2489         2017 
TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-5457 TCGA-CZ-5988 TCGA-DV-5573 TCGA-DV-5574 
        3222         2552         1683          693         1130          723 
TCGA-DV-5575 TCGA-EU-5905 
        1729          119 

$subtype2
TCGA-A3-3358 TCGA-AK-3440 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5399 TCGA-B0-5402 
        1307         1745           26           96          652          449 
TCGA-B0-5690 TCGA-B0-5692 TCGA-B0-5693 TCGA-B0-5695 TCGA-B0-5696 TCGA-B0-5698 
        2408         1487         3076         1420         1727         2583 
TCGA-B0-5699 TCGA-B0-5700 TCGA-B0-5703 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 
        2741         1082         1203         3668         1459         2931 
TCGA-B0-5712 TCGA-B0-5713 TCGA-B2-3924 TCGA-B2-5639 TCGA-B2-A4SR TCGA-B4-5377 
        2722         1865         1092          417          507          291 
TCGA-B4-5378 TCGA-B4-5834 TCGA-B4-5843 TCGA-B4-5844 TCGA-B8-4146 TCGA-B8-4153 
         175           38           11            7          511          762 
TCGA-B8-5546 TCGA-B8-5549 TCGA-B8-5553 TCGA-B8-A54J TCGA-BP-4759 TCGA-BP-4965 
         505          194          435           66         2372         1871 
TCGA-BP-4969 TCGA-BP-4973 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4987 TCGA-BP-4992 
        1794         1384         1433         1632         1124          501 
TCGA-BP-4995 TCGA-BP-5001 TCGA-BP-5007 TCGA-CJ-4870 TCGA-CJ-4878 TCGA-CJ-4899 
        1371         1177         1140         1498         2186         1528 
TCGA-CJ-5675 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 TCGA-CJ-5686 TCGA-CJ-6032 
        2430         1883         1889         2231         2038         2548 
TCGA-CW-5581 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6093 TCGA-CZ-4863 
        2799         2609         2226         2378         3146         1928 
TCGA-CZ-4864 TCGA-CZ-4866 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5458 TCGA-CZ-5459 
        2830         1868         1929           25         1732         1683 
TCGA-CZ-5460 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-CZ-5986 TCGA-CZ-5989 
        1430          662         1446         2439          373         1905 
TCGA-DV-5565 TCGA-DV-5566 TCGA-DV-5569 TCGA-EU-5904 TCGA-EU-5906 TCGA-GK-A6C7 
        1329         1398          355          551          206           61 

$subtype3
TCGA-AK-3458 TCGA-B0-5400 TCGA-B0-5697 TCGA-B0-5701 TCGA-B0-5706 TCGA-B0-5707 
        1168         1132         1835         1732         2414         2828 
TCGA-B2-3923 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-5641 TCGA-B4-5832 TCGA-B4-5835 
         992          358          315          656            7           16 
TCGA-B8-4621 TCGA-B8-5551 TCGA-B8-A54D TCGA-B8-A54F TCGA-B8-A54G TCGA-B8-A54I 
         788           15          830          519           53          150 
TCGA-BP-4761 TCGA-BP-4797 TCGA-BP-4959 TCGA-BP-4960 TCGA-BP-4967 TCGA-BP-4968 
         182         1107         2660         2172          205         1746 
TCGA-BP-4971 TCGA-BP-4977 TCGA-BP-4986 TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-5000 
        1487          454          785          118         1308          563 
TCGA-CJ-4635 TCGA-CJ-4875 TCGA-CJ-4876 TCGA-CJ-4881 TCGA-CJ-5676 TCGA-CJ-5681 
        1416         2353         1955         2014         2575          552 
TCGA-CJ-6027 TCGA-CW-5591 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5452 TCGA-CZ-5456 
        1855         2271         1404         1943         1789         1712 
TCGA-CZ-5461 TCGA-CZ-5464 TCGA-CZ-5466 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5470 
         330         1740          685           59          946          386 
TCGA-CZ-5984 TCGA-CZ-5985 TCGA-CZ-5987 TCGA-DV-5567 TCGA-DV-5568 TCGA-EU-5907 
        2067         1997          435         1470          370          127 

subtype1 subtype2 subtype3 
     110        7        7 
subtype1 subtype2 subtype3 
    3431     3668     2828 
subtype1 subtype2 subtype3 
  1294.5   1439.5   1049.5 
[1] "110.0 - 3431.0 (1294.5)" "7.0 - 3668.0 (1439.5)"  
[3] "7.0 - 2828.0 (1049.5)"  
D11V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      36        3         6        7
  subtype2      46       14        21       10
  subtype3      30       10        21       26
D11V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         36       46       30
  STAGE II         3       14       10
  STAGE III        6       21       21
  STAGE IV         7       10       26
[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 37  3  9  3
  subtype2 46 16 28  1
  subtype3 33 11 41  2
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       37       46       33
  T2        3       16       11
  T3        9       28       41
  T4        3        1        2
[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"
D11V5, binary
          cls
clus        0  1
  subtype1 17  2
  subtype2 40  1
  subtype3 41  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17    2
  subtype2   40    1
  subtype3   41    5
   clus
vv  subtype1 subtype2 subtype3
  0       17       40       41
  1        2        1        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 43  6  2
  subtype2 80  9  2
  subtype3 58 25  4
D11V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       43       80       58
  M1        6        9       25
  MX        2        2        4
[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"
D11V7, binary
          cls
clus        0  1
  subtype1 18 34
  subtype2 37 54
  subtype3 16 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   34
  subtype2   37   54
  subtype3   16   71
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       37       16
  MALE         34       54       71
[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"
D11V8, continuous
D11V9, continuous
[1] "Remove cluster labels:" "subtype2"              
clus
subtype2 subtype3 
       1        4 
[1] "subtype3" "subtype3" "subtype3" "subtype3"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         6    43
  subtype2     2                         7    81
  subtype3     1                         9    75
D11V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        2        1
  BLACK OR AFRICAN AMERICAN        6        7        9
  WHITE                           43       81       75
[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"
D11V11, binary
          cls
clus        0  1
  subtype1  2 33
  subtype2  3 70
  subtype3  4 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   33
  subtype2    3   70
  subtype3    4   64
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        3        4
  NOT HISPANIC OR LATINO       33       70       64
[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(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 54  4
  subtype2 75  3
  subtype3 31  3
subtype1 subtype2 subtype3 
      58       78       34 
subtype1 subtype2 subtype3 
       4        3        3 
$subtype1
TCGA-A3-3317 TCGA-AK-3440 TCGA-AK-3465 TCGA-B0-5400 TCGA-B0-5691 TCGA-B0-5702 
        1491         1745          369         1132         3431         1605 
TCGA-B0-5706 TCGA-B0-5707 TCGA-B0-5709 TCGA-B2-3923 TCGA-B2-5636 TCGA-B2-5641 
        2414         2828         3117          992          919          656 
TCGA-B4-5378 TCGA-B4-5832 TCGA-B4-5835 TCGA-B4-5838 TCGA-B8-5545 TCGA-B8-5550 
         175            7           16          166          522          434 
TCGA-B8-5551 TCGA-B8-5552 TCGA-B8-A54F TCGA-B8-A54H TCGA-B8-A54I TCGA-B8-A7U6 
          15         1046          519          256          150          110 
TCGA-BP-4173 TCGA-BP-4761 TCGA-BP-4804 TCGA-BP-4960 TCGA-BP-4970 TCGA-BP-4971 
        1893          182         1459         2172          433         1487 
TCGA-BP-4989 TCGA-BP-4994 TCGA-BP-4998 TCGA-BP-5000 TCGA-BP-5008 TCGA-CJ-4635 
         118         1308          932          563         1071         1416 
TCGA-CJ-4881 TCGA-CJ-4889 TCGA-CJ-4890 TCGA-CJ-5671 TCGA-CJ-6027 TCGA-CJ-6031 
        2014         1946         2085         1943         1855         1906 
TCGA-CW-5588 TCGA-CW-6088 TCGA-CW-6090 TCGA-CZ-4854 TCGA-CZ-4858 TCGA-CZ-5456 
        2017         3222         2552         1404         1943         1712 
TCGA-CZ-5464 TCGA-CZ-5468 TCGA-CZ-5469 TCGA-CZ-5988 TCGA-DV-5567 TCGA-DV-5568 
        1740           59          946          693         1470          370 
TCGA-DV-5573 TCGA-DV-5574 TCGA-EU-5905 TCGA-EU-5907 
        1130          723          119          127 

$subtype2
TCGA-A3-3358 TCGA-B0-4706 TCGA-B0-4710 TCGA-B0-5399 TCGA-B0-5690 TCGA-B0-5693 
        1307           26           96          652         2408         3076 
TCGA-B0-5695 TCGA-B0-5700 TCGA-B0-5705 TCGA-B0-5710 TCGA-B0-5711 TCGA-B0-5712 
        1420         1082         3668         1459         2931         2722 
TCGA-B0-5713 TCGA-B0-5812 TCGA-B2-3924 TCGA-B2-5633 TCGA-B2-5635 TCGA-B2-A4SR 
        1865         2963         1092          358          315          507 
TCGA-B4-5377 TCGA-B4-5834 TCGA-B4-5843 TCGA-B8-4146 TCGA-B8-4153 TCGA-B8-5549 
         291           38           11          511          762          194 
TCGA-B8-5553 TCGA-B8-A54D TCGA-B8-A54J TCGA-BP-4759 TCGA-BP-4789 TCGA-BP-4797 
         435          830           66         2372         1489         1107 
TCGA-BP-4807 TCGA-BP-4959 TCGA-BP-4961 TCGA-BP-4965 TCGA-BP-4967 TCGA-BP-4968 
         211         2660         1935         1871          205         1746 
TCGA-BP-4969 TCGA-BP-4975 TCGA-BP-4976 TCGA-BP-4977 TCGA-BP-4982 TCGA-BP-4987 
        1794         1433         1632          454         1014         1124 
TCGA-BP-4992 TCGA-BP-4995 TCGA-BP-5001 TCGA-BP-5007 TCGA-CJ-4870 TCGA-CJ-4875 
         501         1371         1177         1140         1498         2353 
TCGA-CJ-4878 TCGA-CJ-4899 TCGA-CJ-5676 TCGA-CJ-5682 TCGA-CJ-5683 TCGA-CJ-5684 
        2186         1528         2575         1883         1889         2231 
TCGA-CJ-6032 TCGA-CW-5583 TCGA-CW-5585 TCGA-CW-5587 TCGA-CW-5589 TCGA-CW-6093 
        2548         2489         2609         2226         2378         3146 
TCGA-CZ-4863 TCGA-CZ-4864 TCGA-CZ-5451 TCGA-CZ-5453 TCGA-CZ-5457 TCGA-CZ-5459 
        1928         2830         1929           25         1683         1683 
TCGA-CZ-5460 TCGA-CZ-5461 TCGA-CZ-5463 TCGA-CZ-5465 TCGA-CZ-5982 TCGA-DV-5565 
        1430          330          662         1446         2439         1329 
TCGA-DV-5566 TCGA-DV-5569 TCGA-DV-5575 TCGA-EU-5904 TCGA-EU-5906 TCGA-GK-A6C7 
        1398          355         1729          551          206           61 

$subtype3
TCGA-A3-3387 TCGA-AK-3458 TCGA-B0-5402 TCGA-B0-5692 TCGA-B0-5696 TCGA-B0-5697 
         617         1168          449         1487         1727         1835 
TCGA-B0-5698 TCGA-B0-5699 TCGA-B0-5701 TCGA-B0-5703 TCGA-B2-5639 TCGA-B4-5836 
        2583         2741         1732         1203          417          141 
TCGA-B4-5844 TCGA-B8-4621 TCGA-B8-5546 TCGA-B8-A54G TCGA-BP-4973 TCGA-BP-4986 
           7          788          505           53         1384          785 
TCGA-CJ-4876 TCGA-CJ-5675 TCGA-CJ-5681 TCGA-CJ-5686 TCGA-CW-5581 TCGA-CW-5591 
        1955         2430          552         2038         2799         2271 
TCGA-CZ-4866 TCGA-CZ-5452 TCGA-CZ-5458 TCGA-CZ-5466 TCGA-CZ-5470 TCGA-CZ-5984 
        1868         1789         1732          685          386         2067 
TCGA-CZ-5985 TCGA-CZ-5986 TCGA-CZ-5987 TCGA-CZ-5989 
        1997          373          435         1905 

subtype1 subtype2 subtype3 
       7       11        7 
subtype1 subtype2 subtype3 
    3431     3668     2799 
subtype1 subtype2 subtype3 
  1100.5   1431.5   1435.5 
[1] "7.0 - 3431.0 (1100.5)"  "11.0 - 3668.0 (1431.5)" "7.0 - 2799.0 (1435.5)" 
D12V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      43       10        17       20
  subtype2      52       10        23       11
  subtype3      17        7         8       12
D12V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         43       52       17
  STAGE II        10       10        7
  STAGE III       17       23        8
  STAGE IV        20       11       12
[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 44 10 32  4
  subtype2 55 11 29  1
  subtype3 17  9 17  1
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       44       55       17
  T2       10       11        9
  T3       32       29       17
  T4        4        1        1
[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 36  6
  subtype2 36  2
  subtype3 26  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    6
  subtype2   36    2
  subtype3   26    0
   clus
vv  subtype1 subtype2 subtype3
  0       36       36       26
  1        6        2        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 67 18  4
  subtype2 82 11  3
  subtype3 32 11  1
D12V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       67       82       32
  M1       18       11       11
  MX        4        3        1
[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 24 66
  subtype2 36 60
  subtype3 11 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24   66
  subtype2   36   60
  subtype3   11   33
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       24       36       11
  MALE         66       60       33
[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"               "subtype2"              
[4] "subtype3"              
clus
subtype1 subtype2 subtype3 
       1        2        2 
character(0)
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                        10    76
  subtype2     2                         7    86
  subtype3     0                         5    37
D12V10, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        2        0
  BLACK OR AFRICAN AMERICAN       10        7        5
  WHITE                           76       86       37
[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  3 64
  subtype2  3 69
  subtype3  3 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   64
  subtype2    3   69
  subtype3    3   34
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        3        3
  NOT HISPANIC OR LATINO       64       69       34
[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"
