[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"        "-oTLUAD-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/LUAD-TP/10006018/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/10667984/LUAD-TP.mergedcluster.txt"

nPatients in clinical file=474, in cluster file=511, common to both=472
[1]  12 472
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
 5  9 12  6 
 1  2  3  4 
 5  9 12  6 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
14 11  7 
 1  2  3 
14 11  7 
[1] "CN_CNMF"
[1] 3
  1   2   3 
181 194  87 
  1   2   3 
181 194  87 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
 84 120 109  96 
  1   2   3   4 
 84 120 109  96 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
95 68 74 
 1  2  3 
95 68 74 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3 
113  71  53 
  1   2   3 
113  71  53 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5 
134 102  72 101  49 
  1   2   3   4   5 
134 102  72 101  49 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
81 52 43 78 43 47 47 16 51 
 1  2  3  4  5  6  7  8  9 
81 52 43 78 43 47 47 16 51 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
163 222  75 
  1   2   3 
163 222  75 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5   6 
 61  41 115 128  80  35 
  1   2   3   4   5   6 
 61  41 115 128  80  35 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
142 179  76 
  1   2   3 
142 179  76 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
167 200  30 
  1   2   3 
167 200  30 
[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] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 472 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-05-4244 TCGA-05-4249 TCGA-05-4250 TCGA-05-4382 TCGA-05-4384 TCGA-05-4389 
          NA         1523           NA          607          426         1369 
TCGA-05-4390 TCGA-05-4395 TCGA-05-4396 TCGA-05-4397 TCGA-05-4398 TCGA-05-4402 
        1126           NA           NA           NA         1431           NA 
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4415 TCGA-05-4417 TCGA-05-4418 
         578          610           NA           NA          455           NA 
TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4426 TCGA-05-4427 
         912          365          913          669          791          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-4434 TCGA-05-5420 TCGA-05-5423 
         761          761          730           NA          457          151 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5429 TCGA-05-5715 TCGA-35-3615 TCGA-35-4122 
         882          670           30           62           14          225 
TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 
         182          264         2973         3674         1147         1492 
TCGA-38-4629 TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-38-7271 
         864         1073          354         1357          448           NA 
TCGA-38-A44F TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
         133         1324         1429          400         1367          741 
TCGA-44-2662 TCGA-44-2664 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
        1280         1251         1301           97          246         1130 
TCGA-44-3398 TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 
        1163         1183         1036          190          722         1013 
TCGA-44-5644 TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 
         863          383          723          328          302          845 
TCGA-44-6148 TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 
         704          658          705         1938           NA         1864 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 
          NA          444          592          366          218          557 
TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 
          NA          882          535          719          385           99 
TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
         260          486          466          287          337          351 
TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 
         415           76         2318           NA           NA           NA 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 
        1081         1421          428          999          268          896 
TCGA-49-4512 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         157         1700          445          369          890          522 
TCGA-49-6761 TCGA-49-6767 TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
         354           NA           NA         2174         2146          455 
TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
         785          944         1499          246          282          267 
TCGA-50-5932 TCGA-50-5933 TCGA-50-5935 TCGA-50-5936 TCGA-50-5939 TCGA-50-5941 
        1091         2370          653           NA           NA          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-5946 TCGA-50-6590 TCGA-50-6591 TCGA-50-6592 
         883          764          686           NA           NA           NA 
TCGA-50-6593 TCGA-50-6594 TCGA-50-6595 TCGA-50-6597 TCGA-50-6673 TCGA-50-7109 
          NA           NA           NA         1015           NA          255 
TCGA-50-8460 TCGA-53-7624 TCGA-53-7626 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         105           NA           NA          424          280          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 
        1178         1479         1375           87            2          993 
TCGA-55-6712 TCGA-55-6968 TCGA-55-6969 TCGA-55-6970 TCGA-55-6971 TCGA-55-6972 
          24           NA         1239           NA           25         1475 
TCGA-55-6975 TCGA-55-6978 TCGA-55-6979 TCGA-55-6980 TCGA-55-6981 TCGA-55-6982 
          NA           NA           NA           67           NA           NA 
TCGA-55-6983 TCGA-55-6984 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 TCGA-55-7227 
        1826           NA         1233         2151         1170           53 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7570 TCGA-55-7573 TCGA-55-7574 
          18           35          121            6            4           95 
TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7727 TCGA-55-7728 
          40           NA           39           39           34           24 
TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 
          54           44           19           16          197           21 
TCGA-55-7914 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
           3           31            5           33           21          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6           43           26            4           47           15 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 
          NA           33           46           66          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          23           29           11            8           15          228 
TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
           9            3          146          202          536           15 
TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y 
          48           49           66          106           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          29           48           NA            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 TCGA-62-8398 
          47          162           NA         1216         1289           NA 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R TCGA-62-A46S 
        2696         1445           NA           NA           NA           NA 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 TCGA-62-A472 
        2067         2199           NA           NA         1246          910 
TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 TCGA-64-1681 
        1728          628         1189         1686         1126           NA 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-64-5815 
        2676           62         1305          864         1559          866 
TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-4679 
          31          610          573          427          385           NA 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 TCGA-69-7763 
         174          141          422          202          186          690 
TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
         414          165          230          184           70           89 
TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 
         382          100           77          129          214           61 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 TCGA-73-4668 
           3         1600          711          912          800          467 
TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 TCGA-73-7499 
         131           40          164           38          621          519 
TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 TCGA-75-5147 TCGA-75-6203 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 TCGA-75-6212 TCGA-75-6214 
          NA           NA           NA           NA           NA           NA 
TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 TCGA-78-7143 TCGA-78-7145 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 
          NA           NA           NA         1093           NA         1202 
TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7158 TCGA-78-7159 
         760           NA           NA           NA           NA         1221 
TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7166 TCGA-78-7167 
         678          215           NA         6812           NA           NA 
TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 
          NA           NA           NA           NA          327          881 
TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 
          NA          994         6346           NA         2360           NA 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 TCGA-83-5908 TCGA-86-6562 
          NA           NA           NA           NA          824           NA 
TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7714 TCGA-86-7953 
          NA           11          630          422           NA          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8056 TCGA-86-8073 
          NA          508          745           10           NA           13 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8280 
          24          479          489          476          482           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8668 TCGA-86-8669 
          NA           19           26           35           45           34 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 
          18           15          455          405           10           30 
TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
          NA           14           39          323           NA           60 
TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 
         310           79          417          372          842          224 
TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-8499 TCGA-91-A4BC 
          35          492          197          174           36           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         218          297          127          186           34            2 
TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 
         568          377          477          476          121          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7938 
        1965         1932         1332          775          181           NA 
TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
          22          107          182           NA           87          147 
TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-7458 
          15          148          115          197          271          392 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         427          459           44          170          154          114 
TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A443 
         287          282          238          578          435          116 
TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV TCGA-L9-A8F4 
           6          266           NA          312          111          102 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4SY 
         285          622          353           NA           NA           NA 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH 
          NA           NA           NA           NA           NA          142 
TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 
          NA           NA           NA         1490 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=120,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=286,	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=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	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=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=39,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=7,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=92,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=57,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=23,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                                   
 [2] "NEOPLASM.DISEASESTAGE"                 
 [3] "PATHOLOGY.T.STAGE"                     
 [4] "PATHOLOGY.N.STAGE"                     
 [5] "PATHOLOGY.M.STAGE"                     
 [6] "GENDER"                                
 [7] "KARNOFSKY.PERFORMANCE.SCORE"           
 [8] "HISTOLOGICAL.TYPE"                     
 [9] "RADIATIONS.RADIATION.REGIMENINDICATION"
[10] "NUMBERPACKYEARSSMOKED"                 
[11] "COMPLETENESS.OF.RESECTION"             
[12] "RACE"                                  
[13] "ETHNICITY"                             
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 472 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=51, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=8, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
145 264  42  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
145 264  42  18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
145 264  42  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
145 264  42  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
299  89  71   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  299    89    73 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
299  89  71   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  299    89    73 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=7, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=12, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=92, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1  4  0
  subtype2  7  1
  subtype3 10  2
  subtype4  4  2
subtype1 subtype2 subtype3 subtype4 
       4        8       12        6 
subtype1 subtype2 subtype3 subtype4 
       0        1        2        2 
$subtype1
TCGA-35-4123 TCGA-44-2665 TCGA-44-3919 TCGA-55-1595 
         182         1301          190         1479 

$subtype2
TCGA-05-4249 TCGA-35-4122 TCGA-44-2656 TCGA-44-2662 TCGA-44-2668 TCGA-44-3398 
        1523          225         1429         1280          246         1163 
TCGA-44-3918 TCGA-64-1676 
        1036         1728 

$subtype3
TCGA-35-3615 TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 TCGA-44-2666 
          14         1324          400         1367          741           97 
TCGA-44-4112 TCGA-64-1680 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         722         1126           31          573          427          385 

$subtype4
TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-64-1677 TCGA-64-1678 TCGA-67-3771 
         701         1178         1375          628         1189          610 

subtype1 subtype2 subtype3 subtype4 
     182      225       14      610 
subtype1 subtype2 subtype3 subtype4 
    1479     1728     1367     1375 
subtype1 subtype2 subtype3 subtype4 
   745.5   1221.5    500.0    939.5 
[1] "182.0 - 1479.0 (745.5)"  "225.0 - 1728.0 (1221.5)"
[3] "14.0 - 1367.0 (500.0)"   "610.0 - 1375.0 (939.5)" 
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IV
  subtype1        3        0         0         1          0        1
  subtype2        4        4         0         0          1        0
  subtype3        3        7         0         1          0        1
  subtype4        2        0         1         1          2        0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE IA          3        4        3        2
  STAGE IB          0        4        7        0
  STAGE IIA         0        0        0        1
  STAGE IIB         1        0        1        1
  STAGE IIIA        0        1        0        2
  STAGE IV          1        0        1        0
[1] 6 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3
  subtype1  3  2  0
  subtype2  4  4  1
  subtype3  4  8  0
  subtype4  1  5  0
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        3        4        4        1
  T2        2        4        8        5
  T3        0        1        0        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1  3  1     1
  subtype2  8  1     0
  subtype3  9  1     1
  subtype4  3  1     2
D1V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0           3        8        9        3
  N1           1        1        1        1
  N2+N3        1        0        1        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1
  subtype1  4  1
  subtype2  9  0
  subtype3 11  1
  subtype4  6  0
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0        4        9       11        6
  M1        1        0        1        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus       0 1
  subtype1 3 2
  subtype2 3 6
  subtype3 9 3
  subtype4 3 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3    2
  subtype2    3    6
  subtype3    9    3
  subtype4    3    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        3        3        9        3
  MALE          2        6        3        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype2"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype4 
       1        1        1 
character(0)
          vv
clus       LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                                 0
  subtype2                                 0
  subtype3                                 1
  subtype4                                 0
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                  4
  subtype2                                                  9
  subtype3                                                 11
  subtype4                                                  6
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA
  subtype1                              1
  subtype2                              0
  subtype3                              0
  subtype4                              0
D1V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         0        0        1
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)        4        9       11
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
                                                    clus
vv                                                   subtype4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)        6
  LUNG CLEAR CELL ADENOCARCINOMA                            0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
          cls
clus        0  1
  subtype1  0  5
  subtype2  0  9
  subtype3  1 11
  subtype4  0  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    5
  subtype2    0    9
  subtype3    1   11
  subtype4    0    6
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         0        0        1        0
  YES        5        9       11        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       2        9        6        3 
 [1] "subtype2" "subtype2" "subtype2" "subtype3" "subtype2" "subtype3"
 [7] "subtype3" "subtype2" "subtype3" "subtype2" "subtype2" "subtype2"
[13] "subtype3" "subtype4" "subtype2" "subtype4" "subtype4" "subtype3"
          vv
clus       R0 R2 RX
  subtype1  3  0  1
  subtype2  7  1  0
  subtype3 10  0  1
  subtype4  6  0  0
D1V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0        3        7       10        6
  R2        0        1        0        0
  RX        1        0        1        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0     3
  subtype2     0                         0     7
  subtype3     0                         0    12
  subtype4     1                         1     4
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        0        1
  BLACK OR AFRICAN AMERICAN        0        0        0        1
  WHITE                            3        7       12        4
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
          cls
clus        0  1
  subtype1  0  4
  subtype2  0  7
  subtype3  1 11
  subtype4  0  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0    4
  subtype2    0    7
  subtype3    1   11
  subtype4    0    6
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        0        1        0
  NOT HISPANIC OR LATINO        4        7       11        6
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = MRNA_CHIERARCHICAL
D2V1, survival
          sevent
clus2       0  1
  subtype1 11  2
  subtype2  9  1
  subtype3  5  2
subtype1 subtype2 subtype3 
      13       10        7 
subtype1 subtype2 subtype3 
       2        1        2 
$subtype1
TCGA-35-3615 TCGA-44-2655 TCGA-44-2656 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
          14         1324         1429          400         1367          741 
TCGA-44-2666 TCGA-44-4112 TCGA-64-1680 TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 
          97          722         1126           31          573          427 
TCGA-67-3774 
         385 

$subtype2
TCGA-05-4249 TCGA-35-4122 TCGA-35-4123 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 
        1523          225          182         1280         1301          246 
TCGA-44-3398 TCGA-44-3918 TCGA-44-3919 TCGA-64-1676 
        1163         1036          190         1728 

$subtype3
TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-64-1677 TCGA-64-1678 
         701         1178         1479         1375          628         1189 
TCGA-67-3771 
         610 

subtype1 subtype2 subtype3 
      14      182      610 
subtype1 subtype2 subtype3 
    1429     1728     1479 
subtype1 subtype2 subtype3 
   573.0   1099.5   1178.0 
[1] "14.0 - 1429.0 (573.0)"   "182.0 - 1728.0 (1099.5)"
[3] "610.0 - 1479.0 (1178.0)"
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IV
  subtype1        3        8         0         1          0        2
  subtype2        6        3         0         1          1        0
  subtype3        3        0         1         1          2        0
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE IA          3        6        3
  STAGE IB          8        3        0
  STAGE IIA         0        0        1
  STAGE IIB         1        1        1
  STAGE IIIA        0        1        2
  STAGE IV          2        0        0
[1] 6 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  4 10  0
  subtype2  6  4  1
  subtype3  2  5  0
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        4        6        2
  T2       10        4        5
  T3        0        1        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"
          vv
clus       N0 N1 N2+N3
  subtype1 10  1     2
  subtype2  9  2     0
  subtype3  4  1     2
D2V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          10        9        4
  N1           1        2        1
  N2+N3        2        0        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"
          vv
clus       M0 M1
  subtype1 12  2
  subtype2 11  0
  subtype3  7  0
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       12       11        7
  M1        2        0        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"
D2V7, binary
          cls
clus       0 1
  subtype1 9 5
  subtype2 5 6
  subtype3 4 3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9    5
  subtype2    5    6
  subtype3    4    3
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        9        5        4
  MALE          5        6        3
[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"
D2V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
clus
subtype2 subtype3 
       2        1 
character(0)
          vv
clus       LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                                 1
  subtype2                                 0
  subtype3                                 0
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 13
  subtype2                                                 11
  subtype3                                                  6
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA
  subtype1                              0
  subtype2                              0
  subtype3                              1
D2V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         1        0        0
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       13       11        6
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        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"
D2V10, binary
          cls
clus        0  1
  subtype1  1 13
  subtype2  0 11
  subtype3  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   13
  subtype2    0   11
  subtype3    0    7
     clus
vv    subtype1 subtype2 subtype3
  NO         1        0        0
  YES       13       11        7
[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"
D2V11, continuous
          vv
clus       R0 R2 RX
  subtype1 10  0  2
  subtype2 10  1  0
  subtype3  6  0  0
D2V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       10       10        6
  R2        0        1        0
  RX        2        0        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         0    13
  subtype2     0                         0     9
  subtype3     2                         1     4
D2V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        0        2
  BLACK OR AFRICAN AMERICAN        0        0        1
  WHITE                           13        9        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"
D2V14, binary
          cls
clus        0  1
  subtype1  1 12
  subtype2  0  9
  subtype3  0  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   12
  subtype2    0    9
  subtype3    0    7
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        0
  NOT HISPANIC OR LATINO       12        9        7
[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(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2        0   1
  subtype1 124  33
  subtype2 135  33
  subtype3  62  16
subtype1 subtype2 subtype3 
     157      168       78 
subtype1 subtype2 subtype3 
      33       33       16 
$subtype1
TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4420 TCGA-05-4425 TCGA-05-4426 
        1431          610         1958          912          669          791 
TCGA-05-4427 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-4123 
         791          151          882          670           62          182 
TCGA-38-4629 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2656 TCGA-44-2659 
         864          354         1357          448         1429         1367 
TCGA-44-2662 TCGA-44-3919 TCGA-44-5644 TCGA-44-6144 TCGA-44-6775 TCGA-44-6777 
        1280          190          863          723          705         1942 
TCGA-44-6779 TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4501 
        1978          218          385          260           76         1421 
TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-6761 TCGA-50-5045 TCGA-50-5933 
         428          268          157          354         2174         2370 
TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-55-1592 TCGA-55-1594 
         764          686         1015         1986          701         1178 
TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 
        1479         1375            2           24         1475           67 
TCGA-55-6985 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 TCGA-55-7727 
        1233           35            4           40           39           34 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8091 TCGA-55-8096 TCGA-55-8207 
         197           31            5           43           47           66 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8616 
          23           11          228            9          202           48 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          29           48         1952          162         1216         1289 
TCGA-62-8399 TCGA-62-8402 TCGA-62-A46U TCGA-62-A472 TCGA-64-1676 TCGA-64-1678 
        2696         1445         2067          910         1728         1189 
TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-67-6217 
        1686         1968         1305           31          573          422 
TCGA-69-7760 TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 
         202           89          382          214           61          912 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 
         467          131          164          519         1970         1973 
TCGA-78-7147 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7161 TCGA-78-7163 
        1950         1963         1948         1957          215         1950 
TCGA-78-7535 TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 
        1972          327         1952         1949         1981         1964 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 
         824         1959          630          422          591         1963 
TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 
         508          745           10           24          479          482 
TCGA-86-8280 TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8673 TCGA-91-6829 
          16           19           26           45          455         1940 
TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-95-7039 TCGA-95-7567 
         417          842          224           36           34          568 
TCGA-95-7947 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 
         477          121          964          775          181          107 
TCGA-97-8547 TCGA-97-A4M7 TCGA-99-8025 TCGA-J2-8192 TCGA-J2-8194 TCGA-J2-A4AD 
         148          271          427          154          114          287 
TCGA-J2-A4AE TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         282          578            6          285          622          353 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TF 
        1967         1951         1954         1957         1944         1970 
TCGA-MP-A4TK 
        1971 

$subtype2
TCGA-05-4249 TCGA-05-4382 TCGA-05-4384 TCGA-05-4396 TCGA-05-4403 TCGA-05-4422 
        1523          607          426         1947          578          365 
TCGA-05-4430 TCGA-05-4433 TCGA-05-5420 TCGA-05-5429 TCGA-35-3615 TCGA-35-4122 
         761          730          457           30           14          225 
TCGA-38-4626 TCGA-38-4627 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 
        1962         1147         1073         1971          133         1324 
TCGA-44-2657 TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 
         400          741         1301           97          246         1130 
TCGA-44-3398 TCGA-44-4112 TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 
        1163          722          383          328          302          704 
TCGA-44-6776 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A479 
        1938          444          366          535          719          486 
TCGA-44-A47A TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 
         466          337          351          415         1932         1081 
TCGA-49-4506 TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 
         999         1700          445          369          890          522 
TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 
        2146          785          944         1499          246          282 
TCGA-50-5932 TCGA-50-5942 TCGA-50-8460 TCGA-53-7626 TCGA-55-6642 TCGA-55-6983 
        1091          883          105         1971          993         1826 
TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7284 TCGA-55-7574 TCGA-55-7724 
        2151         1170           18          121           95         1958 
TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7911 TCGA-55-7914 TCGA-55-8087 
          39           24           54           21            3           21 
TCGA-55-8089 TCGA-55-8090 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8299 
         100            6           15           33           46          216 
TCGA-55-8301 TCGA-55-8505 TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
          44           29           15            3          146           49 
TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 
          66          106           33           42            1           28 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-A46V TCGA-64-1680 TCGA-64-5781 TCGA-64-5815 
          47         1970         2199         1126         1559          866 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-69-7761 TCGA-69-7763 
         427          385          174          141          186          690 
TCGA-69-7765 TCGA-69-7974 TCGA-69-7978 TCGA-69-8253 TCGA-69-8254 TCGA-73-4658 
         165          184           70          100           77         1600 
TCGA-73-4666 TCGA-73-4677 TCGA-73-7498 TCGA-75-7025 TCGA-78-7148 TCGA-78-7152 
         800           38          621         1967         1944         1202 
TCGA-78-7153 TCGA-78-7156 TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 
         760         1961         1963          678         1940         1934 
TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 TCGA-78-8648 TCGA-78-8660 TCGA-80-5607 
        1944          881          994         1971         1954         1965 
TCGA-86-7714 TCGA-86-8056 TCGA-86-8073 TCGA-86-8076 TCGA-86-8278 TCGA-86-8281 
        1968         1963           13          489          476         1955 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 
          18           15          405           10           14           39 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BC 
          60           79           35          197          174           44 
TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7944 TCGA-97-7547 TCGA-97-7552 
         218          297          127          377         1965         1932 
TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 
        1332           22          182         1965           87          147 
TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 TCGA-J2-A4AG TCGA-L4-A4E6 
         115          197          392          459          238          435 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A5C7 
        1954         1980         1951          142         1955         1490 

$subtype3
TCGA-05-4389 TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4424 TCGA-05-4432 
        1369         1126         1997          455          913          761 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-44-3918 TCGA-44-5643 TCGA-44-6147 
         264         1952         1492         1036         1013          845 
TCGA-44-6774 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         658         1864          592          557         1970          882 
TCGA-44-8119 TCGA-44-A47B TCGA-49-4510 TCGA-50-5051 TCGA-50-5931 TCGA-50-5935 
          99          287          896          455          267          653 
TCGA-50-5941 TCGA-50-7109 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6969 
         567          255          424          280           87         1239 
TCGA-55-6971 TCGA-55-7570 TCGA-55-7903 TCGA-55-7907 TCGA-55-8085 TCGA-55-8092 
          25            6           19           16           33           26 
TCGA-55-8094 TCGA-55-8507 TCGA-55-8614 TCGA-55-8615 TCGA-55-A494 TCGA-62-A471 
           4            8          536           15            5         1246 
TCGA-64-1677 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-69-7764 
         628         1959           62          864          610          414 
TCGA-69-7973 TCGA-69-8255 TCGA-73-4659 TCGA-73-4675 TCGA-75-7027 TCGA-75-7031 
         230          129          711           40         1956         1965 
TCGA-78-7146 TCGA-78-7149 TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1988         1093         1221         1937         1965         1949 
TCGA-80-5608 TCGA-86-7701 TCGA-86-8585 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 
        1972           11           35           34           30          323 
TCGA-91-6831 TCGA-91-6840 TCGA-91-7771 TCGA-93-8067 TCGA-95-7043 TCGA-95-7948 
         310          372          492          186            2          476 
TCGA-97-8179 TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 TCGA-MP-A4SV TCGA-MP-A4TE 
          15           44          170          116         1946         1970 

subtype1 subtype2 subtype3 
       2        1        2 
subtype1 subtype2 subtype3 
    2696     2199     1997 
subtype1 subtype2 subtype3 
   519.0    426.5    484.0 
[1] "2.0 - 2696.0 (519.0)" "1.0 - 2199.0 (426.5)" "2.0 - 1997.0 (484.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       2       36       52        20        31         26          5
  subtype2       1       55       56        17        28         24          3
  subtype3       1       22       23         6        10         17          3
          vv
clus       STAGE IV
  subtype1        9
  subtype2        9
  subtype3        5
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        1        1
  STAGE IA         36       55       22
  STAGE IB         52       56       23
  STAGE IIA        20       17        6
  STAGE IIB        31       28       10
  STAGE IIIA       26       24       17
  STAGE IIIB        5        3        3
  STAGE IV          9        9        5
[1] 8 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  49 108  19   5
  subtype2  68 104  13   9
  subtype3  26  47   8   4
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       49       68       26
  T2      108      104       47
  T3       19       13        8
  T4        5        9        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"
          vv
clus        N0  N1 N2+N3
  subtype1 111  36    32
  subtype2 127  37    25
  subtype3  57  12    15
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         111      127       57
  N1          36       37       12
  N2+N3       32       25       15
[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"
          vv
clus        M0  M1 M1A M1B  MX
  subtype1 122   8   1   0  48
  subtype2 136   6   0   2  48
  subtype3  59   4   0   1  23
D3V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       122      136       59
  M1         8        6        4
  M1A        1        0        0
  M1B        0        2        1
  MX        48       48       23
[1] 5 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 109  72
  subtype2 106  88
  subtype3  33  54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  109   72
  subtype2  106   88
  subtype3   33   54
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      109      106       33
  MALE         72       88       54
[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
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          6                                34
  subtype2                          3                                43
  subtype3                          4                                16
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                120
  subtype2                                                114
  subtype3                                                 60
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          2
  subtype2                                          2
  subtype3                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             9
  subtype2                                             9
  subtype3                                             1
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  3
  subtype2                              1                                  1
  subtype3                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             5
  subtype2                            2                            11
  subtype3                            0                             3
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               1
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             1
  subtype3                                             2
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            6
  subtype3                            1
D3V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                6        3        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        34       43       16
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      120      114       60
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        2        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             9        9        1
  LUNG CLEAR CELL ADENOCARCINOMA                            1        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        3        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        2        0
  LUNG PAPILLARY ADENOCARCINOMA                             5       11        3
  LUNG SIGNET RING ADENOCARCINOMA                           0        1        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        1        2
  MUCINOUS (COLLOID) CARCINOMA                              0        6        1
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V10, binary
          cls
clus         0   1
  subtype1   5 176
  subtype2  10 184
  subtype3   6  81
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  176
  subtype2   10  184
  subtype3    6   81
     clus
vv    subtype1 subtype2 subtype3
  NO         5       10        6
  YES      176      184       81
[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"
D3V11, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 128   5   1   9
  subtype2 133   4   2   6
  subtype3  57   2   1   4
D3V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      128      133       57
  R1        5        4        2
  R2        1        2        1
  RX        9        6        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                        10
  subtype2                                0     1                        10
  subtype3                                0     1                         6
          vv
clus       WHITE
  subtype1   140
  subtype2   155
  subtype3    67
D3V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   4        1        1
  BLACK OR AFRICAN AMERICAN              10       10        6
  WHITE                                 140      155       67
[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"
D3V14, binary
          cls
clus         0   1
  subtype1   3 127
  subtype2   1 145
  subtype3   3  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  127
  subtype2    1  145
  subtype3    3   60
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        3
  NOT HISPANIC OR LATINO      127      145       60
[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 61 13
  subtype2 82 24
  subtype3 80 18
  subtype4 66 13
subtype1 subtype2 subtype3 subtype4 
      74      106       98       79 
subtype1 subtype2 subtype3 subtype4 
      13       24       18       13 
$subtype1
TCGA-05-4384 TCGA-05-5423 TCGA-05-5715 TCGA-44-2665 TCGA-44-2666 TCGA-44-5645 
         426          151           62         1301           97          383 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-7659 TCGA-44-A47F TCGA-49-4512 
         302          704         1938          444          337          157 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-8460 TCGA-53-7626 
        1091          653          883          764          105         1971 
TCGA-55-6543 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7573 TCGA-55-7725 
           2         1826         1233         2151            4           39 
TCGA-55-8087 TCGA-55-8091 TCGA-55-8097 TCGA-55-8206 TCGA-55-8512 TCGA-55-8513 
          21           43           15           46            3          146 
TCGA-55-A492 TCGA-62-8395 TCGA-62-8397 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
           1         1216         1289          174          141          422 
TCGA-69-7760 TCGA-69-7763 TCGA-69-8253 TCGA-69-8254 TCGA-73-7498 TCGA-75-7025 
         202          690          100           77          621         1967 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7537 TCGA-80-5607 TCGA-86-7714 TCGA-86-8280 
        1940         1950         1944         1965         1968           16 
TCGA-86-8668 TCGA-86-A4P7 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
          45           14           35          197          174          218 
TCGA-93-7347 TCGA-93-7348 TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 
         297          127          476          964         1965         1332 
TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 
          22          182         1965          147          115          197 
TCGA-99-7458 TCGA-J2-8192 TCGA-J2-A4AE TCGA-L9-A50W TCGA-MP-A4T2 TCGA-MP-A4T7 
         392          154          282          266         1951         1954 
TCGA-MP-A4T9 TCGA-MP-A4TH 
        1980          142 

$subtype2
TCGA-05-4390 TCGA-05-4415 TCGA-05-4424 TCGA-05-5425 TCGA-35-5375 TCGA-38-4631 
        1126         1997          913          882          264          354 
TCGA-44-5644 TCGA-44-6144 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 
         863          723          592          557         1970          882 
TCGA-44-7671 TCGA-44-8119 TCGA-44-A4SU TCGA-49-6742 TCGA-50-5051 TCGA-50-5072 
         535           99           76          445          455          246 
TCGA-50-5931 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
         267          686          255         1986          424          280 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6972 TCGA-55-7570 TCGA-55-7910 TCGA-55-7995 
          87          993         1475            6          197            5 
TCGA-55-8085 TCGA-55-8094 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 
          33            4            8           15          202          536 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 
          15           66           42           29           48            5 
TCGA-55-A4DF TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A471 TCGA-64-1681 
          47         1970         2696         1445         1246         1968 
TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 
        1959         1305          864          414          230           89 
TCGA-69-7980 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 
         382          519         1970         1956         1965         1988 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
        1944         1093         1963         1948         1957         1961 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 
        1221          215         1934         1937         1965         1949 
TCGA-78-7633 TCGA-78-8640 TCGA-78-8662 TCGA-80-5608 TCGA-86-7713 TCGA-86-7955 
         994         1949         1964         1972          422          508 
TCGA-86-8054 TCGA-86-8075 TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 
         745          479          482         1955           19           26 
TCGA-86-8669 TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 
          34          405           30         1940          310          372 
TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VK 
         842          492           36            2          477          121 
TCGA-97-8171 TCGA-97-8179 TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L9-A443 
         107           15           44          114          287          116 
TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4TF TCGA-MP-A5C7 
         111          622         1970         1490 

$subtype3
TCGA-05-4396 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4425 TCGA-05-4427 
        1947          610         1958          455          669          791 
TCGA-05-4433 TCGA-05-5428 TCGA-05-5429 TCGA-38-4632 TCGA-38-6178 TCGA-44-3917 
         730          670           30         1357          448         1183 
TCGA-44-3918 TCGA-44-4112 TCGA-44-7662 TCGA-44-7672 TCGA-44-8117 TCGA-44-8120 
        1036          722          218          719          385          260 
TCGA-44-A47A TCGA-44-A47B TCGA-49-6745 TCGA-49-6761 TCGA-50-5933 TCGA-50-6597 
         466          287          522          354         2370         1015 
TCGA-55-6712 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 
          24           53           18           35          121           40 
TCGA-55-7727 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 
          34           54           19           16           21            3 
TCGA-55-7994 TCGA-55-8090 TCGA-55-8092 TCGA-55-8205 TCGA-55-8207 TCGA-55-8506 
          31            6           26           33           66           11 
TCGA-55-8511 TCGA-55-8616 TCGA-55-A4DG TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 
           9           48          162         2067         2199          910 
TCGA-64-5775 TCGA-64-5815 TCGA-69-7765 TCGA-69-7974 TCGA-69-A59K TCGA-71-6725 
          62          866          165          184          214           61 
TCGA-71-8520 TCGA-73-4658 TCGA-73-4676 TCGA-78-7145 TCGA-78-7147 TCGA-78-7152 
           3         1600          164         1973         1950         1202 
TCGA-78-7153 TCGA-78-7158 TCGA-78-7535 TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 
         760         1963         1972          327          881         1952 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-8056 
        1981         1954          824         1959           11         1963 
TCGA-86-8073 TCGA-86-8074 TCGA-86-8278 TCGA-86-8672 TCGA-86-8673 TCGA-86-A456 
          13           24          476           15          455           10 
TCGA-91-6828 TCGA-91-6836 TCGA-93-8067 TCGA-95-7039 TCGA-95-7567 TCGA-97-7554 
         323          417          186           34          568          775 
TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 TCGA-97-A4M7 TCGA-99-8025 TCGA-L4-A4E5 
         181           87          148          271          427          578 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T8 
           6          285          353         1946         1967         1957 
TCGA-MP-A4TC TCGA-MP-A4TE 
        1944         1970 

$subtype4
TCGA-05-5420 TCGA-38-7271 TCGA-38-A44F TCGA-44-2656 TCGA-44-2668 TCGA-44-5643 
         457         1971          133         1429          246         1013 
TCGA-44-6145 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6778 
         328          845          658          705         1942         1864 
TCGA-44-6779 TCGA-44-7661 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SS TCGA-49-4514 
        1978          366          486          351          415         1700 
TCGA-49-6743 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 
         369          890         2174         2146          785          944 
TCGA-50-5068 TCGA-50-5930 TCGA-50-5941 TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 
        1499          282          567         1239           25           67 
TCGA-55-6987 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 TCGA-55-7816 
        1170           95         1958           39           24           44 
TCGA-55-8089 TCGA-55-8096 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
         100           47          216           44           23           29 
TCGA-55-8510 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A491 TCGA-55-A493 
         228           49          106           33         1952           28 
TCGA-64-1679 TCGA-64-5781 TCGA-69-7761 TCGA-69-7978 TCGA-69-8255 TCGA-78-7160 
        1686         1559          186           70          129          678 
TCGA-78-8648 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 TCGA-86-8055 TCGA-86-8076 
        1971          630          591         1963           10          489 
TCGA-86-8585 TCGA-86-8671 TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 
          35           18           39           60           79          224 
TCGA-91-A4BC TCGA-95-7944 TCGA-97-7552 TCGA-99-8028 TCGA-99-8033 TCGA-J2-A4AG 
          44          377         1932          459          170          238 
TCGA-L4-A4E6 TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MP-A4T4 TCGA-MP-A4TA TCGA-MP-A4TI 
         435          312          102         1954         1951         1955 
TCGA-MP-A4TK 
        1971 

subtype1 subtype2 subtype3 subtype4 
       1        2        3       10 
subtype1 subtype2 subtype3 subtype4 
    2151     2696     2370     2174 
subtype1 subtype2 subtype3 subtype4 
   289.5    487.0    369.5    377.0 
[1] "1.0 - 2151.0 (289.5)"  "2.0 - 2696.0 (487.0)"  "3.0 - 2370.0 (369.5)" 
[4] "10.0 - 2174.0 (377.0)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       30       19         8        13         10          0
  subtype2       2       26       32        15        13         18          5
  subtype3       1       15       36        10        21         18          3
  subtype4       0       27       30        10        12         13          1
          vv
clus       STAGE IV
  subtype1        2
  subtype2        9
  subtype3        5
  subtype4        3
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        2        1        0
  STAGE IA         30       26       15       27
  STAGE IB         19       32       36       30
  STAGE IIA         8       15       10       10
  STAGE IIB        13       13       21       12
  STAGE IIIA       10       18       18       13
  STAGE IIIB        0        5        3        1
  STAGE IV          2        9        5        3
[1] 8 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 38 38  7  1
  subtype2 32 71 11  5
  subtype3 24 65 13  7
  subtype4 34 53  5  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       38       32       24       34
  T2       38       71       65       53
  T3        7       11       13        5
  T4        1        5        7        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 57 15     9
  subtype2 76 19    23
  subtype3 69 23    17
  subtype4 60 18    14
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          57       76       69       60
  N1          15       19       23       18
  N2+N3        9       23       17       14
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B MX
  subtype1 50  1   0   1 30
  subtype2 81  5   1   3 29
  subtype3 75  4   0   0 29
  subtype4 59  2   0   0 35
D4V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        50       81       75       59
  M1         1        5        4        2
  M1A        0        1        0        0
  M1B        1        3        0        0
  MX        30       29       29       35
[1] 5 4
[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 57 27
  subtype2 49 71
  subtype3 54 55
  subtype4 59 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57   27
  subtype2   49   71
  subtype3   54   55
  subtype4   59   37
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       57       49       54       59
  MALE         27       71       55       37
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          5                                17
  subtype2                          6                                25
  subtype3                          1                                27
  subtype4                          1                                10
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 42
  subtype2                                                 74
  subtype3                                                 70
  subtype4                                                 72
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          2
  subtype2                                          0
  subtype3                                          1
  subtype4                                          1
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            10
  subtype2                                             3
  subtype3                                             4
  subtype4                                             2
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  1
  subtype2                              0                                  0
  subtype3                              0                                  2
  subtype4                              1                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            2                             3
  subtype2                            0                             8
  subtype3                            0                             3
  subtype4                            0                             4
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             1
  subtype3                                             1
  subtype4                                             2
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            2
  subtype2                            3
  subtype3                            0
  subtype4                            2
D4V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                5        6        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        17       25       27
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       42       74       70
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            10        3        4
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        2
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             3        8        3
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        1        1
  MUCINOUS (COLLOID) CARCINOMA                              2        3        0
                                                    clus
vv                                                   subtype4
  LUNG ACINAR ADENOCARCINOMA                                1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        10
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       72
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             2
  LUNG CLEAR CELL ADENOCARCINOMA                            1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0
  LUNG MUCINOUS ADENOCARCINOMA                              0
  LUNG PAPILLARY ADENOCARCINOMA                             4
  LUNG SIGNET RING ADENOCARCINOMA                           1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2
  MUCINOUS (COLLOID) CARCINOMA                              2
[1] 12  4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, binary
          cls
clus         0   1
  subtype1   2  82
  subtype2   5 115
  subtype3   3 106
  subtype4   8  88
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   82
  subtype2    5  115
  subtype3    3  106
  subtype4    8   88
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        5        3        8
  YES       82      115      106       88
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 53  1  0  4
  subtype2 83  4  0  5
  subtype3 80  4  0  5
  subtype4 56  1  1  2
D4V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       53       83       80       56
  R1        1        4        4        1
  R2        0        0        0        1
  RX        4        5        5        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         6    68
  subtype2     1                         8    99
  subtype3     4                         7    80
  subtype4     0                         8    79
D4V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        1        4        0
  BLACK OR AFRICAN AMERICAN        6        8        7        8
  WHITE                           68       99       80       79
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
          cls
clus        0  1
  subtype1  1 65
  subtype2  3 87
  subtype3  0 76
  subtype4  3 69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   65
  subtype2    3   87
  subtype3    0   76
  subtype4    3   69
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        3        0        3
  NOT HISPANIC OR LATINO       65       87       76       69
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 56 14
  subtype2 50 14
  subtype3 45 21
subtype1 subtype2 subtype3 
      70       64       66 
subtype1 subtype2 subtype3 
      14       14       21 
$subtype1
TCGA-05-4396 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4422 
        1947         1431          610         1958          455          365 
TCGA-05-4430 TCGA-05-5423 TCGA-05-5429 TCGA-38-6178 TCGA-44-2656 TCGA-44-2661 
         761          151           30          448         1429          741 
TCGA-44-2664 TCGA-44-2665 TCGA-44-3918 TCGA-44-3919 TCGA-44-5645 TCGA-44-6144 
        1251         1301         1036          190          383          723 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-49-4494 
         302          845          705         1938         1942         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 
        1421          428          157          369          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5068 TCGA-50-5941 TCGA-50-5942 
        2174         2146          944         1499          567          883 
TCGA-50-5944 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
         764         1015          701         1178         1375           87 
TCGA-55-6543 TCGA-55-6712 TCGA-55-7573 TCGA-55-7911 TCGA-64-1676 TCGA-64-1679 
           2           24            4           21         1728         1686 
TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
        1968         1305         1559          174          141          422 
TCGA-69-7760 TCGA-71-6725 TCGA-73-4675 TCGA-75-7031 TCGA-78-7145 TCGA-78-7535 
         202           61           40         1965         1973         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 
         824         1959          323         1940           60           79 
TCGA-91-6840 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 
         372           34          568          476 

$subtype2
TCGA-05-4249 TCGA-05-4384 TCGA-05-4426 TCGA-05-5420 TCGA-05-5425 TCGA-35-3615 
        1523          426          791          457          882           14 
TCGA-38-4626 TCGA-38-4627 TCGA-44-2657 TCGA-44-3396 TCGA-44-3398 TCGA-44-7659 
        1962         1147          400         1130         1163          444 
TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-49-4486 TCGA-49-4510 TCGA-49-6742 
         366          535          719         1932          896          445 
TCGA-49-6744 TCGA-50-5051 TCGA-50-5932 TCGA-50-7109 TCGA-53-7626 TCGA-53-7813 
         890          455         1091          255         1971          424 
TCGA-55-7574 TCGA-55-7728 TCGA-55-7815 TCGA-64-1680 TCGA-69-7761 TCGA-69-7763 
          95           24           54         1126          186          690 
TCGA-69-7764 TCGA-73-4658 TCGA-73-4659 TCGA-73-4670 TCGA-73-4676 TCGA-73-7498 
         414         1600          711          131          164          621 
TCGA-78-7147 TCGA-78-7149 TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 
        1950         1093         1961         1963          215         1940 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 TCGA-80-5607 
        1950         1937         1944          327          994         1965 
TCGA-80-5608 TCGA-86-7713 TCGA-86-7954 TCGA-91-6849 TCGA-91-7771 TCGA-93-7348 
        1972          422         1963           35          492          127 
TCGA-95-7043 TCGA-95-7944 TCGA-95-7947 TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 
           2          377          477          964         1932         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-99-7458 
         775          181           22          392 

$subtype3
TCGA-05-4420 TCGA-05-4427 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-35-5375 
         912          791           62          225          182          264 
TCGA-38-4625 TCGA-38-4629 TCGA-44-2668 TCGA-44-3917 TCGA-44-4112 TCGA-44-5643 
        1952          864          246         1183          722         1013 
TCGA-44-5644 TCGA-44-6145 TCGA-44-6148 TCGA-44-6774 TCGA-44-6778 TCGA-44-6779 
         863          328          704          658         1864         1978 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-49-4506 
         592          218          557         1970          882          999 
TCGA-49-4507 TCGA-49-4514 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 
         268         1700          246          282          267         2370 
TCGA-50-5946 TCGA-53-7624 TCGA-55-6969 TCGA-55-6971 TCGA-55-7910 TCGA-64-1677 
         686         1986         1239           25          197          628 
TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-64-5815 TCGA-67-3771 TCGA-69-7765 
        1189         1959          864          866          610          165 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7148 TCGA-78-7150 
         519         1970         1956         1988         1944         1963 
TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 
        1202          760         1948         1957         1221          678 
TCGA-78-7166 TCGA-78-7536 TCGA-78-7540 TCGA-78-7542 TCGA-86-7701 TCGA-86-7711 
        1934         1949          881         1952           11          630 
TCGA-86-7953 TCGA-86-7955 TCGA-91-6831 TCGA-91-6836 TCGA-91-6847 TCGA-91-6848 
         591          508          310          417          842          224 

subtype1 subtype2 subtype3 
       2        2       11 
subtype1 subtype2 subtype3 
    2174     1972     2370 
subtype1 subtype2 subtype3 
   714.0    700.5    816.5 
[1] "2.0 - 2174.0 (714.0)"  "2.0 - 1972.0 (700.5)"  "11.0 - 2370.0 (816.5)"
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       0       26       25         6        15         16          3
  subtype2       1       18       17         7         8         10          3
  subtype3       0       11       26         6         9         16          1
          vv
clus       STAGE IV
  subtype1        4
  subtype2        4
  subtype3        5
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        1        0
  STAGE IA         26       18       11
  STAGE IB         25       17       26
  STAGE IIA         6        7        6
  STAGE IIB        15        8        9
  STAGE IIIA       16       10       16
  STAGE IIIB        3        3        1
  STAGE IV          4        4        5
[1] 8 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 30 51  9  5
  subtype2 19 41  2  5
  subtype3 14 51  6  3
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       30       19       14
  T2       51       41       51
  T3        9        2        6
  T4        5        5        3
[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       N0 N1 N2+N3
  subtype1 51 24    16
  subtype2 45 11    11
  subtype3 45 11    17
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          51       45       45
  N1          24       11       11
  N2+N3       16       11       17
[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"
          vv
clus       M0 M1 MX
  subtype1 73  4 16
  subtype2 47  4 17
  subtype3 55  4 14
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       73       47       55
  M1        4        4        4
  MX       16       17       14
[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"
D5V7, binary
          cls
clus        0  1
  subtype1 59 36
  subtype2 36 32
  subtype3 36 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   59   36
  subtype2   36   32
  subtype3   36   38
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       59       36       36
  MALE         36       32       38
[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"
D5V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          2                                19
  subtype2                          3                                18
  subtype3                          1                                15
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 65
  subtype2                                                 33
  subtype3                                                 55
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          1
  subtype2                                          1
  subtype3                                          1
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             2
  subtype2                                             7
  subtype3                                             0
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  1
  subtype2                              0                                  1
  subtype3                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             1
  subtype2                            0                             3
  subtype3                            1                             1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             0
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            1
  subtype2                            2
  subtype3                            0
D5V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                2        3        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        19       18       15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       65       33       55
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                1        1        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             2        7        0
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              1        0        1
  LUNG PAPILLARY ADENOCARCINOMA                             1        3        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        0        0
  MUCINOUS (COLLOID) CARCINOMA                              1        2        0
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
          cls
clus        0  1
  subtype1  4 91
  subtype2  3 65
  subtype3  9 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   91
  subtype2    3   65
  subtype3    9   65
     clus
vv    subtype1 subtype2 subtype3
  NO         4        3        9
  YES       91       65       65
[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"
D5V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 57  3  3  6
  subtype2 47  4  0  1
  subtype3 44  1  0  3
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       57       47       44
  R1        3        4        1
  R2        3        0        0
  RX        6        1        3
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         4    66
  subtype2     0                         3    54
  subtype3     0                         7    60
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN        4        3        7
  WHITE                           66       54       60
[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"
D5V14, binary
          cls
clus        0  1
  subtype1  1 57
  subtype2  0 44
  subtype3  3 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   57
  subtype2    0   44
  subtype3    3   45
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        3
  NOT HISPANIC OR LATINO       57       44       45
[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(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 66 18
  subtype2 50 17
  subtype3 35 14
subtype1 subtype2 subtype3 
      84       67       49 
subtype1 subtype2 subtype3 
      18       17       14 
$subtype1
TCGA-05-4249 TCGA-05-4398 TCGA-05-4405 TCGA-05-4410 TCGA-05-4427 TCGA-05-4430 
        1523         1431          610         1958          791          761 
TCGA-05-5423 TCGA-05-5715 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-6178 
         151           62          225          182         1952          448 
TCGA-44-2656 TCGA-44-2661 TCGA-44-2664 TCGA-44-2665 TCGA-44-3918 TCGA-44-3919 
        1429          741         1251         1301         1036          190 
TCGA-44-4112 TCGA-44-5645 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 
         722          383          845          704          705         1938 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7660 TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 
        1942         1978          592         1421          428          268 
TCGA-49-4512 TCGA-49-6743 TCGA-49-6745 TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 
         157          369          522          354         2174         2146 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 
         944         1499          267         2370          567          883 
TCGA-50-5944 TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 
         764         1015          701         1178         1375           24 
TCGA-55-6969 TCGA-55-7573 TCGA-55-7815 TCGA-55-7911 TCGA-64-1676 TCGA-64-1679 
        1239            4           54           21         1728         1686 
TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 TCGA-64-5815 TCGA-67-6215 
        1126         1968         1305         1559          866          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-71-6725 TCGA-73-4675 TCGA-75-7031 
         141          422          202           61           40         1965 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7155 TCGA-78-7535 TCGA-83-5908 TCGA-86-6851 
        1973         1950         1957         1972          824         1959 
TCGA-86-7954 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6835 TCGA-91-6840 
        1963          323         1940           60           79          372 
TCGA-91-6847 TCGA-91-6848 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7948 
         842          224           34            2          568          476 

$subtype2
TCGA-05-4384 TCGA-05-4396 TCGA-05-4422 TCGA-05-4426 TCGA-05-5420 TCGA-05-5425 
         426         1947          365          791          457          882 
TCGA-05-5429 TCGA-35-3615 TCGA-38-4626 TCGA-38-4627 TCGA-44-2657 TCGA-44-3396 
          30           14         1962         1147          400         1130 
TCGA-44-3398 TCGA-44-6146 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 
        1163          302          444          366          535          719 
TCGA-49-4486 TCGA-49-4494 TCGA-49-4510 TCGA-49-6742 TCGA-49-6744 TCGA-50-5051 
        1932         1081          896          445          890          455 
TCGA-50-5932 TCGA-53-7626 TCGA-55-6543 TCGA-55-7574 TCGA-55-7728 TCGA-69-7761 
        1091         1971            2           95           24          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-73-4658 TCGA-73-4659 TCGA-73-4670 
         690          414          165         1600          711          131 
TCGA-73-4676 TCGA-73-7498 TCGA-73-7499 TCGA-78-7148 TCGA-78-7149 TCGA-78-7153 
         164          621          519         1944         1093          760 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 
        1961         1963          215         1940         1950         1937 
TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-80-5607 TCGA-80-5608 
        1944          327          881          994         1965         1972 
TCGA-86-7713 TCGA-91-6849 TCGA-91-7771 TCGA-93-7348 TCGA-95-7944 TCGA-95-7947 
         422           35          492          127          377          477 
TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 
         964         1932         1332          775          181           22 
TCGA-99-7458 
         392 

$subtype3
TCGA-05-4417 TCGA-05-4420 TCGA-35-5375 TCGA-38-4629 TCGA-44-2668 TCGA-44-3917 
         455          912          264          864          246         1183 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6145 TCGA-44-6774 TCGA-44-6778 
        1013          863          723          328          658         1864 
TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-49-4506 TCGA-49-4514 
         218          557         1970          882          999         1700 
TCGA-50-5072 TCGA-50-5930 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 
         246          282          686          255         1986          424 
TCGA-55-5899 TCGA-55-6971 TCGA-55-7910 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 
          87           25          197          628         1189         1959 
TCGA-64-5779 TCGA-67-3771 TCGA-75-6214 TCGA-75-7027 TCGA-78-7146 TCGA-78-7150 
         864          610         1970         1956         1988         1963 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7159 TCGA-78-7160 TCGA-78-7166 TCGA-78-7536 
        1202         1948         1221          678         1934         1949 
TCGA-78-7542 TCGA-86-7701 TCGA-86-7711 TCGA-86-7953 TCGA-86-7955 TCGA-91-6831 
        1952           11          630          591          508          310 
TCGA-91-6836 
         417 

subtype1 subtype2 subtype3 
       2        2       11 
subtype1 subtype2 subtype3 
    2370     1972     1988 
subtype1 subtype2 subtype3 
   762.5    690.0    723.0 
[1] "2.0 - 2370.0 (762.5)"  "2.0 - 1972.0 (690.0)"  "11.0 - 1988.0 (723.0)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       0       28       35         7        17         17          3
  subtype2       0       18       17         7        10         12          3
  subtype3       1        9       16         5         5         13          1
          vv
clus       STAGE IV
  subtype1        6
  subtype2        4
  subtype3        3
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        1
  STAGE IA         28       18        9
  STAGE IB         35       17       16
  STAGE IIA         7        7        5
  STAGE IIB        17       10        5
  STAGE IIIA       17       12       13
  STAGE IIIB        3        3        1
  STAGE IV          6        4        3
[1] 8 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 31 69  7  5
  subtype2 19 40  6  6
  subtype3 13 34  4  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       31       19       13
  T2       69       40       34
  T3        7        6        4
  T4        5        6        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"
          vv
clus       N0 N1 N2+N3
  subtype1 64 27    18
  subtype2 46 12    12
  subtype3 31  7    14
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          64       46       31
  N1          27       12        7
  N2+N3       18       12       14
[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"
          vv
clus       M0 M1 MX
  subtype1 83  6 22
  subtype2 52  3 16
  subtype3 40  3  9
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       83       52       40
  M1        6        3        3
  MX       22       16        9
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 71 42
  subtype2 35 36
  subtype3 25 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   71   42
  subtype2   35   36
  subtype3   25   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       71       35       25
  MALE         42       36       28
[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
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          2                                22
  subtype2                          3                                22
  subtype3                          1                                 8
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 79
  subtype2                                                 32
  subtype3                                                 42
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          3
  subtype3                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             4
  subtype2                                             4
  subtype3                                             1
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  1
  subtype2                              0                                  1
  subtype3                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             1
  subtype2                            1                             3
  subtype3                            0                             1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             0
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            1
  subtype2                            2
  subtype3                            0
D6V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                2        3        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        22       22        8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       79       32       42
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        3        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             4        4        1
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              1        1        0
  LUNG PAPILLARY ADENOCARCINOMA                             1        3        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        0        0
  MUCINOUS (COLLOID) CARCINOMA                              1        2        0
[1] 11  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V10, binary
          cls
clus         0   1
  subtype1   7 106
  subtype2   2  69
  subtype3   7  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  106
  subtype2    2   69
  subtype3    7   46
     clus
vv    subtype1 subtype2 subtype3
  NO         7        2        7
  YES      106       69       46
[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"
D6V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 68  3  3  6
  subtype2 50  4  0  1
  subtype3 30  1  0  3
D6V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       68       50       30
  R1        3        4        1
  R2        3        0        0
  RX        6        1        3
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         4    84
  subtype2     0                         4    54
  subtype3     0                         6    42
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        0
  BLACK OR AFRICAN AMERICAN        4        4        6
  WHITE                           84       54       42
[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"
D6V14, binary
          cls
clus        0  1
  subtype1  1 71
  subtype2  0 43
  subtype3  3 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   71
  subtype2    0   43
  subtype3    3   32
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        0        3
  NOT HISPANIC OR LATINO       71       43       32
[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 84 28
  subtype2 79 16
  subtype3 41 19
  subtype4 76 14
  subtype5 39  3
subtype1 subtype2 subtype3 subtype4 subtype5 
     112       95       60       90       42 
subtype1 subtype2 subtype3 subtype4 subtype5 
      28       16       19       14        3 
$subtype1
TCGA-05-4382 TCGA-05-4398 TCGA-05-4405 TCGA-05-4426 TCGA-05-4427 TCGA-05-5428 
         607         1431          610          791          791          670 
TCGA-35-4123 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 TCGA-38-4632 TCGA-38-6178 
         182         1147         1492          864         1357          448 
TCGA-44-2656 TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 
        1429         1280         1301          246         1130         1036 
TCGA-44-3919 TCGA-44-4112 TCGA-44-6775 TCGA-44-6777 TCGA-44-7661 TCGA-44-7662 
         190          722          705         1942          366          218 
TCGA-44-8117 TCGA-44-A4SU TCGA-49-4494 TCGA-49-4505 TCGA-49-4512 TCGA-49-6745 
         385           76         1081          428          157          522 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5933 TCGA-50-5941 
         354         2174         2146          944         2370          567 
TCGA-55-1595 TCGA-55-6712 TCGA-55-6980 TCGA-55-7281 TCGA-55-7576 TCGA-55-7903 
        1479           24           67           18           40           19 
TCGA-55-7907 TCGA-55-7911 TCGA-55-7994 TCGA-55-8096 TCGA-55-8301 TCGA-55-8302 
          16           21           31           47           44           23 
TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-A48Z TCGA-55-A491 TCGA-55-A493 
          11          228            9           29         1952           28 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1679 
        2067         2199          910         1728          628         1686 
TCGA-64-5775 TCGA-64-5778 TCGA-64-5815 TCGA-69-7760 TCGA-69-7765 TCGA-69-7978 
          62         1305          866          202          165           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
          89          382          214           61            3         1600 
TCGA-73-4666 TCGA-73-4668 TCGA-73-4676 TCGA-78-7145 TCGA-78-7146 TCGA-78-7535 
         800          467          164         1973         1988         1972 
TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 TCGA-86-7711 TCGA-86-8055 
        1981         1954          824         1959          630           10 
TCGA-86-8074 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 TCGA-86-8673 TCGA-91-6829 
          24          479          476          482          455         1940 
TCGA-91-6836 TCGA-91-6848 TCGA-95-7039 TCGA-95-7567 TCGA-95-7948 TCGA-97-7554 
         417          224           34          568          476          775 
TCGA-97-7937 TCGA-97-8547 TCGA-99-8028 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 
         181          148          459          154          287          578 
TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T4 
           6          285          622          353         1946         1954 
TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        1980         1944         1955         1971 

$subtype2
TCGA-05-4249 TCGA-05-4384 TCGA-05-4425 TCGA-05-5423 TCGA-05-5715 TCGA-35-3615 
        1523          426          669          151           62           14 
TCGA-38-4626 TCGA-38-7271 TCGA-44-2655 TCGA-44-2657 TCGA-44-2659 TCGA-44-2661 
        1962         1971         1324          400         1367          741 
TCGA-44-2666 TCGA-44-3398 TCGA-44-6776 TCGA-44-8120 TCGA-44-A47A TCGA-49-4486 
          97         1163         1938          260          466         1932 
TCGA-49-4501 TCGA-49-6744 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 
        1421          890         1091          653          883          764 
TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-55-6543 TCGA-55-6986 TCGA-55-7227 
        1015          105         1971            2         2151           53 
TCGA-55-7283 TCGA-55-7574 TCGA-55-7725 TCGA-55-7727 TCGA-55-7914 TCGA-55-8087 
          35           95           39           34            3           21 
TCGA-55-8090 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 TCGA-55-8514 TCGA-55-A492 
           6           15           46           66          202            1 
TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-67-3770 TCGA-67-3772 
         162         1216         1289         2696           31          573 
TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7763 
         427          385          174          141          422          690 
TCGA-69-7764 TCGA-69-8253 TCGA-73-4662 TCGA-73-4677 TCGA-73-7498 TCGA-78-7152 
         414          100          912           38          621         1202 
TCGA-78-7156 TCGA-78-7158 TCGA-78-7162 TCGA-78-7537 TCGA-78-7539 TCGA-78-7633 
        1961         1963         1940         1944          327          994 
TCGA-78-8648 TCGA-86-7714 TCGA-86-8056 TCGA-86-8073 TCGA-86-8281 TCGA-86-8668 
        1971         1968         1963           13         1955           45 
TCGA-86-8671 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6849 TCGA-91-8496 
          18           10           14           39           35          197 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 
         174          218          297          964         1965         1332 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M2 TCGA-99-7458 
         182         1965          147           15          197          392 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4SW TCGA-MP-A4TH 
         282          238          435         1967          142 

$subtype3
TCGA-05-4403 TCGA-05-4415 TCGA-05-4433 TCGA-05-5420 TCGA-05-5425 TCGA-05-5429 
         578         1997          730          457          882           30 
TCGA-35-4122 TCGA-38-4625 TCGA-38-4631 TCGA-44-5643 TCGA-44-6145 TCGA-44-6146 
         225         1952          354         1013          328          302 
TCGA-44-6779 TCGA-44-A4SS TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 
        1978          415          999          268         1700          445 
TCGA-49-6743 TCGA-50-5072 TCGA-50-5930 TCGA-53-7624 TCGA-55-6987 TCGA-55-7284 
         369          246          282         1986         1170          121 
TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 TCGA-55-8089 TCGA-55-8092 TCGA-55-8205 
        1958           39           24          100           26           33 
TCGA-55-8299 TCGA-55-8505 TCGA-55-8619 TCGA-62-8398 TCGA-62-A471 TCGA-64-5781 
         216           29           49         1970         1246         1559 
TCGA-69-7761 TCGA-73-4670 TCGA-75-6214 TCGA-75-7027 TCGA-78-7148 TCGA-78-7150 
         186          131         1970         1956         1944         1963 
TCGA-78-7154 TCGA-78-7160 TCGA-78-7166 TCGA-78-7220 TCGA-78-7540 TCGA-78-7542 
        1948          678         1934         1965          881         1952 
TCGA-80-5607 TCGA-86-8585 TCGA-86-8672 TCGA-91-6830 TCGA-93-8067 TCGA-95-7944 
        1965           35           15           60          186          377 
TCGA-95-A4VK TCGA-97-8175 TCGA-99-8033 TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TF 
         121           87          170         1954         1951         1970 

$subtype4
TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 
        1369         1126         1947          455          912          365 
TCGA-05-4424 TCGA-05-4432 TCGA-35-5375 TCGA-38-4630 TCGA-44-5644 TCGA-44-6774 
         913          761          264         1073          863          658 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-8119 TCGA-44-A479 
        1864          592          557         1970           99          486 
TCGA-44-A47B TCGA-49-4510 TCGA-50-5051 TCGA-50-5931 TCGA-50-5946 TCGA-50-7109 
         287          896          455          267          686          255 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 
         424          280          701         1178         1375           87 
TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-7570 TCGA-55-7815 
         993         1239           25         1475            6           54 
TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 TCGA-55-8094 TCGA-55-8507 TCGA-55-8508 
         197            5           33            4            8           15 
TCGA-55-8615 TCGA-55-8620 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8402 TCGA-64-1678 
          15           66            5           47         1445         1189 
TCGA-64-5774 TCGA-64-5779 TCGA-67-3771 TCGA-69-7973 TCGA-69-8255 TCGA-73-4659 
        1959          864          610          230          129          711 
TCGA-75-7031 TCGA-78-7149 TCGA-78-7153 TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 
        1965         1093          760         1957         1221          215 
TCGA-78-7163 TCGA-78-7167 TCGA-78-7536 TCGA-78-8640 TCGA-78-8662 TCGA-80-5608 
        1950         1937         1949         1949         1964         1972 
TCGA-86-7701 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
          11          422          591         1963          508          745 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6828 
          19           26           34          405           30          323 
TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 TCGA-91-8499 TCGA-91-A4BC 
         310          372          842          492           36           44 
TCGA-95-7043 TCGA-97-8171 TCGA-99-8032 TCGA-J2-8194 TCGA-MP-A4T8 TCGA-MP-A5C7 
           2          107           44          114         1957         1490 

$subtype5
TCGA-05-4410 TCGA-05-4430 TCGA-38-A44F TCGA-44-5645 TCGA-44-6147 TCGA-44-6148 
        1958          761          133          383          845          704 
TCGA-44-7659 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47G TCGA-50-5055 
         444          882          535          719          351          785 
TCGA-50-5068 TCGA-55-6983 TCGA-55-6985 TCGA-55-7573 TCGA-55-8091 TCGA-55-8512 
        1499         1826         1233            4           43            3 
TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-55-8621 TCGA-55-A48X TCGA-64-1680 
         146          536           48          106           33         1126 
TCGA-64-1681 TCGA-69-7974 TCGA-69-8254 TCGA-73-4675 TCGA-73-7499 TCGA-75-7025 
        1968          184           77           40          519         1967 
TCGA-78-7147 TCGA-86-8076 TCGA-86-8280 TCGA-91-6835 TCGA-93-7348 TCGA-95-7947 
        1950          489           16           79          127          477 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8552 TCGA-97-A4M7 TCGA-99-8025 TCGA-L9-A443 
        1932           22          115          271          427          116 

subtype1 subtype2 subtype3 subtype4 subtype5 
       3        1       15        2        3 
subtype1 subtype2 subtype3 subtype4 subtype5 
    2370     2696     1997     1972     1968 
subtype1 subtype2 subtype3 subtype4 subtype5 
   502.0    400.0    451.0    500.0    435.5 
[1] "3.0 - 2370.0 (502.0)"  "1.0 - 2696.0 (400.0)"  "15.0 - 1997.0 (451.0)"
[4] "2.0 - 1972.0 (500.0)"  "3.0 - 1968.0 (435.5)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       2       21       39        15        26         21          4
  subtype2       0       40       29         9         9         12          1
  subtype3       0       11       17         2        17         17          3
  subtype4       1       22       35        10        11         12          3
  subtype5       1       17       12         4         5          6          0
          vv
clus       STAGE IV
  subtype1        6
  subtype2        2
  subtype3        5
  subtype4        7
  subtype5        3
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           2        0        0        1        1
  STAGE IA         21       40       11       22       17
  STAGE IB         39       29       17       35       12
  STAGE IIA        15        9        2       10        4
  STAGE IIB        26        9       17       11        5
  STAGE IIIA       21       12       17       12        6
  STAGE IIIB        4        1        3        3        0
  STAGE IV          6        2        5        7        3
[1] 8 5
[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 31 85 12  6
  subtype2 47 45  6  4
  subtype3 14 43 10  4
  subtype4 26 63  8  3
  subtype5 23 20  5  1
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       31       47       14       26       23
  T2       85       45       43       63       20
  T3       12        6       10        8        5
  T4        6        4        4        3        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 73 34    25
  subtype2 75 14    10
  subtype3 38 15    18
  subtype4 74 13    13
  subtype5 31  9     6
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          73       75       38       74       31
  N1          34       14       15       13        9
  N2+N3       25       10       18       13        6
[1] 3 5
[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 M1A M1B MX
  subtype1 92  5   0   0 36
  subtype2 71  2   0   0 29
  subtype3 53  5   0   0 14
  subtype4 69  4   1   2 24
  subtype5 29  2   0   1 15
D7V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        92       71       53       69       29
  M1         5        2        5        4        2
  M1A        0        0        0        1        0
  M1B        0        0        0        2        1
  MX        36       29       14       24       15
[1] 5 5
[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 78 56
  subtype2 67 35
  subtype3 35 37
  subtype4 38 63
  subtype5 31 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78   56
  subtype2   67   35
  subtype3   35   37
  subtype4   38   63
  subtype5   31   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       78       67       35       38       31
  MALE         56       35       37       63       18
[1] 2 5
[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
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          2                                23
  subtype2                          5                                22
  subtype3                          1                                15
  subtype4                          4                                19
  subtype5                          1                                14
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 98
  subtype2                                                 58
  subtype3                                                 44
  subtype4                                                 66
  subtype5                                                 24
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          2
  subtype3                                          1
  subtype4                                          0
  subtype5                                          1
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             5
  subtype2                                             8
  subtype3                                             1
  subtype4                                             2
  subtype5                                             3
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  3
  subtype2                              0                                  1
  subtype3                              1                                  0
  subtype4                              0                                  0
  subtype5                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             2
  subtype2                            0                             6
  subtype3                            1                             2
  subtype4                            0                             7
  subtype5                            1                             2
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               0
  subtype5                               1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             0
  subtype3                                             2
  subtype4                                             2
  subtype5                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            0
  subtype3                            4
  subtype4                            1
  subtype5                            2
D7V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                2        5        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        23       22       15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       98       58       44
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        2        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             5        8        1
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        3        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        1
  LUNG PAPILLARY ADENOCARCINOMA                             2        6        2
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        0        2
  MUCINOUS (COLLOID) CARCINOMA                              0        0        4
                                                    clus
vv                                                   subtype4 subtype5
  LUNG ACINAR ADENOCARCINOMA                                4        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        19       14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       66       24
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             2        3
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        1
  LUNG PAPILLARY ADENOCARCINOMA                             7        2
  LUNG SIGNET RING ADENOCARCINOMA                           0        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2        0
  MUCINOUS (COLLOID) CARCINOMA                              1        2
[1] 12  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, binary
          cls
clus         0   1
  subtype1   6 128
  subtype2   4  98
  subtype3   6  66
  subtype4   3  98
  subtype5   2  47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  128
  subtype2    4   98
  subtype3    6   66
  subtype4    3   98
  subtype5    2   47
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         6        4        6        3        2
  YES      128       98       66       98       47
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 91  3  1  5
  subtype2 73  3  0  3
  subtype3 49  2  1  2
  subtype4 71  3  0  4
  subtype5 32  0  2  3
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       91       73       49       71       32
  R1        3        3        2        3        0
  R2        1        0        1        0        2
  RX        5        3        2        4        3
[1] 4 5
[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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         9
  subtype2                                0     1                         5
  subtype3                                0     1                         1
  subtype4                                0     2                         8
  subtype5                                0     0                         3
          vv
clus       WHITE
  subtype1   104
  subtype2    85
  subtype3    56
  subtype4    73
  subtype5    39
D7V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   3        1        1        2        0
  BLACK OR AFRICAN AMERICAN               9        5        1        8        3
  WHITE                                 104       85       56       73       39
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V14, binary
          cls
clus         0   1
  subtype1   2 100
  subtype2   1  78
  subtype3   1  44
  subtype4   2  67
  subtype5   1  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  100
  subtype2    1   78
  subtype3    1   44
  subtype4    2   67
  subtype5    1   39
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        1        1        2        1
  NOT HISPANIC OR LATINO      100       78       44       67       39
[1] 2 5
[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 59 14
  subtype2 41  7
  subtype3 23  8
  subtype4 52 13
  subtype5 29 10
  subtype6 39  5
  subtype7 22 17
  subtype8 13  1
  subtype9 41  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      73       48       31       65       39       44       39       14 
subtype9 
      46 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      14        7        8       13       10        5       17        1 
subtype9 
       5 
$subtype1
TCGA-05-4405 TCGA-05-4426 TCGA-05-4427 TCGA-05-5428 TCGA-38-4628 TCGA-38-4632 
         610          791          791          670         1492         1357 
TCGA-44-2656 TCGA-44-2665 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-6777 
        1429         1301         1163          190          722         1942 
TCGA-44-7661 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47B TCGA-49-4494 TCGA-49-4505 
         366          385          260          287         1081          428 
TCGA-49-4512 TCGA-50-5941 TCGA-55-1595 TCGA-55-6971 TCGA-55-6980 TCGA-55-6987 
         157          567         1479           25           67         1170 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7574 TCGA-55-7576 TCGA-55-7727 TCGA-55-7903 
          53           18           95           40           34           19 
TCGA-55-7911 TCGA-55-8207 TCGA-55-8299 TCGA-55-8301 TCGA-55-8506 TCGA-55-8510 
          21           66          216           44           11          228 
TCGA-55-8514 TCGA-62-8399 TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-5815 
         202         2696         2067         2199          910          866 
TCGA-69-7760 TCGA-69-7765 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 
         202          165          214           61            3         1600 
TCGA-73-4662 TCGA-73-4668 TCGA-78-7145 TCGA-78-7535 TCGA-78-8648 TCGA-78-8655 
         912          467         1973         1972         1971         1981 
TCGA-86-8073 TCGA-86-8279 TCGA-86-8673 TCGA-93-7347 TCGA-95-7039 TCGA-95-7567 
          13          482          455          297           34          568 
TCGA-95-7948 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 TCGA-99-7458 
         476          775          181           87          148          392 
TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4T9 
         238          578            6          353         1946         1980 
TCGA-MP-A4TK 
        1971 

$subtype2
TCGA-05-4249 TCGA-05-4425 TCGA-05-5423 TCGA-05-5715 TCGA-38-4626 TCGA-38-7271 
        1523          669          151           62         1962         1971 
TCGA-44-2659 TCGA-44-2666 TCGA-44-A47A TCGA-49-4501 TCGA-49-6744 TCGA-50-5935 
        1367           97          466         1421          890          653 
TCGA-50-5944 TCGA-50-6597 TCGA-53-7626 TCGA-55-6986 TCGA-55-7283 TCGA-55-7725 
         764         1015         1971         2151           35           39 
TCGA-55-7914 TCGA-55-8087 TCGA-55-8097 TCGA-55-8206 TCGA-55-A4DG TCGA-62-8397 
           3           21           15           46          162         1289 
TCGA-67-3770 TCGA-67-3772 TCGA-67-3773 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
          31          573          427          174          141          422 
TCGA-78-7158 TCGA-78-7539 TCGA-80-5607 TCGA-86-7714 TCGA-86-8278 TCGA-86-8668 
        1963          327         1965         1968          476           45 
TCGA-86-8671 TCGA-86-A456 TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-8496 TCGA-93-7348 
          18           10           14           39          197          127 
TCGA-97-7546 TCGA-97-7547 TCGA-97-8171 TCGA-97-8172 TCGA-97-8177 TCGA-L4-A4E6 
         964         1965          107          182          147          435 

$subtype3
TCGA-05-4398 TCGA-35-4122 TCGA-35-4123 TCGA-38-4625 TCGA-38-4629 TCGA-44-2662 
        1431          225          182         1952          864         1280 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 TCGA-44-7662 TCGA-49-6745 TCGA-49-6761 
         246         1130         1036          218          522          354 
TCGA-50-5066 TCGA-50-5933 TCGA-55-6712 TCGA-55-7726 TCGA-55-7994 TCGA-55-8205 
         944         2370           24           39           31           33 
TCGA-55-8302 TCGA-55-A493 TCGA-64-1676 TCGA-69-7978 TCGA-73-4666 TCGA-73-4676 
          23           28         1728           70          800          164 
TCGA-78-7146 TCGA-78-7542 TCGA-78-8660 TCGA-83-5908 TCGA-91-6836 TCGA-MP-A4TC 
        1988         1952         1954          824          417         1944 
TCGA-MP-A4TI 
        1955 

$subtype4
TCGA-05-4382 TCGA-05-4389 TCGA-05-4424 TCGA-35-5375 TCGA-38-4627 TCGA-38-4630 
         607         1369          913          264         1147         1073 
TCGA-38-6178 TCGA-44-5643 TCGA-44-6775 TCGA-44-6778 TCGA-44-7660 TCGA-44-7669 
         448         1013          705         1864          592         1970 
TCGA-44-7670 TCGA-44-A4SU TCGA-49-6743 TCGA-50-5931 TCGA-50-5946 TCGA-53-A4EZ 
         882           76          369          267          686          280 
TCGA-55-1592 TCGA-55-5899 TCGA-55-6543 TCGA-55-7570 TCGA-55-7724 TCGA-55-7995 
         701           87            2            6         1958            5 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A491 
          43           47          536           66           29         1952 
TCGA-55-A4DF TCGA-64-1677 TCGA-64-1679 TCGA-64-5775 TCGA-67-3771 TCGA-69-7979 
          47          628         1686           62          610           89 
TCGA-69-7980 TCGA-73-7499 TCGA-75-6214 TCGA-78-7147 TCGA-78-7155 TCGA-78-7163 
         382          519         1970         1950         1957         1950 
TCGA-78-8640 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 
        1949         1964         1959          630          591         1963 
TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8358 TCGA-91-6829 
         508           10           24          479           19         1940 
TCGA-91-6830 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 TCGA-95-7043 
          60          372          842          224           36            2 
TCGA-95-7947 TCGA-J2-8192 TCGA-J2-A4AD TCGA-MN-A4N1 TCGA-MN-A4N4 
         477          154          287          285          622 

$subtype5
TCGA-05-4384 TCGA-05-4396 TCGA-05-4422 TCGA-35-3615 TCGA-44-2655 TCGA-44-6776 
         426         1947          365           14         1324         1938 
TCGA-44-7671 TCGA-49-4486 TCGA-49-4510 TCGA-50-5932 TCGA-55-6972 TCGA-55-8085 
         535         1932          896         1091         1475           33 
TCGA-55-A492 TCGA-62-8395 TCGA-67-3774 TCGA-69-7763 TCGA-69-7764 TCGA-69-8253 
           1         1216          385          690          414          100 
TCGA-73-4675 TCGA-73-4677 TCGA-73-7498 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 
          40           38          621         1093         1202          760 
TCGA-78-7156 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7633 TCGA-86-8281 
        1961         1940         1937         1944          994         1955 
TCGA-86-8674 TCGA-91-6849 TCGA-91-7771 TCGA-91-8497 TCGA-97-8174 TCGA-97-8179 
         405           35          492          174         1965           15 
TCGA-J2-8194 TCGA-MP-A4TH TCGA-MP-A5C7 
         114          142         1490 

$subtype6
TCGA-05-4390 TCGA-05-4417 TCGA-05-4420 TCGA-05-4432 TCGA-44-5644 TCGA-44-6774 
        1126          455          912          761          863          658 
TCGA-44-7667 TCGA-44-8119 TCGA-44-A479 TCGA-50-5051 TCGA-50-7109 TCGA-53-7813 
         557           99          486          455          255          424 
TCGA-55-1594 TCGA-55-6642 TCGA-55-6969 TCGA-55-7815 TCGA-55-7910 TCGA-55-8094 
        1178          993         1239           54          197            4 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8615 TCGA-55-A494 TCGA-62-8402 TCGA-64-1678 
           8           15           15            5         1445         1189 
TCGA-64-5774 TCGA-64-5779 TCGA-69-7973 TCGA-73-4659 TCGA-75-7031 TCGA-78-7159 
        1959          864          230          711         1965         1221 
TCGA-78-7161 TCGA-78-7536 TCGA-80-5608 TCGA-86-7701 TCGA-86-7713 TCGA-86-8054 
         215         1949         1972           11          422          745 
TCGA-86-8359 TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6831 TCGA-91-A4BC 
          26           34           30          323          310           44 
TCGA-99-8032 TCGA-MP-A4T8 
          44         1957 

$subtype7
TCGA-05-4415 TCGA-05-5420 TCGA-05-5425 TCGA-38-4631 TCGA-44-6145 TCGA-44-6779 
        1997          457          882          354          328         1978 
TCGA-44-A4SS TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6742 TCGA-50-5072 
         415          999          268         1700          445          246 
TCGA-50-5930 TCGA-53-7624 TCGA-55-1596 TCGA-55-8089 TCGA-55-8092 TCGA-55-8505 
         282         1986         1375          100           26           29 
TCGA-62-8398 TCGA-62-A471 TCGA-64-5781 TCGA-69-8255 TCGA-73-4670 TCGA-75-7027 
        1970         1246         1559          129          131         1956 
TCGA-78-7148 TCGA-78-7150 TCGA-78-7154 TCGA-78-7160 TCGA-78-7166 TCGA-78-7220 
        1944         1963         1948          678         1934         1965 
TCGA-86-8585 TCGA-86-8672 TCGA-93-8067 TCGA-95-7944 TCGA-95-A4VK TCGA-99-8033 
          35           15          186          377          121          170 
TCGA-MP-A4T7 TCGA-MP-A4TA TCGA-MP-A4TF 
        1954         1951         1970 

$subtype8
TCGA-05-4403 TCGA-05-4433 TCGA-05-5429 TCGA-38-A44F TCGA-44-6146 TCGA-55-7284 
         578          730           30          133          302          121 
TCGA-55-7728 TCGA-55-8513 TCGA-55-8619 TCGA-69-7761 TCGA-69-8254 TCGA-78-7540 
          24          146           49          186           77          881 
TCGA-97-7552 TCGA-97-7941 
        1932           22 

$subtype9
TCGA-05-4410 TCGA-05-4430 TCGA-44-2657 TCGA-44-2661 TCGA-44-5645 TCGA-44-6147 
        1958          761          400          741          383          845 
TCGA-44-6148 TCGA-44-7659 TCGA-44-7672 TCGA-44-A47G TCGA-50-5045 TCGA-50-5049 
         704          444          719          351         2174         2146 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5942 TCGA-50-8460 TCGA-55-6983 TCGA-55-6985 
         785         1499          883          105         1826         1233 
TCGA-55-7573 TCGA-55-7907 TCGA-55-8090 TCGA-55-8511 TCGA-55-8512 TCGA-55-8616 
           4           16            6            9            3           48 
TCGA-55-8621 TCGA-55-A48X TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-69-7974 
         106           33         1126         1968         1305          184 
TCGA-75-7025 TCGA-86-8056 TCGA-86-8076 TCGA-86-8280 TCGA-91-6835 TCGA-91-A4BD 
        1967         1963          489           16           79          218 
TCGA-97-7553 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8028 
        1332          115          197          271          427          459 
TCGA-J2-A4AE TCGA-L9-A443 TCGA-MP-A4SW TCGA-MP-A4T4 
         282          116         1967         1954 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       3        3       23        2        1        4       15       22 
subtype9 
       3 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    2696     2151     2370     1970     1965     1972     1997     1932 
subtype9 
    2174 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   428.0    374.5    800.0    519.0    690.0    455.0    678.0    139.5 
subtype9 
   451.5 
[1] "3.0 - 2696.0 (428.0)"  "3.0 - 2151.0 (374.5)"  "23.0 - 2370.0 (800.0)"
[4] "2.0 - 1970.0 (519.0)"  "1.0 - 1965.0 (690.0)"  "4.0 - 1972.0 (455.0)" 
[7] "15.0 - 1997.0 (678.0)" "22.0 - 1932.0 (139.5)" "3.0 - 2174.0 (451.5)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       17       28         3        17         11          0
  subtype2       0       15       16         7         6          5          1
  subtype3       0        6       12         4         7         10          3
  subtype4       1       20       23        12         5         10          2
  subtype5       0       15       13         2         6          3          2
  subtype6       1        6       15         6         5         11          1
  subtype7       0        7        8         1        12         12          2
  subtype8       0        1        7         0         6          1          0
  subtype9       1       24       10         5         4          5          0
          vv
clus       STAGE IV
  subtype1        4
  subtype2        2
  subtype3        1
  subtype4        5
  subtype5        2
  subtype6        2
  subtype7        5
  subtype8        0
  subtype9        2
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I           1        0        0        1        0        1        0
  STAGE IA         17       15        6       20       15        6        7
  STAGE IB         28       16       12       23       13       15        8
  STAGE IIA         3        7        4       12        2        6        1
  STAGE IIB        17        6        7        5        6        5       12
  STAGE IIIA       11        5       10       10        3       11       12
  STAGE IIIB        0        1        3        2        2        1        2
  STAGE IV          4        2        1        5        2        2        5
            clus
vv           subtype8 subtype9
  STAGE I           0        1
  STAGE IA          1       24
  STAGE IB          7       10
  STAGE IIA         0        5
  STAGE IIB         6        4
  STAGE IIIA        1        5
  STAGE IIIB        0        0
  STAGE IV          0        2
[1] 8 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1 21 48  9  3
  subtype2 21 28  2  1
  subtype3  9 25  6  3
  subtype4 31 41  2  3
  subtype5 14 22  4  3
  subtype6  8 33  5  1
  subtype7  8 30  5  3
  subtype8  1  9  6  0
  subtype9 28 20  2  1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1       21       21        9       31       14        8        8        1
  T2       48       28       25       41       22       33       30        9
  T3        9        2        6        2        4        5        5        6
  T4        3        1        3        3        3        1        3        0
    clus
vv   subtype9
  T1       28
  T2       20
  T3        2
  T4        1
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 54 16    10
  subtype2 34 10     7
  subtype3 24  8    11
  subtype4 47 19    11
  subtype5 33  7     2
  subtype6 32  3    11
  subtype7 21 11    14
  subtype8 13  1     1
  subtype9 33 10     5
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0          54       34       24       47       33       32       21       13
  N1          16       10        8       19        7        3       11        1
  N2+N3       10        7       11       11        2       11       14        1
       clus
vv      subtype9
  N0          33
  N1          10
  N2+N3        5
[1] 3 9
[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 M1A M1B MX
  subtype1 55  3   0   0 23
  subtype2 35  1   1   0 15
  subtype3 32  1   0   0 10
  subtype4 45  4   0   1 27
  subtype5 34  2   0   0  7
  subtype6 33  1   0   1 11
  subtype7 37  5   0   0  5
  subtype8  8  0   0   0  7
  subtype9 35  1   0   1 13
D8V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  M0        55       35       32       45       34       33       37        8
  M1         3        1        1        4        2        1        5        0
  M1A        0        1        0        0        0        0        0        0
  M1B        0        0        0        1        0        1        0        0
  MX        23       15       10       27        7       11        5        7
     clus
vv    subtype9
  M0        35
  M1         1
  M1A        0
  M1B        1
  MX        13
[1] 5 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 50 31
  subtype2 45  7
  subtype3 20 23
  subtype4 44 34
  subtype5 14 29
  subtype6 19 28
  subtype7 18 29
  subtype8  6 10
  subtype9 33 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   31
  subtype2   45    7
  subtype3   20   23
  subtype4   44   34
  subtype5   14   29
  subtype6   19   28
  subtype7   18   29
  subtype8    6   10
  subtype9   33   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       50       45       20       44       14       19       18
  MALE         31        7       23       34       29       28       29
        clus
vv       subtype8 subtype9
  FEMALE        6       33
  MALE         10       18
[1] 2 9
[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:" "subtype8"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      12       10        7       17        6       12        5        2 
subtype9 
      10 
 [1] "subtype3" "subtype3" "subtype4" "subtype4" "subtype2" "subtype9"
 [7] "subtype2" "subtype6" "subtype2" "subtype7" "subtype4" "subtype3"
[13] "subtype6" "subtype6" "subtype9" "subtype9" "subtype4" "subtype4"
[19] "subtype6" "subtype4" "subtype5" "subtype2" "subtype7" "subtype1"
[25] "subtype6" "subtype7" "subtype5" "subtype9" "subtype5" "subtype1"
[31] "subtype1" "subtype9" "subtype6" "subtype7" "subtype1" "subtype4"
[37] "subtype9" "subtype9" "subtype9" "subtype1" "subtype1" "subtype6"
[43] "subtype1" "subtype3" "subtype1" "subtype3" "subtype5" "subtype4"
[49] "subtype3" "subtype3" "subtype6" "subtype4" "subtype6" "subtype2"
[55] "subtype4" "subtype4" "subtype4" "subtype9" "subtype4" "subtype4"
[61] "subtype9" "subtype2" "subtype1" "subtype5" "subtype4" "subtype6"
[67] "subtype2" "subtype6" "subtype2" "subtype6" "subtype1" "subtype2"
[73] "subtype5" "subtype2" "subtype7" "subtype1" "subtype4" "subtype4"
[79] "subtype1"
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          2                                14
  subtype2                          3                                 9
  subtype3                          0                                 4
  subtype4                          2                                13
  subtype5                          1                                17
  subtype6                          3                                 8
  subtype7                          0                                13
  subtype8                          2                                 4
  subtype9                          0                                11
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 52
  subtype2                                                 30
  subtype3                                                 38
  subtype4                                                 57
  subtype5                                                 18
  subtype6                                                 34
  subtype7                                                 28
  subtype8                                                  3
  subtype9                                                 30
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          1
  subtype3                                          0
  subtype4                                          1
  subtype5                                          0
  subtype6                                          0
  subtype7                                          0
  subtype8                                          2
  subtype9                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             5
  subtype2                                             4
  subtype3                                             0
  subtype4                                             2
  subtype5                                             1
  subtype6                                             1
  subtype7                                             0
  subtype8                                             1
  subtype9                                             5
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  3
  subtype2                              0                                  1
  subtype3                              0                                  0
  subtype4                              1                                  0
  subtype5                              0                                  0
  subtype6                              0                                  0
  subtype7                              0                                  0
  subtype8                              0                                  0
  subtype9                              0                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             3
  subtype2                            0                             4
  subtype3                            0                             1
  subtype4                            0                             1
  subtype5                            0                             6
  subtype6                            0                             0
  subtype7                            0                             2
  subtype8                            1                             0
  subtype9                            1                             2
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               0
  subtype5                               0
  subtype6                               0
  subtype7                               0
  subtype8                               0
  subtype9                               1
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             0
  subtype3                                             0
  subtype4                                             1
  subtype5                                             0
  subtype6                                             0
  subtype7                                             2
  subtype8                                             0
  subtype9                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            0
  subtype3                            0
  subtype4                            0
  subtype5                            0
  subtype6                            1
  subtype7                            2
  subtype8                            3
  subtype9                            1
D8V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                2        3        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        14        9        4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       52       30       38
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        1        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             5        4        0
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        3        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             3        4        1
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        0        0
  MUCINOUS (COLLOID) CARCINOMA                              0        0        0
                                                    clus
vv                                                   subtype4 subtype5 subtype6
  LUNG ACINAR ADENOCARCINOMA                                2        1        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        13       17        8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       57       18       34
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                1        0        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             2        1        1
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             1        6        0
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        0        0
  MUCINOUS (COLLOID) CARCINOMA                              0        0        1
                                                    clus
vv                                                   subtype7 subtype8 subtype9
  LUNG ACINAR ADENOCARCINOMA                                0        2        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        13        4       11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       28        3       30
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        2        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             0        1        5
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        1        1
  LUNG PAPILLARY ADENOCARCINOMA                             2        0        2
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2        0        0
  MUCINOUS (COLLOID) CARCINOMA                              2        3        1
[1] 12  9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
          cls
clus        0  1
  subtype1  2 79
  subtype2  2 50
  subtype3  3 40
  subtype4  1 77
  subtype5  0 43
  subtype6  3 44
  subtype7  5 42
  subtype8  0 16
  subtype9  5 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   79
  subtype2    2   50
  subtype3    3   40
  subtype4    1   77
  subtype5    0   43
  subtype6    3   44
  subtype7    5   42
  subtype8    0   16
  subtype9    5   46
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         2        2        3        1        0        3        5        0
  YES       79       50       40       77       43       44       42       16
     clus
vv    subtype9
  NO         5
  YES       46
[1] 2 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 57  3  0  3
  subtype2 40  2  0  0
  subtype3 30  0  2  0
  subtype4 46  3  2  5
  subtype5 27  0  0  3
  subtype6 35  1  0  1
  subtype7 33  2  0  2
  subtype8 11  0  0  0
  subtype9 37  0  0  3
D8V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0       57       40       30       46       27       35       33       11
  R1        3        2        0        3        0        1        2        0
  R2        0        0        2        2        0        0        0        0
  RX        3        0        0        5        3        1        2        0
    clus
vv   subtype9
  R0       37
  R1        0
  R2        0
  RX        3
[1] 4 9
[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       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         6
  subtype2                                0     2                         1
  subtype3                                0     0                         2
  subtype4                                0     0                         6
  subtype5                                0     0                         4
  subtype6                                0     0                         3
  subtype7                                0     2                         0
  subtype8                                0     0                         0
  subtype9                                0     0                         4
          vv
clus       WHITE
  subtype1    61
  subtype2    42
  subtype3    33
  subtype4    61
  subtype5    33
  subtype6    35
  subtype7    38
  subtype8    11
  subtype9    43
D8V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   3        2        0        0        0
  BLACK OR AFRICAN AMERICAN               6        1        2        6        4
  WHITE                                  61       42       33       61       33
                                  clus
vv                                 subtype6 subtype7 subtype8 subtype9
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0
  ASIAN                                   0        2        0        0
  BLACK OR AFRICAN AMERICAN               3        0        0        4
  WHITE                                  35       38       11       43
[1] 4 9
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V14, binary
          cls
clus        0  1
  subtype1  0 62
  subtype2  1 39
  subtype3  0 29
  subtype4  4 54
  subtype5  0 29
  subtype6  0 32
  subtype7  2 29
  subtype8  0 10
  subtype9  0 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   62
  subtype2    1   39
  subtype3    0   29
  subtype4    4   54
  subtype5    0   29
  subtype6    0   32
  subtype7    2   29
  subtype8    0   10
  subtype9    0   44
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        4        0        0
  NOT HISPANIC OR LATINO       62       39       29       54       29       32
                        clus
vv                       subtype7 subtype8 subtype9
  HISPANIC OR LATINO            2        0        0
  NOT HISPANIC OR LATINO       29       10       44
[1] 2 9
[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 117  27
  subtype2 159  38
  subtype3  45  16
subtype1 subtype2 subtype3 
     144      197       61 
subtype1 subtype2 subtype3 
      27       38       16 
$subtype1
TCGA-05-4384 TCGA-05-4403 TCGA-05-4410 TCGA-05-4426 TCGA-05-5429 TCGA-35-3615 
         426          578         1958          791           30           14 
TCGA-35-4122 TCGA-38-4626 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
         225         1962         1971          133         1324          400 
TCGA-44-2661 TCGA-44-2666 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 TCGA-44-5645 
         741           97         1163          190          722          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 
         328          302          704         1938         1942          444 
TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
         366          535          719          287          337          351 
TCGA-49-4486 TCGA-49-4505 TCGA-49-4510 TCGA-49-6744 TCGA-49-6745 TCGA-50-5045 
        1932          428          896          890          522         2174 
TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 TCGA-50-5932 TCGA-50-5941 TCGA-50-5942 
         455          785         1499         1091          567          883 
TCGA-50-5944 TCGA-50-8460 TCGA-53-7626 TCGA-55-6712 TCGA-55-6972 TCGA-55-6986 
         764          105         1971           24         1475         2151 
TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 TCGA-55-7724 
          53           18           35            4           40         1958 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-8090 
          39           34           19           21            3            6 
TCGA-55-8097 TCGA-55-8205 TCGA-55-8207 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 
          15           33           66            3          146           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 
         106           33            1         1216         1289         2696 
TCGA-62-A46V TCGA-62-A472 TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-64-5815 
        2199          910         1126         1968         1305          866 
TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 
          31          427          385          174          141          422 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-8253 TCGA-69-8254 
         186          690          414          165          100           77 
TCGA-73-4662 TCGA-73-4675 TCGA-73-4676 TCGA-73-7498 TCGA-78-7145 TCGA-78-7148 
         912           40          164          621         1973         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7160 
        1093         1202          760         1948         1961          678 
TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 TCGA-78-7633 
        1940         1934         1937         1944          881          994 
TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-86-7714 TCGA-86-8076 TCGA-86-8278 
        1981         1954         1965         1968          489          476 
TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-A4P8 TCGA-91-6849 TCGA-91-7771 
          16         1955           45           39           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-95-7567 TCGA-95-7947 
         197          174          218          297          568          477 
TCGA-95-7948 TCGA-95-A4VK TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-8174 
         476          121          964         1932         1332         1965 
TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-99-8028 
          87           15          115          197          392          459 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4T7 TCGA-MP-A4TH TCGA-MP-A4TK 
         282          238          435         1954          142         1971 

$subtype2
TCGA-05-4382 TCGA-05-4389 TCGA-05-4390 TCGA-05-4396 TCGA-05-4398 TCGA-05-4415 
         607         1369         1126         1947         1431         1997 
TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-05-4424 TCGA-05-4425 TCGA-05-4427 
         455          912          365          913          669          791 
TCGA-05-4430 TCGA-05-4432 TCGA-05-4433 TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 
         761          761          730          457          151          882 
TCGA-05-5428 TCGA-05-5715 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 
         670           62          182          264         1952         1492 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-44-2656 TCGA-44-2659 TCGA-44-2662 
        1073          354         1357         1429         1367         1280 
TCGA-44-2668 TCGA-44-3396 TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 
         246         1130         1036         1013          863          592 
TCGA-44-7667 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A 
         557          882          385           99          486          466 
TCGA-44-A4SS TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 
         415         1081         1421          999          268         1700 
TCGA-49-6743 TCGA-50-5049 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 
         369         2146          944          282          267          653 
TCGA-50-5946 TCGA-50-6597 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-1592 
         686         1015         1986          424          280          701 
TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 TCGA-55-6971 
        1178         1479         1375           87         1239           25 
TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 
        1170          121            6           24           54           16 
TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 
         197           31            5           33           21          100 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8206 TCGA-55-8301 TCGA-55-8302 
          26            4           47           46           44           23 
TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 
          29           11            8           15          228            9 
TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
         202           15           48           66           42           29 
TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG 
          48         1952           28            5           47          162 
TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 TCGA-64-1677 TCGA-64-1678 
        1970         1445         2067         1246          628         1189 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 TCGA-69-7760 
        1959           62          864          610          573          202 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 
         230          184           70           89          382          129 
TCGA-69-A59K TCGA-71-6725 TCGA-73-4659 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 
         214           61          711          519         1970         1965 
TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 TCGA-78-7158 TCGA-78-7159 
        1988         1950         1963         1957         1963         1221 
TCGA-78-7161 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 
         215         1965         1972         1949          327         1952 
TCGA-78-8640 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 
        1949         1964         1972          824         1959           11 
TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 
         630          422          591         1963          508          745 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 
        1963           13          479          482           19           26 
TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 
          35           34           18          455           10           30 
TCGA-91-6828 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
         323           60          310           79          417          372 
TCGA-91-6847 TCGA-91-8499 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         842           36           44          186           34            2 
TCGA-95-7944 TCGA-97-7547 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-99-8025 
         377         1965           22          107          182          427 
TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 
          44          170          114          287          578            6 
TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 
         285          622          353         1946         1967         1954 
TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A5C7 
        1957         1980         1951         1970         1490 

$subtype3
TCGA-05-4249 TCGA-05-4405 TCGA-38-4627 TCGA-38-4629 TCGA-38-6178 TCGA-44-2665 
        1523          610         1147          864          448         1301 
TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 TCGA-44-6779 
         723          845          658          705         1864         1978 
TCGA-44-7662 TCGA-44-7669 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4512 TCGA-49-6742 
         218         1970          260           76          157          445 
TCGA-49-6761 TCGA-50-5072 TCGA-50-5933 TCGA-50-7109 TCGA-55-6543 TCGA-55-6642 
         354          246         2370          255            2          993 
TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-7574 TCGA-55-7726 TCGA-55-7816 
          67         1826         1233           95           39           44 
TCGA-55-8091 TCGA-55-8299 TCGA-55-8614 TCGA-64-1676 TCGA-64-1679 TCGA-64-5781 
          43          216          536         1728         1686         1559 
TCGA-71-8520 TCGA-73-4658 TCGA-75-7025 TCGA-75-7027 TCGA-78-7163 TCGA-78-8648 
           3         1600         1967         1956         1950         1971 
TCGA-86-8055 TCGA-86-8074 TCGA-86-8672 TCGA-86-8674 TCGA-86-A4P7 TCGA-91-6829 
          10           24           15          405           14         1940 
TCGA-91-6848 TCGA-93-7348 TCGA-97-7554 TCGA-97-7937 TCGA-97-8177 TCGA-97-8547 
         224          127          775          181          147          148 
TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TF 
         271          154          116         1951         1944         1970 
TCGA-MP-A4TI 
        1955 

subtype1 subtype2 subtype3 
       1        2        2 
subtype1 subtype2 subtype3 
    2696     2146     2370 
subtype1 subtype2 subtype3 
   467.5    455.0    536.0 
[1] "1.0 - 2696.0 (467.5)" "2.0 - 2146.0 (455.0)" "2.0 - 2370.0 (536.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       55       35        14        25         21          2
  subtype2       2       44       74        20        32         31          8
  subtype3       1       13       23         9        10         16          1
          vv
clus       STAGE IV
  subtype1        9
  subtype2       11
  subtype3        2
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        2        1
  STAGE IA         55       44       13
  STAGE IB         35       74       23
  STAGE IIA        14       20        9
  STAGE IIB        25       32       10
  STAGE IIIA       21       31       16
  STAGE IIIB        2        8        1
  STAGE IV          9       11        2
[1] 8 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  64  77  15   7
  subtype2  55 135  20  10
  subtype3  23  44   6   1
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       64       55       23
  T2       77      135       44
  T3       15       20        6
  T4        7       10        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"
          vv
clus        N0  N1 N2+N3
  subtype1 101  36    20
  subtype2 148  36    35
  subtype3  44  12    17
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         101      148       44
  N1          36       36       12
  N2+N3       20       35       17
[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"
          vv
clus        M0  M1 M1A M1B  MX
  subtype1 113   7   0   1  40
  subtype2 156   8   1   2  54
  subtype3  46   1   0   0  27
D9V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       113      156       46
  M1         7        8        1
  M1A        0        1        0
  M1B        1        2        0
  MX        40       54       27
[1] 5 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  92  71
  subtype2 115 107
  subtype3  40  35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   92   71
  subtype2  115  107
  subtype3   40   35
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       92      115       40
  MALE         71      107       35
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          5                                36
  subtype2                          8                                50
  subtype3                          0                                 6
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 91
  subtype2                                                143
  subtype3                                                 60
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          3
  subtype2                                          0
  subtype3                                          1
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            12
  subtype2                                             5
  subtype3                                             2
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  1
  subtype2                              2                                  0
  subtype3                              0                                  2
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            2                             8
  subtype2                            0                             9
  subtype3                            0                             2
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             3
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            3
  subtype2                            2
  subtype3                            2
D9V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                5        8        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        36       50        6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       91      143       60
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3        0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            12        5        2
  LUNG CLEAR CELL ADENOCARCINOMA                            0        2        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        2
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             8        9        2
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        3        0
  MUCINOUS (COLLOID) CARCINOMA                              3        2        2
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, binary
          cls
clus         0   1
  subtype1   7 156
  subtype2   9 213
  subtype3   4  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  156
  subtype2    9  213
  subtype3    4   71
     clus
vv    subtype1 subtype2 subtype3
  NO         7        9        4
  YES      156      213       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"
D9V11, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 109   2   2   8
  subtype2 160   6   2   8
  subtype3  46   3   0   3
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      109      160       46
  R1        2        6        3
  R2        2        2        0
  RX        8        8        3
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                        10   134
  subtype2     6                        12   165
  subtype3     1                         4    61
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        6        1
  BLACK OR AFRICAN AMERICAN       10       12        4
  WHITE                          134      165       61
[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"
D9V14, binary
          cls
clus         0   1
  subtype1   1 119
  subtype2   5 155
  subtype3   1  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  119
  subtype2    5  155
  subtype3    1   56
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        1
  NOT HISPANIC OR LATINO      119      155       56
[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 43 15
  subtype2 30  7
  subtype3 75 21
  subtype4 92 18
  subtype5 58 13
  subtype6 23  7
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      58       37       96      110       71       30 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      15        7       21       18       13        7 
$subtype1
TCGA-05-4384 TCGA-35-3615 TCGA-44-2656 TCGA-44-3398 TCGA-44-3919 TCGA-44-4112 
         426           14         1429         1163          190          722 
TCGA-44-6776 TCGA-44-6777 TCGA-44-7659 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47B 
        1938         1942          444          535          719          287 
TCGA-44-A47F TCGA-49-4486 TCGA-50-5045 TCGA-50-5932 TCGA-50-5942 TCGA-50-5944 
         337         1932         2174         1091          883          764 
TCGA-55-6972 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7573 TCGA-55-7727 
        1475         2151           53           18            4           34 
TCGA-55-7911 TCGA-55-8207 TCGA-55-A491 TCGA-55-A492 TCGA-62-8397 TCGA-62-A472 
          21           66         1952            1         1289          910 
TCGA-64-5815 TCGA-67-6215 TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 TCGA-69-8253 
         866          174          422          690          165          100 
TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7156 TCGA-78-7167 TCGA-78-7537 
         621         1944         1093         1961         1937         1944 
TCGA-78-7633 TCGA-78-8660 TCGA-86-7714 TCGA-86-8281 TCGA-91-8496 TCGA-93-7347 
         994         1954         1968         1955          197          297 
TCGA-95-A4VK TCGA-97-8174 TCGA-97-8179 TCGA-99-7458 TCGA-J2-A4AG TCGA-L4-A4E6 
         121         1965           15          392          238          435 
TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A4TH TCGA-MP-A4TK 
        1954         1944          142         1971 

$subtype2
TCGA-05-4390 TCGA-05-4417 TCGA-05-5423 TCGA-05-5715 TCGA-38-4628 TCGA-44-5644 
        1126          455          151           62         1492          863 
TCGA-44-A47A TCGA-49-4501 TCGA-50-5051 TCGA-50-5935 TCGA-50-7109 TCGA-53-7813 
         466         1421          455          653          255          424 
TCGA-55-1595 TCGA-55-6642 TCGA-55-7910 TCGA-55-8615 TCGA-55-A494 TCGA-62-8395 
        1479          993          197           15            5         1216 
TCGA-64-1678 TCGA-67-3772 TCGA-69-7760 TCGA-69-7973 TCGA-69-A59K TCGA-73-4659 
        1189          573          202          230          214          711 
TCGA-73-4662 TCGA-78-7159 TCGA-78-7161 TCGA-80-5608 TCGA-86-7701 TCGA-86-8669 
         912         1221          215         1972           11           34 
TCGA-86-A4D0 TCGA-91-6828 TCGA-97-8171 TCGA-99-8032 TCGA-MP-A4SW TCGA-MP-A4TE 
          30          323          107           44         1967         1970 
TCGA-MP-A5C7 
        1490 

$subtype3
TCGA-05-4396 TCGA-05-4398 TCGA-05-4422 TCGA-05-4425 TCGA-05-5420 TCGA-05-5425 
        1947         1431          365          669          457          882 
TCGA-05-5428 TCGA-35-4123 TCGA-35-5375 TCGA-38-4625 TCGA-38-4630 TCGA-38-4631 
         670          182          264         1952         1073          354 
TCGA-38-4632 TCGA-44-2659 TCGA-44-2662 TCGA-44-2666 TCGA-44-2668 TCGA-44-3918 
        1357         1367         1280           97          246         1036 
TCGA-44-5643 TCGA-44-7662 TCGA-44-8117 TCGA-44-A4SS TCGA-49-4494 TCGA-49-4506 
        1013          218          385          415         1081          999 
TCGA-49-4507 TCGA-49-4514 TCGA-49-6761 TCGA-50-5066 TCGA-50-5930 TCGA-50-5933 
         268         1700          354          944          282         2370 
TCGA-53-7624 TCGA-53-A4EZ TCGA-55-1596 TCGA-55-6971 TCGA-55-7815 TCGA-55-7907 
        1986          280         1375           25           54           16 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8301 TCGA-55-8302 TCGA-55-8510 
           5           33          100           44           23          228 
TCGA-55-8511 TCGA-55-8616 TCGA-55-A48Z TCGA-55-A4DG TCGA-62-8398 TCGA-62-A46U 
           9           48           29          162         1970         2067 
TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-5781 TCGA-67-3773 TCGA-67-3774 
        1246         1728          628         1559          427          385 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-75-7027 TCGA-78-7146 
         184           70           89          382         1956         1988 
TCGA-78-7155 TCGA-78-7536 TCGA-78-7539 TCGA-78-8662 TCGA-83-5908 TCGA-86-7713 
        1957         1949          327         1964          824          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8359 
         591         1963           13          479          482           26 
TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-91-6830 
          18           15          455          405           10           60 
TCGA-91-6836 TCGA-91-6847 TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         417          842           44          186           34            2 
TCGA-95-7944 TCGA-97-8547 TCGA-99-8025 TCGA-99-8033 TCGA-J2-8194 TCGA-L4-A4E5 
         377          148          427          170          114          578 
TCGA-L9-A444 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
           6          622          353         1957         1980         1951 

$subtype4
TCGA-05-4403 TCGA-05-4405 TCGA-05-4410 TCGA-05-4426 TCGA-05-4433 TCGA-05-5429 
         578          610         1958          791          730           30 
TCGA-35-4122 TCGA-38-4629 TCGA-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 
         225          864         1971          133          400          741 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6774 
         383          328          302          845          704          658 
TCGA-44-6775 TCGA-44-6779 TCGA-44-7661 TCGA-44-8120 TCGA-44-A47G TCGA-49-4505 
         705         1978          366          260          351          428 
TCGA-49-4510 TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-50-5055 TCGA-50-5068 
         896          157          890          522          785         1499 
TCGA-50-5941 TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-55-6712 TCGA-55-6980 
         567         1015          105         1971           24           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 TCGA-55-7284 TCGA-55-7574 TCGA-55-7576 
        1826         1233           35          121           95           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 TCGA-55-7816 TCGA-55-7903 
        1958           39           39           24           44           19 
TCGA-55-7914 TCGA-55-8087 TCGA-55-8090 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 
           3           21            6           15           33           46 
TCGA-55-8299 TCGA-55-8506 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 
         216           11            3          146          536           49 
TCGA-55-8621 TCGA-55-A48X TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 TCGA-67-3770 
         106           33         1126         1968         1305           31 
TCGA-69-7761 TCGA-69-7764 TCGA-69-8254 TCGA-71-6725 TCGA-73-4676 TCGA-75-7025 
         186          414           77           61          164         1967 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7158 
        1973         1950         1202          760         1948         1963 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7535 TCGA-78-7540 TCGA-78-8655 TCGA-86-8056 
         678         1940         1972          881         1981         1963 
TCGA-86-8076 TCGA-86-8280 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6849 TCGA-91-7771 
         489           16           39           79           35          492 
TCGA-91-8497 TCGA-91-A4BD TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-97-7546 
         174          218          568          477          476          964 
TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 TCGA-97-8175 
        1965         1932         1332           22          182           87 
TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8028 TCGA-J2-A4AE TCGA-MN-A4N1 
         147          115          197          459          282          285 
TCGA-MP-A4T4 TCGA-MP-A4TI 
        1954         1955 

$subtype5
TCGA-05-4382 TCGA-05-4389 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 TCGA-05-4427 
         607         1369         1997          912          913          791 
TCGA-05-4430 TCGA-05-4432 TCGA-44-3396 TCGA-44-6144 TCGA-44-6778 TCGA-44-7660 
         761          761         1130          723         1864          592 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 TCGA-44-A479 TCGA-49-6742 
         557         1970          882           99          486          445 
TCGA-49-6743 TCGA-50-5049 TCGA-50-5072 TCGA-50-5931 TCGA-50-5946 TCGA-55-1592 
         369         2146          246          267          686          701 
TCGA-55-1594 TCGA-55-5899 TCGA-55-6969 TCGA-55-6987 TCGA-55-7570 TCGA-55-7994 
        1178           87         1239         1170            6           31 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 
          26            4           47           29            8           15 
TCGA-55-8514 TCGA-55-8620 TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8399 
         202           66           48           28           47         2696 
TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-69-8255 
        1686         1959           62          864          610          129 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 TCGA-78-7150 TCGA-78-7220 TCGA-78-7542 
         519         1970         1965         1963         1965         1952 
TCGA-78-8640 TCGA-78-8648 TCGA-86-6851 TCGA-86-7711 TCGA-86-7955 TCGA-86-8054 
        1949         1971         1959          630          508          745 
TCGA-86-8055 TCGA-86-8358 TCGA-86-8585 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 
          10           19           35         1940          310          372 
TCGA-91-6848 TCGA-91-8499 TCGA-97-7937 TCGA-J2-A4AD TCGA-MP-A4SV 
         224           36          181          287         1946 

$subtype6
TCGA-05-4249 TCGA-38-4626 TCGA-38-4627 TCGA-38-6178 TCGA-44-2655 TCGA-44-2665 
        1523         1962         1147          448         1324         1301 
TCGA-44-A4SU TCGA-55-6543 TCGA-55-8091 TCGA-55-A48Y TCGA-62-8402 TCGA-62-A46V 
          76            2           43           42         1445         2199 
TCGA-67-6216 TCGA-71-8520 TCGA-73-4658 TCGA-73-4675 TCGA-78-7163 TCGA-78-7166 
         141            3         1600           40         1950         1934 
TCGA-80-5607 TCGA-86-8074 TCGA-86-8278 TCGA-86-8668 TCGA-86-A4P7 TCGA-93-7348 
        1965           24          476           45           14          127 
TCGA-97-7554 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 TCGA-MP-A4T2 TCGA-MP-A4TF 
         775          271          154          116         1951         1970 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
       1        5        2        3        4        2 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    2174     1972     2370     1981     2696     2199 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   720.5    455.0    410.0    407.0    607.0    462.0 
[1] "1.0 - 2174.0 (720.5)" "5.0 - 1972.0 (455.0)" "2.0 - 2370.0 (410.0)"
[4] "3.0 - 1981.0 (407.0)" "4.0 - 2696.0 (607.0)" "2.0 - 2199.0 (462.0)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       0       23       14         2         9          8          1
  subtype2       1        8       12         5         7          4          2
  subtype3       2       19       39        10        16         19          5
  subtype4       1       36       36        11        19         16          2
  subtype5       0       17       24         8        11         15          1
  subtype6       0        9        7         7         5          6          0
          vv
clus       STAGE IV
  subtype1        4
  subtype2        2
  subtype3        5
  subtype4        6
  subtype5        4
  subtype6        1
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           0        1        2        1        0        0
  STAGE IA         23        8       19       36       17        9
  STAGE IB         14       12       39       36       24        7
  STAGE IIA         2        5       10       11        8        7
  STAGE IIB         9        7       16       19       11        5
  STAGE IIIA        8        4       19       16       15        6
  STAGE IIIB        1        2        5        2        1        0
  STAGE IV          4        2        5        6        4        1
[1] 8 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 25 29  3  4
  subtype2  9 25  5  2
  subtype3 26 72 10  5
  subtype4 46 62 14  5
  subtype5 24 46  8  2
  subtype6 12 22  1  0
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1       25        9       26       46       24       12
  T2       29       25       72       62       46       22
  T3        3        5       10       14        8        1
  T4        4        2        5        5        2        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 41 11     6
  subtype2 30  4     6
  subtype3 71 21    22
  subtype4 81 24    18
  subtype5 50 14    15
  subtype6 20 10     5
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0          41       30       71       81       50       20
  N1          11        4       21       24       14       10
  N2+N3        6        6       22       18       15        5
[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"
          vv
clus       M0 M1 M1A M1B MX
  subtype1 41  3   0   0 17
  subtype2 32  1   1   0  6
  subtype3 81  5   0   0 29
  subtype4 82  4   0   1 39
  subtype5 53  2   0   2 23
  subtype6 26  1   0   0  7
D10V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0        41       32       81       82       53       26
  M1         3        1        5        4        2        1
  M1A        0        1        0        0        0        0
  M1B        0        0        0        1        2        0
  MX        17        6       29       39       23        7
[1] 5 6
[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 30 31
  subtype2 25 16
  subtype3 60 55
  subtype4 79 49
  subtype5 27 53
  subtype6 26  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   31
  subtype2   25   16
  subtype3   60   55
  subtype4   79   49
  subtype5   27   53
  subtype6   26    9
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       30       25       60       79       27       26
  MALE         31       16       55       49       53        9
[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"
D10V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          3                                15
  subtype2                          1                                10
  subtype3                          2                                24
  subtype4                          4                                26
  subtype5                          3                                14
  subtype6                          0                                 3
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 35
  subtype2                                                 27
  subtype3                                                 78
  subtype4                                                 72
  subtype5                                                 54
  subtype6                                                 28
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          0
  subtype4                                          2
  subtype5                                          0
  subtype6                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             4
  subtype2                                             1
  subtype3                                             3
  subtype4                                            10
  subtype5                                             1
  subtype6                                             0
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  0
  subtype2                              1                                  0
  subtype3                              0                                  1
  subtype4                              0                                  0
  subtype5                              1                                  1
  subtype6                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             4
  subtype2                            0                             1
  subtype3                            0                             7
  subtype4                            2                             5
  subtype5                            0                             1
  subtype6                            0                             1
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               0
  subtype4                               1
  subtype5                               0
  subtype6                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             0
  subtype3                                             0
  subtype4                                             1
  subtype5                                             3
  subtype6                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            0
  subtype3                            0
  subtype4                            5
  subtype5                            2
  subtype6                            0
D10V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                3        1        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        15       10       24
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       35       27       78
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        0        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             4        1        3
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             4        1        7
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        0        0
  MUCINOUS (COLLOID) CARCINOMA                              0        0        0
                                                    clus
vv                                                   subtype4 subtype5 subtype6
  LUNG ACINAR ADENOCARCINOMA                                4        3        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        26       14        3
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       72       54       28
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            10        1        0
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        1        1
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             5        1        1
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        3        0
  MUCINOUS (COLLOID) CARCINOMA                              5        2        0
[1] 12  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V10, binary
          cls
clus         0   1
  subtype1   3  58
  subtype2   1  40
  subtype3   6 109
  subtype4   5 123
  subtype5   4  76
  subtype6   1  34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   58
  subtype2    1   40
  subtype3    6  109
  subtype4    5  123
  subtype5    4   76
  subtype6    1   34
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO         3        1        6        5        4        1
  YES       58       40      109      123       76       34
[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"
D10V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 39  1  0  2
  subtype2 28  1  0  2
  subtype3 81  3  1  5
  subtype4 83  4  2  6
  subtype5 54  1  1  3
  subtype6 30  1  0  1
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       39       28       81       83       54       30
  R1        1        1        3        4        1        1
  R2        0        0        1        2        1        0
  RX        2        2        5        6        3        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         5    49
  subtype2     2                         2    31
  subtype3     3                         5    90
  subtype4     1                         7   105
  subtype5     0                         7    55
  subtype6     1                         0    30
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            0        2        3        1        0
  BLACK OR AFRICAN AMERICAN        5        2        5        7        7
  WHITE                           49       31       90      105       55
                           clus
vv                          subtype6
  ASIAN                            1
  BLACK OR AFRICAN AMERICAN        0
  WHITE                           30
[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"
D10V14, binary
          cls
clus        0  1
  subtype1  0 43
  subtype2  0 30
  subtype3  3 85
  subtype4  1 93
  subtype5  3 51
  subtype6  0 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   43
  subtype2    0   30
  subtype3    3   85
  subtype4    1   93
  subtype5    3   51
  subtype6    0   28
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        0        3        1        3        0
  NOT HISPANIC OR LATINO       43       30       85       93       51       28
[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(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1 100  25
  subtype2 136  21
  subtype3  46  18
subtype1 subtype2 subtype3 
     125      157       64 
subtype1 subtype2 subtype3 
      25       21       18 
$subtype1
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4410 TCGA-05-4424 TCGA-05-4427 
         426         1947          610         1958          913          791 
TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-38-7271 TCGA-38-A44F TCGA-44-5645 
         730          151           30         1971          133          383 
TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6776 TCGA-44-6777 TCGA-44-6779 
         328          302          845         1938         1942         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47B TCGA-44-A47G 
         444          366          535          719          287          351 
TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-50-5051 TCGA-50-5055 TCGA-50-5068 
        1700          890          522          455          785         1499 
TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 
        1091          653          567          883          764         1015 
TCGA-50-8460 TCGA-53-7626 TCGA-55-6712 TCGA-55-6972 TCGA-55-6986 TCGA-55-7227 
         105         1971           24         1475         2151           53 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 
          18           35            4           95           40         1958 
TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 TCGA-55-8097 
          39           34           19           21            3           15 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 
          46           66            3          146           48           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 TCGA-62-8397 TCGA-62-A472 TCGA-64-1681 
         106           33            1         1289          910         1968 
TCGA-67-6215 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 
         174          422          186          690          414          165 
TCGA-69-8253 TCGA-69-8254 TCGA-73-4676 TCGA-73-7498 TCGA-78-7145 TCGA-78-7147 
         100           77          164          621         1973         1950 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 
        1944         1093         1202          760         1948         1961 
TCGA-78-7158 TCGA-78-7160 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 
        1963          678         1940         1937         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 
         881         1952          994         1968         1963          489 
TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6828 TCGA-91-6835 TCGA-91-6849 TCGA-91-7771 
          10           39          323           79           35          492 
TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-95-7567 TCGA-95-A4VK 
         197          174          218          297          568          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7937 TCGA-97-8172 
         964         1965         1932         1332          181          182 
TCGA-97-8174 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-J2-A4AE 
        1965           15          115          197          392          282 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH 
         238          435         1954         1980          142 

$subtype2
TCGA-05-4390 TCGA-05-4415 TCGA-05-4425 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 
        1126         1997          669          457          882          670 
TCGA-05-5715 TCGA-35-5375 TCGA-38-4632 TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 
          62          264         1357         1013          863          592 
TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A47A 
         882          385           99          260          486          466 
TCGA-44-A47F TCGA-44-A4SS TCGA-49-6743 TCGA-50-5049 TCGA-50-5066 TCGA-50-5930 
         337          415          369         2146          944          282 
TCGA-50-5931 TCGA-50-5946 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
         267          686         1986          424          280           87 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6987 TCGA-55-7284 TCGA-55-7570 
        1239           25           67         1170          121            6 
TCGA-55-7728 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 
          24           16          197           31            5           33 
TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
          21          100            6           26            4           47 
TCGA-55-8205 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 
          33           44           23           29           11            8 
TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 
          15          228            9          202           15           66 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 TCGA-55-A494 
          42           29           48         1952           28            5 
TCGA-55-A4DF TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A471 
          47         1216         1970         2696         2067         1246 
TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 TCGA-69-7973 
        1959           62         1305          864         1559          230 
TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K 
         184           70           89          382          129          214 
TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7150 
         519         1970         1956         1965         1988         1963 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7161 TCGA-78-7535 TCGA-78-7536 TCGA-78-8640 
        1957         1221          215         1972         1949         1949 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1981         1954         1964         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
          11          630          422          591         1963          508 
TCGA-86-8054 TCGA-86-8073 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 
         745           13          479          482           16         1955 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          19           26           35           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 
         455          405           30           60          310          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-8499 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 
         372          842           36          186           34            2 
TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 TCGA-97-7941 TCGA-97-8171 TCGA-97-8175 
         377          477          476           22          107           87 
TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD 
         427          459           44          170          114          287 
TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV 
         578            6          285          622          353         1946 
TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A4TF 
        1967         1954         1957         1951         1970         1970 
TCGA-MP-A5C7 
        1490 

$subtype3
TCGA-05-4417 TCGA-38-4631 TCGA-38-6178 TCGA-44-6144 TCGA-44-6148 TCGA-44-6774 
         455          354          448          723          704          658 
TCGA-44-6775 TCGA-44-6778 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-A4SU 
         705         1864          218          557         1970           76 
TCGA-49-4512 TCGA-49-6742 TCGA-49-6761 TCGA-50-5045 TCGA-50-5072 TCGA-50-5933 
         157          445          354         2174          246         2370 
TCGA-50-7109 TCGA-55-6543 TCGA-55-6642 TCGA-55-6983 TCGA-55-6985 TCGA-55-7726 
         255            2          993         1826         1233           39 
TCGA-55-7815 TCGA-55-7816 TCGA-55-8091 TCGA-55-8299 TCGA-55-8614 TCGA-55-A4DG 
          54           44           43          216          536          162 
TCGA-62-8402 TCGA-62-A46V TCGA-64-1679 TCGA-64-5815 TCGA-67-6216 TCGA-69-7760 
        1445         2199         1686          866          141          202 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-75-7025 TCGA-78-7163 TCGA-78-7166 
          61            3         1600         1967         1950         1934 
TCGA-78-7220 TCGA-78-8648 TCGA-80-5607 TCGA-86-8055 TCGA-86-8074 TCGA-86-8278 
        1965         1971         1965           10           24          476 
TCGA-86-8668 TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6848 TCGA-91-A4BC TCGA-93-7348 
          45           14         1940          224           44          127 
TCGA-97-7554 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 
         775          147          148          271          154          116 
TCGA-MP-A4T2 TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        1951         1944         1955         1971 

subtype1 subtype2 subtype3 
       1        2        2 
subtype1 subtype2 subtype3 
    2151     2696     2370 
subtype1 subtype2 subtype3 
   444.0    372.0    451.5 
[1] "1.0 - 2151.0 (444.0)" "2.0 - 2696.0 (372.0)" "2.0 - 2370.0 (451.5)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       44       35        12        17         21          4
  subtype2       2       38       58        20        26         22          4
  subtype3       1       15       19         8        14         16          1
          vv
clus       STAGE IV
  subtype1        7
  subtype2        9
  subtype3        2
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        2        1
  STAGE IA         44       38       15
  STAGE IB         35       58       19
  STAGE IIA        12       20        8
  STAGE IIB        17       26       14
  STAGE IIIA       21       22       16
  STAGE IIIB        4        4        1
  STAGE IV          7        9        2
[1] 8 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        T1  T2  T3  T4
  subtype1  55  63  14  10
  subtype2  49 108  16   4
  subtype3  22  47   5   1
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       55       49       22
  T2       63      108       47
  T3       14       16        5
  T4       10        4        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"
          vv
clus        N0  N1 N2+N3
  subtype1  91  26    20
  subtype2 123  28    25
  subtype3  42  16    17
D11V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          91      123       42
  N1          26       28       16
  N2+N3       20       25       17
[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"
          vv
clus        M0  M1 M1A M1B  MX
  subtype1  92   5   0   1  42
  subtype2 120   6   1   2  49
  subtype3  44   1   0   0  30
D11V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        92      120       44
  M1         5        6        1
  M1A        0        1        0
  M1B        1        2        0
  MX        42       49       30
[1] 5 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 83 59
  subtype2 87 92
  subtype3 43 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   83   59
  subtype2   87   92
  subtype3   43   33
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       83       87       43
  MALE         59       92       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"
D11V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          6                                39
  subtype2                          6                                31
  subtype3                          1                                 7
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 71
  subtype2                                                119
  subtype3                                                 58
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          2
  subtype2                                          0
  subtype3                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            10
  subtype2                                             8
  subtype3                                             1
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  1
  subtype2                              1                                  0
  subtype3                              0                                  2
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             9
  subtype2                            0                             7
  subtype3                            1                             2
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               1
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             4
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            3
  subtype2                            2
  subtype3                            2
D11V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                6        6        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        39       31        7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       71      119       58
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            10        8        1
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        2
  LUNG MUCINOUS ADENOCARCINOMA                              1        0        1
  LUNG PAPILLARY ADENOCARCINOMA                             9        7        2
  LUNG SIGNET RING ADENOCARCINOMA                           0        1        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        4        0
  MUCINOUS (COLLOID) CARCINOMA                              3        2        2
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D11V10, binary
          cls
clus         0   1
  subtype1   6 136
  subtype2   6 173
  subtype3   6  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  136
  subtype2    6  173
  subtype3    6   70
     clus
vv    subtype1 subtype2 subtype3
  NO         6        6        6
  YES      136      173       70
[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"
D11V11, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  86   4   1   5
  subtype2 129   3   0   6
  subtype3  48   2   0   5
D11V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       86      129       48
  R1        4        3        2
  R2        1        0        0
  RX        5        6        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"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         7   119
  subtype2     2                        14   138
  subtype3     2                         3    61
D11V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        2
  BLACK OR AFRICAN AMERICAN        7       14        3
  WHITE                          119      138       61
[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"
D11V14, binary
          cls
clus         0   1
  subtype1   0  99
  subtype2   5 130
  subtype3   1  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   99
  subtype2    5  130
  subtype3    1   56
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        5        1
  NOT HISPANIC OR LATINO       99      130       56
[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 122  26
  subtype2 141  32
  subtype3  19   6
subtype1 subtype2 subtype3 
     148      173       25 
subtype1 subtype2 subtype3 
      26       32        6 
$subtype1
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4410 TCGA-05-4427 TCGA-05-4433 
         426         1947          610         1958          791          730 
TCGA-05-5423 TCGA-05-5429 TCGA-38-7271 TCGA-38-A44F TCGA-44-5645 TCGA-44-6145 
         151           30         1971          133          383          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 
         302          845          704          705         1938         1942 
TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A47B 
        1978          444          366          535          719          287 
TCGA-44-A47F TCGA-44-A47G TCGA-49-4514 TCGA-49-6744 TCGA-49-6745 TCGA-50-5055 
         337          351         1700          890          522          785 
TCGA-50-5068 TCGA-50-5932 TCGA-50-5933 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
        1499         1091         2370          567          883          764 
TCGA-50-6597 TCGA-50-8460 TCGA-53-7626 TCGA-55-6712 TCGA-55-6972 TCGA-55-6980 
        1015          105         1971           24         1475           67 
TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
        1826         1233         2151           53           18           35 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7725 
         121            4           95           40         1958           39 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7815 TCGA-55-7816 TCGA-55-7903 TCGA-55-7911 
          34           24           54           44           19           21 
TCGA-55-7914 TCGA-55-8087 TCGA-55-8090 TCGA-55-8097 TCGA-55-8206 TCGA-55-8207 
           3           21            6           15           46           66 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 
           3          146          536           48           49          106 
TCGA-55-A48X TCGA-55-A491 TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 
          33         1952            1          162         1216         1289 
TCGA-62-A46U TCGA-62-A472 TCGA-64-1681 TCGA-64-5815 TCGA-67-6215 TCGA-67-6217 
        2067          910         1968          866          174          422 
TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-8253 TCGA-69-8254 
         186          690          414          165          100           77 
TCGA-73-4676 TCGA-73-7498 TCGA-75-7025 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 
         164          621         1967         1973         1950         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7156 TCGA-78-7158 
        1093         1202          760         1948         1961         1963 
TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 TCGA-78-7540 
         678         1940         1934         1937         1944          881 
TCGA-78-7633 TCGA-78-8655 TCGA-78-8660 TCGA-86-7714 TCGA-86-8056 TCGA-86-8076 
         994         1981         1954         1968         1963          489 
TCGA-86-8280 TCGA-86-8281 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6849 
          16         1955           10           39           79           35 
TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-95-A4VK 
         492          197          174          218          297          121 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 TCGA-97-8172 
         964         1965         1932         1332           22          182 
TCGA-97-8174 TCGA-97-8175 TCGA-97-8179 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 
        1965           87           15          115          197          392 
TCGA-99-8025 TCGA-99-8028 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4T4 
         427          459          282          238          435         1954 
TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A5C7 
        1954         1980          142         1490 

$subtype2
TCGA-05-4390 TCGA-05-4415 TCGA-05-4417 TCGA-05-4424 TCGA-05-4425 TCGA-05-5420 
        1126         1997          455          913          669          457 
TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-5375 TCGA-38-4631 TCGA-38-4632 
         882          670           62          264          354         1357 
TCGA-44-5643 TCGA-44-5644 TCGA-44-6144 TCGA-44-6778 TCGA-44-7660 TCGA-44-7662 
        1013          863          723         1864          592          218 
TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         557         1970          882          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A4SS TCGA-49-6742 TCGA-49-6743 TCGA-49-6761 
         486          466          415          445          369          354 
TCGA-50-5049 TCGA-50-5051 TCGA-50-5066 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 
        2146          455          944          246          282          267 
TCGA-50-5935 TCGA-50-5946 TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ 
         653          686          255         1986          424          280 
TCGA-55-5899 TCGA-55-6642 TCGA-55-6969 TCGA-55-6971 TCGA-55-6987 TCGA-55-7570 
          87          993         1239           25         1170            6 
TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 
          16          197           31            5           33          100 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8299 TCGA-55-8301 
          26            4           47           33          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 
          23           29           11            8           15          228 
TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z 
           9          202           15           66           42           29 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8399 
          48           28            5           47         1970         2696 
TCGA-62-A471 TCGA-64-1679 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 
        1246         1686         1959           62         1305          864 
TCGA-64-5781 TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 
        1559          202          230          184           70           89 
TCGA-69-7980 TCGA-69-8255 TCGA-69-A59K TCGA-71-6725 TCGA-73-7499 TCGA-75-6214 
         382          129          214           61          519         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7150 TCGA-78-7155 TCGA-78-7159 
        1956         1965         1988         1963         1957         1221 
TCGA-78-7161 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-7542 
         215         1965         1972         1949          327         1952 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1949         1971         1964         1972          824         1959 
TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
          11          630          422          591         1963          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 TCGA-86-8278 TCGA-86-8279 
         745           10           13          479          476          482 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 
          19           26           35           34           18           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 
         455          405           30          323         1940           60 
TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 
         310          417          372          842          224           36 
TCGA-91-A4BC TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 TCGA-95-7944 
          44          186           34            2          568          377 
TCGA-95-7947 TCGA-95-7948 TCGA-97-7937 TCGA-97-8171 TCGA-97-8547 TCGA-99-8032 
         477          476          181          107          148           44 
TCGA-99-8033 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 
         170          114          287          578            6          285 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TA 
         622          353         1946         1967         1957         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1970         1955         1971 

$subtype3
TCGA-38-6178 TCGA-44-6774 TCGA-44-A4SU TCGA-49-4512 TCGA-50-5045 TCGA-55-6543 
         448          658           76          157         2174            2 
TCGA-55-7726 TCGA-55-8091 TCGA-62-8402 TCGA-62-A46V TCGA-67-6216 TCGA-71-8520 
          39           43         1445         2199          141            3 
TCGA-73-4658 TCGA-78-7163 TCGA-80-5607 TCGA-86-8074 TCGA-86-8668 TCGA-86-A4P7 
        1600         1950         1965           24           45           14 
TCGA-93-7348 TCGA-97-7554 TCGA-97-8177 TCGA-97-A4M7 TCGA-J2-8192 TCGA-L9-A443 
         127          775          147          271          154          116 
TCGA-MP-A4T2 
        1951 

subtype1 subtype2 subtype3 
       1        2        2 
subtype1 subtype2 subtype3 
    2370     2696     2199 
subtype1 subtype2 subtype3 
     474      382      154 
[1] "1.0 - 2370.0 (474.0)" "2.0 - 2696.0 (382.0)" "2.0 - 2199.0 (154.0)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       52       41        11        27         21          5
  subtype2       3       35       64        26        29         30          4
  subtype3       0       10        7         3         1          8          0
          vv
clus       STAGE IV
  subtype1        8
  subtype2        9
  subtype3        1
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        3        0
  STAGE IA         52       35       10
  STAGE IB         41       64        7
  STAGE IIA        11       26        3
  STAGE IIB        27       29        1
  STAGE IIIA       21       30        8
  STAGE IIIB        5        4        0
  STAGE IV          8        9        1
[1] 8 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  63  75  17  11
  subtype2  51 125  18   4
  subtype3  12  18   0   0
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       63       51       12
  T2       75      125       18
  T3       17       18        0
  T4       11        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        N0  N1 N2+N3
  subtype1 107  32    21
  subtype2 132  33    33
  subtype3  17   5     8
D12V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         107      132       17
  N1          32       33        5
  N2+N3       21       33        8
[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"
          vv
clus        M0  M1 M1A M1B  MX
  subtype1 105   5   0   1  54
  subtype2 132   6   1   2  58
  subtype3  19   1   0   0   9
D12V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       105      132       19
  M1         5        6        1
  M1A        0        1        0
  M1B        1        2        0
  MX        54       58        9
[1] 5 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  97  70
  subtype2  90 110
  subtype3  26   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   97   70
  subtype2   90  110
  subtype3   26    4
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       97       90       26
  MALE         70      110        4
[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
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          7                                39
  subtype2                          6                                34
  subtype3                          0                                 4
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 87
  subtype2                                                139
  subtype3                                                 22
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          2
  subtype2                                          0
  subtype3                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            13
  subtype2                                             6
  subtype3                                             0
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  0
  subtype2                              1                                  2
  subtype3                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            2                            10
  subtype2                            0                             7
  subtype3                            0                             1
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             3
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            5
  subtype2                            2
  subtype3                            0
D12V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                7        6        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        39       34        4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       87      139       22
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            13        6        0
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        2        1
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                            10        7        1
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        3        0
  MUCINOUS (COLLOID) CARCINOMA                              5        2        0
[1] 12  3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V10, binary
          cls
clus         0   1
  subtype1   7 160
  subtype2   9 191
  subtype3   2  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  160
  subtype2    9  191
  subtype3    2   28
     clus
vv    subtype1 subtype2 subtype3
  NO         7        9        2
  YES      160      191       28
[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"
D12V11, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 109   4   1   7
  subtype2 133   3   0   9
  subtype3  21   2   0   0
D12V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      109      133       21
  R1        4        3        2
  R2        1        0        0
  RX        7        9        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         9   137
  subtype2     3                        14   156
  subtype3     1                         1    25
D12V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        3        1
  BLACK OR AFRICAN AMERICAN        9       14        1
  WHITE                          137      156       25
[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"
D12V14, binary
          cls
clus         0   1
  subtype1   1 115
  subtype2   5 145
  subtype3   0  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  115
  subtype2    5  145
  subtype3    0   25
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        0
  NOT HISPANIC OR LATINO      115      145       25
[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"
