[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/11541582/LUAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUAD-TP/11590629/LUAD-TP.mergedcluster.txt"

nPatients in clinical file=483, in cluster file=519, common to both=480
[1]  12 480
[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 
185 203  88 
  1   2   3 
185 203  88 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4 
 87 117 106 107 
  1   2   3   4 
 87 117 106 107 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
44 73 64 
 1  2  3 
44 73 64 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
40 33 45 31 32 
 1  2  3  4  5 
40 33 45 31 32 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4   5 
136 103  72 102  51 
  1   2   3   4   5 
136 103  72 102  51 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8  9 
82 52 44 80 43 48 47 16 52 
 1  2  3  4  5  6  7  8  9 
82 52 44 80 43 48 47 16 52 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
172 215  87 
  1   2   3 
172 215  87 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 64 190 129  91 
  1   2   3   4 
 64 190 129  91 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
139 175  84 
  1   2   3 
139 175  84 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
 84 230  84 
  1   2   3 
 84 230  84 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "COMPLETENESS.OF.RESECTION"             
[21] "RACE"                                  
[22] "ETHNICITY"                             
[23] "BATCHNUMBER"                           

Input Data has 23 rows and 480 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-44-2665 TCGA-44-2666 TCGA-44-2668 TCGA-44-3396 TCGA-44-3398 
        1280         1301           97          246         1130         1163 
TCGA-44-3917 TCGA-44-3918 TCGA-44-3919 TCGA-44-4112 TCGA-44-5643 TCGA-44-5644 
        1183         1036          190          722         1013          863 
TCGA-44-5645 TCGA-44-6144 TCGA-44-6145 TCGA-44-6146 TCGA-44-6147 TCGA-44-6148 
         383          723          328          302          845          704 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-44-6778 TCGA-44-6779 
         658          705         1938           NA         1864           NA 
TCGA-44-7659 TCGA-44-7660 TCGA-44-7661 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 
         444          592          366          218          557           NA 
TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 TCGA-44-8117 TCGA-44-8119 TCGA-44-8120 
         882          535          719          385           99          260 
TCGA-44-A479 TCGA-44-A47A TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS 
         486          466          287          337          351          415 
TCGA-44-A4SU TCGA-49-4486 TCGA-49-4487 TCGA-49-4488 TCGA-49-4490 TCGA-49-4494 
          76         2318           NA           NA           NA         1081 
TCGA-49-4501 TCGA-49-4505 TCGA-49-4506 TCGA-49-4507 TCGA-49-4510 TCGA-49-4512 
        1421          428          999          268          896          157 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1700          445          369          890          522          354 
TCGA-49-6767 TCGA-49-AARQ TCGA-50-5044 TCGA-50-5045 TCGA-50-5049 TCGA-50-5051 
          NA         6443           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          705           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          462          100 
TCGA-55-8090 TCGA-55-8091 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8097 
           6          600           26            4           47           15 
TCGA-55-8204 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8208 TCGA-55-8299 
          NA           33           46           66          674          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8512 TCGA-55-8513 TCGA-55-8514 TCGA-55-8614 
         228            9            3          146          202          536 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-8621 TCGA-55-A48X 
          15           48           49           66          106           33 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 
          42           29           48           NA            1           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8394 TCGA-62-8395 TCGA-62-8397 
           5           47          162           NA         1216         1289 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A46O TCGA-62-A46P TCGA-62-A46R 
          NA         2696         1445           NA           NA           NA 
TCGA-62-A46S TCGA-62-A46U TCGA-62-A46V TCGA-62-A46Y TCGA-62-A470 TCGA-62-A471 
          NA         2067         2199           NA           NA         1246 
TCGA-62-A472 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-1679 TCGA-64-1680 
         910         1728          628         1189         1686         1126 
TCGA-64-1681 TCGA-64-5774 TCGA-64-5775 TCGA-64-5778 TCGA-64-5779 TCGA-64-5781 
          NA         2676           62         1305          864         1559 
TCGA-64-5815 TCGA-67-3770 TCGA-67-3771 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 
         866           31          610          573          427          385 
TCGA-67-4679 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7761 
          NA          174          141          422          202          186 
TCGA-69-7763 TCGA-69-7764 TCGA-69-7765 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 
         690          414          165          230          184           70 
TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 TCGA-69-8254 TCGA-69-8255 TCGA-69-A59K 
          89          382          100           77          129          214 
TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 TCGA-73-4666 
          61            3         1600          711          912          800 
TCGA-73-4668 TCGA-73-4670 TCGA-73-4675 TCGA-73-4676 TCGA-73-4677 TCGA-73-7498 
         467          131           40          164           38          621 
TCGA-73-7499 TCGA-73-A9RS TCGA-75-5122 TCGA-75-5125 TCGA-75-5126 TCGA-75-5146 
         519          305           NA           NA           NA           NA 
TCGA-75-5147 TCGA-75-6203 TCGA-75-6205 TCGA-75-6206 TCGA-75-6207 TCGA-75-6211 
          NA           NA           NA           NA           NA           NA 
TCGA-75-6212 TCGA-75-6214 TCGA-75-7025 TCGA-75-7027 TCGA-75-7030 TCGA-75-7031 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7143 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
          NA           NA           NA           NA           NA         1093 
TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 
          NA         1202          760           NA           NA           NA 
TCGA-78-7158 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7162 TCGA-78-7163 
          NA         1221          678          215           NA         6812 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7537 
          NA           NA           NA           NA           NA           NA 
TCGA-78-7539 TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-78-8640 TCGA-78-8648 
         327          881           NA          994         6346           NA 
TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-80-5611 
        2360           NA           NA           NA           NA           NA 
TCGA-83-5908 TCGA-86-6562 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 
         824           NA           NA           11          630          422 
TCGA-86-7714 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 
          NA          591           NA          508          745           10 
TCGA-86-8056 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8076 TCGA-86-8278 
          NA           13           24          479          489          476 
TCGA-86-8279 TCGA-86-8280 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         482           16           NA           19           26           35 
TCGA-86-8668 TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 
          45           34           18           15          455          405 
TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4JF TCGA-86-A4P7 TCGA-86-A4P8 TCGA-91-6828 
          10           30           NA           14           39          323 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6835 TCGA-91-6836 TCGA-91-6840 
          NA           60          310           79          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 
         842          224           35          492          505          174 
TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-93-8067 
          36           44          218          297          127          186 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
          34            2           NA          568          377          477 
TCGA-95-7948 TCGA-95-8039 TCGA-95-8494 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
         476          830           84          121          553          605 
TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 
         964         1965         1932         1332          775          181 
TCGA-97-7938 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 
          NA           22          107          182           NA           87 
TCGA-97-8177 TCGA-97-8179 TCGA-97-8547 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 
         147           15          148          115          197          271 
TCGA-99-7458 TCGA-99-8025 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         392          427          459           44          170          154 
TCGA-J2-8194 TCGA-J2-A4AD TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 
         114          287          282          238          578          435 
TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A50W TCGA-L9-A5IP TCGA-L9-A743 TCGA-L9-A7SV 
         116            6          266           NA          312          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         102          827         1175           84           NA           NA 
TCGA-MP-A4SY TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T6 TCGA-MP-A4T7 TCGA-MP-A4T8 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TD TCGA-MP-A4TE TCGA-MP-A4TF 
          NA           NA           NA           NA           NA           NA 
TCGA-MP-A4TH TCGA-MP-A4TI TCGA-MP-A4TJ TCGA-MP-A4TK TCGA-MP-A5C7 TCGA-S2-AA1A 
         142           NA           NA           NA         1490          121 
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=123,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=293,	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=3,	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=93,	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=26,	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 480 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 
147 269  43  18 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
147 269  43  18 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
147 269  43  18 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
147 269  43  18 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
303  92  72   2 
[1] "table(vv)"
vv
   N0    N1 N2+N3 
  303    92    74 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
303  92  72   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   N0    N1 N2+N3 
  303    92    74 
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=93, 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 122  39
  subtype2 144  33
  subtype3  63  15
subtype1 subtype2 subtype3 
     161      177       78 
subtype1 subtype2 subtype3 
      39       33       15 
$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-44-2668 TCGA-44-3919 TCGA-44-5644 TCGA-44-6144 TCGA-44-6775 
        1280          246          190          863          723          705 
TCGA-44-6777 TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-8117 TCGA-44-8120 
        1942         1978          218         1970          385          260 
TCGA-44-A4SU TCGA-49-4501 TCGA-49-4505 TCGA-49-4507 TCGA-49-4512 TCGA-49-AARQ 
          76         1421          428          268          157         6443 
TCGA-50-5930 TCGA-50-5931 TCGA-50-5933 TCGA-50-5944 TCGA-50-5946 TCGA-50-6597 
         282          267         2370          764          686         1015 
TCGA-53-7624 TCGA-55-1592 TCGA-55-1594 TCGA-55-1595 TCGA-55-1596 TCGA-55-6543 
        1986          701         1178         1479         1375            2 
TCGA-55-6712 TCGA-55-6972 TCGA-55-6985 TCGA-55-7573 TCGA-55-7576 TCGA-55-7726 
          24         1475         1233            4           40           39 
TCGA-55-7727 TCGA-55-7910 TCGA-55-7994 TCGA-55-7995 TCGA-55-8091 TCGA-55-8094 
          34          197           31            5          600            4 
TCGA-55-8096 TCGA-55-8207 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 
          47           66           11          228            9          202 
TCGA-55-8614 TCGA-55-8616 TCGA-55-8620 TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 
         536           48           66           29           48         1952 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-8402 
          47          162         1216         1289         2696         1445 
TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-1676 TCGA-64-1679 TCGA-64-1681 
        2067         1246          910         1728         1686         1968 
TCGA-64-5778 TCGA-67-3770 TCGA-67-3772 TCGA-67-6217 TCGA-69-7760 TCGA-69-7979 
        1305           31          573          422          202           89 
TCGA-69-7980 TCGA-69-A59K TCGA-71-6725 TCGA-73-4662 TCGA-73-4668 TCGA-73-4670 
         382          214           61          912          467          131 
TCGA-73-4676 TCGA-73-7499 TCGA-75-6214 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 
         164          519         1970         1973         1988         1950 
TCGA-78-7149 TCGA-78-7154 TCGA-78-7155 TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 
        1093         1948         1957          215         1950         1972 
TCGA-78-7539 TCGA-78-7542 TCGA-78-8640 TCGA-78-8655 TCGA-78-8662 TCGA-83-5908 
         327         1952         1949         1981         1964          824 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 
        1959          630          422          591         1963          508 
TCGA-86-8054 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8279 TCGA-86-8280 
         745           10           24          479          482           16 
TCGA-86-8358 TCGA-86-8359 TCGA-86-8668 TCGA-86-8673 TCGA-91-6829 TCGA-91-6836 
          19           26           45          455         1940          417 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-95-7039 TCGA-95-7562 TCGA-95-7567 
         372          842          224           34         1973          568 
TCGA-95-7947 TCGA-95-8039 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8547 
         477          830           84          775          181          148 
TCGA-99-8025 TCGA-J2-8192 TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A50W TCGA-L9-A7SV 
         427          154          287          578          266          111 
TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SW TCGA-MP-A4T2 
         102          827         1175           84         1967         1951 
TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TK 
        1954         1957         1944         1970         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-38-4626 
         761          730          457           30           14         1962 
TCGA-38-4627 TCGA-38-4630 TCGA-38-7271 TCGA-38-A44F TCGA-44-2655 TCGA-44-2657 
        1147         1073         1971          133         1324          400 
TCGA-44-2661 TCGA-44-2665 TCGA-44-2666 TCGA-44-3396 TCGA-44-3398 TCGA-44-4112 
         741         1301           97         1130         1163          722 
TCGA-44-5645 TCGA-44-6145 TCGA-44-6146 TCGA-44-6148 TCGA-44-6774 TCGA-44-6776 
         383          328          302          704          658         1938 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7671 TCGA-44-7672 TCGA-44-A479 TCGA-44-A47A 
         444          366          535          719          486          466 
TCGA-44-A47F TCGA-44-A47G TCGA-44-A4SS TCGA-49-4486 TCGA-49-4494 TCGA-49-4506 
         337          351          415         1932         1081          999 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-49-6761 
        1700          445          369          890          522          354 
TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 
        2174         2146          785          944         1499          246 
TCGA-50-5932 TCGA-50-5942 TCGA-50-8460 TCGA-53-7626 TCGA-55-6642 TCGA-55-6980 
        1091          883          105         1971          993           67 
TCGA-55-6983 TCGA-55-6986 TCGA-55-6987 TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 
        1826         2151         1170           18           35          121 
TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7728 TCGA-55-7815 TCGA-55-7911 
          95          705           39           24           54           21 
TCGA-55-7914 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 TCGA-55-8097 TCGA-55-8205 
           3          462          100            6           15           33 
TCGA-55-8206 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 
          46          674          216           44           23           29 
TCGA-55-8508 TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
          15            3          146           49          106           33 
TCGA-55-A48Y TCGA-55-A492 TCGA-55-A493 TCGA-64-1680 TCGA-64-5781 TCGA-64-5815 
          42            1           28         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-73-4677 TCGA-73-7498 TCGA-73-A9RS TCGA-75-7025 TCGA-78-7150 TCGA-78-7152 
          38          621          305         1967         1963         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-86-8585 TCGA-86-8671 TCGA-86-8672 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4P7 
          35           18           15          405           10           14 
TCGA-86-A4P8 TCGA-91-6830 TCGA-91-6835 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 
          39           60           79           35          505          174 
TCGA-91-A4BC TCGA-91-A4BD TCGA-93-7347 TCGA-93-7348 TCGA-95-7944 TCGA-95-A4VK 
          44          218          297          127          377          121 
TCGA-95-A4VN TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         553          964         1965         1932         1332           22 
TCGA-97-8172 TCGA-97-8174 TCGA-97-8175 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 
         182         1965           87          147          115          197 
TCGA-97-A4M7 TCGA-99-7458 TCGA-99-8028 TCGA-J2-8194 TCGA-J2-A4AE TCGA-J2-A4AG 
         271          392          459          114          282          238 
TCGA-L4-A4E6 TCGA-L9-A743 TCGA-MP-A4T7 TCGA-MP-A4T9 TCGA-MP-A4TA TCGA-MP-A4TH 
         435          312         1954         1980         1951          142 
TCGA-MP-A4TI TCGA-MP-A5C7 TCGA-S2-AA1A 
        1955         1490          121 

$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-35-4122 TCGA-35-5375 TCGA-38-4625 TCGA-38-4628 TCGA-44-3918 TCGA-44-5643 
         225          264         1952         1492         1036         1013 
TCGA-44-6147 TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7670 TCGA-44-8119 
         845         1864          592          557          882           99 
TCGA-44-A47B TCGA-49-4510 TCGA-50-5051 TCGA-50-5935 TCGA-50-5941 TCGA-50-7109 
         287          896          455          653          567          255 
TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 TCGA-55-6969 TCGA-55-6971 TCGA-55-7570 
         424          280           87         1239           25            6 
TCGA-55-7903 TCGA-55-7907 TCGA-55-8085 TCGA-55-8092 TCGA-55-8507 TCGA-55-8615 
          19           16           33           26            8           15 
TCGA-55-A494 TCGA-62-8398 TCGA-62-A46V TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 
           5         1970         2199          628         1189         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-69-7764 TCGA-69-7973 TCGA-69-8255 
          62          864          610          414          230          129 
TCGA-73-4659 TCGA-73-4666 TCGA-73-4675 TCGA-75-7027 TCGA-75-7031 TCGA-78-7148 
         711          800           40         1956         1965         1944 
TCGA-78-7159 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-80-5608 TCGA-86-7701 
        1221         1937         1965         1949         1972           11 
TCGA-86-8669 TCGA-86-A4D0 TCGA-91-6828 TCGA-91-6831 TCGA-91-7771 TCGA-91-8499 
          34           30          323          310          492           36 
TCGA-93-8067 TCGA-95-7043 TCGA-95-7948 TCGA-95-A4VP TCGA-97-8171 TCGA-97-8179 
         186            2          476          605          107           15 
TCGA-99-8032 TCGA-99-8033 TCGA-L9-A443 TCGA-L9-A444 TCGA-MP-A4SV TCGA-MP-A4TE 
          44          170          116            6         1946         1970 

subtype1 subtype2 subtype3 
       2        1        2 
subtype1 subtype2 subtype3 
    6443     2174     2199 
subtype1 subtype2 subtype3 
     578      426      484 
[1] "2.0 - 6443.0 (578.0)" "1.0 - 2174.0 (426.0)" "2.0 - 2199.0 (484.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       3       32       55        24        29         25          6
  subtype2       1       60       56        19        31         25          3
  subtype3       1       24       21         6        10         18          2
          vv
clus       STAGE IV
  subtype1       11
  subtype2        7
  subtype3        6
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           3        1        1
  STAGE IA         32       60       24
  STAGE IB         55       56       21
  STAGE IIA        24       19        6
  STAGE IIB        29       31       10
  STAGE IIIA       25       25       18
  STAGE IIIB        6        3        2
  STAGE IV         11        7        6
[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  48 113  18   6
  subtype2  72 107  15   9
  subtype3  27  47   9   3
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       48       72       27
  T2      113      107       47
  T3       18       15        9
  T4        6        9        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 112  40    31
  subtype2 132  40    26
  subtype3  57  11    17
D3V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         112      132       57
  N1          40       40       11
  N2+N3       31       26       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 125   8   0   3  47
  subtype2 141   5   0   1  54
  subtype3  60   5   1   0  22
D3V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       125      141       60
  M1         8        5        5
  M1A        0        0        1
  M1B        3        1        0
  MX        47       54       22
[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 104  81
  subtype2 116  87
  subtype3  35  53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  104   81
  subtype2  116   87
  subtype3   35   53
        clus
vv       subtype1 subtype2 subtype3
  FEMALE      104      116       35
  MALE         81       87       53
[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                                35
  subtype2                          4                                42
  subtype3                          5                                17
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                126
  subtype2                                                119
  subtype3                                                 58
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          2
  subtype2                                          3
  subtype3                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             7
  subtype2                                            11
  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                             4
  subtype2                            2                            10
  subtype3                            0                             5
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               1
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             3
  subtype3                                             1
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            6
  subtype3                            1
D3V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                6        4        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        35       42       17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      126      119       58
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        3        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             7       11        1
  LUNG CLEAR CELL ADENOCARCINOMA                            1        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        3        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        2        0
  LUNG PAPILLARY ADENOCARCINOMA                             4       10        5
  LUNG SIGNET RING ADENOCARCINOMA                           0        1        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        3        1
  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   5 180
  subtype2  10 193
  subtype3   6  82
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  180
  subtype2   10  193
  subtype3    6   82
     clus
vv    subtype1 subtype2 subtype3
  NO         5       10        6
  YES      180      193       82
[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 133   6   1  10
  subtype2 138   4   2   7
  subtype3  56   2   1   4
D3V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      133      138       56
  R1        6        4        2
  R2        1        2        1
  RX       10        7        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                        16
  subtype2                                0     1                        14
  subtype3                                0     2                         5
          vv
clus       WHITE
  subtype1   139
  subtype2   161
  subtype3    67
D3V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   3        1        2
  BLACK OR AFRICAN AMERICAN              16       14        5
  WHITE                                 139      161       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   3 133
  subtype2   1 152
  subtype3   3  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  133
  subtype2    1  152
  subtype3    3   60
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        3
  NOT HISPANIC OR LATINO      133      152       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 63 14
  subtype2 79 24
  subtype3 77 18
  subtype4 73 16
subtype1 subtype2 subtype3 subtype4 
      77      103       95       89 
subtype1 subtype2 subtype3 subtype4 
      14       24       18       16 
$subtype1
TCGA-05-4384 TCGA-05-5423 TCGA-05-5715 TCGA-38-6178 TCGA-44-2665 TCGA-44-2666 
         426          151           62          448         1301           97 
TCGA-44-5645 TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-7659 TCGA-44-A47F 
         383          302          704         1938          444          337 
TCGA-49-4512 TCGA-50-5932 TCGA-50-5935 TCGA-50-5942 TCGA-50-5944 TCGA-50-8460 
         157         1091          653          883          764          105 
TCGA-53-7626 TCGA-55-6543 TCGA-55-6972 TCGA-55-6983 TCGA-55-6985 TCGA-55-6986 
        1971            2         1475         1826         1233         2151 
TCGA-55-7573 TCGA-55-7725 TCGA-55-8087 TCGA-55-8091 TCGA-55-8097 TCGA-55-8206 
           4           39          462          600           15           46 
TCGA-55-8207 TCGA-55-8512 TCGA-55-8513 TCGA-55-A492 TCGA-62-8395 TCGA-62-8397 
          66            3          146            1         1216         1289 
TCGA-64-5778 TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7763 
        1305          174          141          422          202          690 
TCGA-69-8253 TCGA-69-8254 TCGA-73-7498 TCGA-75-7025 TCGA-78-7158 TCGA-78-7162 
         100           77          621         1967         1963         1940 
TCGA-78-7163 TCGA-78-7537 TCGA-80-5607 TCGA-86-7714 TCGA-86-8056 TCGA-86-8280 
        1950         1944         1965         1968         1963           16 
TCGA-86-8668 TCGA-91-6849 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD TCGA-93-7348 
          45           35          505          174          218          127 
TCGA-95-7948 TCGA-97-7546 TCGA-97-7547 TCGA-97-7941 TCGA-97-8171 TCGA-97-8172 
         476          964         1965           22          107          182 
TCGA-97-8174 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-7458 TCGA-J2-A4AE 
        1965          147          115          197          392          282 
TCGA-L9-A443 TCGA-L9-A50W TCGA-MP-A4T2 TCGA-MP-A4T7 TCGA-MP-A4TH 
         116          266         1951         1954          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-55-7570 TCGA-55-7910 TCGA-55-7995 TCGA-55-8085 
          87          993            6          197            5           33 
TCGA-55-8094 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 
           4            8           15          202          536           15 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A494 TCGA-55-A4DF 
          66           42           29           48            5           47 
TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 TCGA-62-A471 TCGA-64-1681 TCGA-64-5774 
        1970         2696         1445         1246         1968         1959 
TCGA-64-5779 TCGA-69-7764 TCGA-69-7973 TCGA-69-7979 TCGA-69-7980 TCGA-73-7499 
         864          414          230           89          382          519 
TCGA-75-6214 TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7148 TCGA-78-7149 
        1970         1956         1965         1988         1944         1093 
TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 TCGA-78-7156 TCGA-78-7159 TCGA-78-7161 
        1963         1948         1957         1961         1221          215 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7536 TCGA-78-7633 TCGA-78-8640 
        1934         1937         1965         1949          994         1949 
TCGA-78-8662 TCGA-80-5608 TCGA-86-7713 TCGA-86-7955 TCGA-86-8054 TCGA-86-8075 
        1964         1972          422          508          745          479 
TCGA-86-8279 TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8669 TCGA-86-8674 
         482         1955           19           26           34          405 
TCGA-86-A4D0 TCGA-91-6829 TCGA-91-6831 TCGA-91-6840 TCGA-91-6847 TCGA-91-7771 
          30         1940          310          372          842          492 
TCGA-91-8499 TCGA-95-7043 TCGA-95-7947 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-8179 
          36            2          477          121          605           15 
TCGA-99-8032 TCGA-J2-8194 TCGA-J2-A4AD TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4TF 
          44          114          287          111         1175         1970 
TCGA-MP-A5C7 
        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-44-3917 TCGA-44-3918 
         730          670           30         1357         1183         1036 
TCGA-44-4112 TCGA-44-7662 TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A47B 
         722          218          385          260          466          287 
TCGA-49-6745 TCGA-49-6761 TCGA-50-5933 TCGA-50-6597 TCGA-55-6712 TCGA-55-7227 
         522          354         2370         1015           24           53 
TCGA-55-7281 TCGA-55-7283 TCGA-55-7284 TCGA-55-7576 TCGA-55-7727 TCGA-55-7815 
          18           35          121           40           34           54 
TCGA-55-7903 TCGA-55-7907 TCGA-55-7911 TCGA-55-7914 TCGA-55-7994 TCGA-55-8090 
          19           16           21            3           31            6 
TCGA-55-8092 TCGA-55-8205 TCGA-55-8506 TCGA-55-8511 TCGA-55-8616 TCGA-55-A4DG 
          26           33           11            9           48          162 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A472 TCGA-64-5775 TCGA-64-5815 TCGA-69-7765 
        2067         2199          910           62          866          165 
TCGA-69-7974 TCGA-69-A59K TCGA-71-6725 TCGA-71-8520 TCGA-73-4658 TCGA-73-4676 
         184          214           61            3         1600          164 
TCGA-78-7145 TCGA-78-7147 TCGA-78-7152 TCGA-78-7153 TCGA-78-7535 TCGA-78-7539 
        1973         1950         1202          760         1972          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-8655 TCGA-78-8660 TCGA-83-5908 TCGA-86-6851 
         881         1952         1981         1954          824         1959 
TCGA-86-7701 TCGA-86-8073 TCGA-86-8074 TCGA-86-8278 TCGA-86-8672 TCGA-86-8673 
          11           13           24          476           15          455 
TCGA-86-A456 TCGA-91-6828 TCGA-91-6836 TCGA-93-8067 TCGA-95-7039 TCGA-95-7562 
          10          323          417          186           34         1973 
TCGA-95-7567 TCGA-95-8039 TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 
         568          830           84          775          181           87 
TCGA-97-8547 TCGA-97-A4M7 TCGA-99-8025 TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 
         148          271          427          578            6          827 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T8 TCGA-MP-A4TE 
          84         1946         1967         1957         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-44-7672 TCGA-44-A479 TCGA-44-A47G TCGA-44-A4SS 
        1978          366          719          486          351          415 
TCGA-49-4514 TCGA-49-6743 TCGA-49-6744 TCGA-50-5045 TCGA-50-5049 TCGA-50-5055 
        1700          369          890         2174         2146          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5930 TCGA-50-5941 TCGA-55-6969 TCGA-55-6971 
         944         1499          282          567         1239           25 
TCGA-55-6980 TCGA-55-6987 TCGA-55-7574 TCGA-55-7724 TCGA-55-7726 TCGA-55-7728 
          67         1170           95          705           39           24 
TCGA-55-7816 TCGA-55-8089 TCGA-55-8096 TCGA-55-8208 TCGA-55-8299 TCGA-55-8301 
          44          100           47          674          216           44 
TCGA-55-8302 TCGA-55-8505 TCGA-55-8510 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
          23           29          228           49          106           33 
TCGA-55-A491 TCGA-55-A493 TCGA-64-1679 TCGA-64-5781 TCGA-69-7761 TCGA-69-7978 
        1952           28         1686         1559          186           70 
TCGA-69-8255 TCGA-78-7160 TCGA-78-8648 TCGA-86-7711 TCGA-86-7953 TCGA-86-7954 
         129          678         1971          630          591         1963 
TCGA-86-8055 TCGA-86-8076 TCGA-86-8585 TCGA-86-8671 TCGA-86-A4P7 TCGA-86-A4P8 
          10          489           35           18           14           39 
TCGA-91-6830 TCGA-91-6835 TCGA-91-6848 TCGA-91-A4BC TCGA-93-7347 TCGA-95-7944 
          60           79          224           44          297          377 
TCGA-95-A4VN TCGA-97-7552 TCGA-97-7553 TCGA-99-8028 TCGA-99-8033 TCGA-J2-8192 
         553         1932         1332          459          170          154 
TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A743 TCGA-L9-A8F4 TCGA-MP-A4T4 TCGA-MP-A4T9 
         238          435          312          102         1954         1980 
TCGA-MP-A4TA TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK TCGA-S2-AA1A 
        1951         1944         1955         1971          121 

subtype1 subtype2 subtype3 subtype4 
       1        2        3       10 
subtype1 subtype2 subtype3 subtype4 
    2151     2696     2370     2174 
subtype1 subtype2 subtype3 subtype4 
     392      492      354      415 
[1] "1.0 - 2151.0 (392.0)"  "2.0 - 2696.0 (492.0)"  "3.0 - 2370.0 (354.0)" 
[4] "10.0 - 2174.0 (415.0)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       29       22         7        12         11          1
  subtype2       2       25       30        15        13         19          5
  subtype3       1       15       35        12        21         15          2
  subtype4       0       32       31        12        13         15          1
          vv
clus       STAGE IV
  subtype1        3
  subtype2        8
  subtype3        5
  subtype4        3
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        2        1        0
  STAGE IA         29       25       15       32
  STAGE IB         22       30       35       31
  STAGE IIA         7       15       12       12
  STAGE IIB        12       13       21       13
  STAGE IIIA       11       19       15       15
  STAGE IIIB        1        5        2        1
  STAGE IV          3        8        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 37 40  7  3
  subtype2 31 69 11  5
  subtype3 23 65 13  5
  subtype4 40 58  5  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       37       31       23       40
  T2       40       69       65       58
  T3        7       11       13        5
  T4        3        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       N0 N1 N2+N3
  subtype1 60 13    11
  subtype2 73 19    23
  subtype3 67 25    14
  subtype4 66 21    16
D4V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          60       73       67       66
  N1          13       19       25       21
  N2+N3       11       23       14       16
[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 53  1   1   1 28
  subtype2 80  5   0   3 28
  subtype3 73  4   0   0 29
  subtype4 66  2   0   0 39
D4V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        53       80       73       66
  M1         1        5        4        2
  M1A        1        0        0        0
  M1B        1        3        0        0
  MX        28       28       29       39
[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 55 32
  subtype2 49 68
  subtype3 50 56
  subtype4 69 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55   32
  subtype2   49   68
  subtype3   50   56
  subtype4   69   38
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       55       49       50       69
  MALE         32       68       56       38
[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                          6                                18
  subtype2                          7                                25
  subtype3                          1                                25
  subtype4                          1                                11
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 41
  subtype2                                                 73
  subtype3                                                 69
  subtype4                                                 79
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          2
  subtype2                                          0
  subtype3                                          1
  subtype4                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            10
  subtype2                                             2
  subtype3                                             4
  subtype4                                             3
          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                             5
  subtype2                            0                             6
  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                                             3
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            2
  subtype2                            3
  subtype3                            0
  subtype4                            2
D4V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                6        7        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        18       25       25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       41       73       69
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            10        2        4
  LUNG CLEAR CELL ADENOCARCINOMA                            0        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        2
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             5        6        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                        11
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       79
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             3
  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             3
  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  85
  subtype2   5 112
  subtype3   3 103
  subtype4   8  99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   85
  subtype2    5  112
  subtype3    3  103
  subtype4    8   99
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        5        3        8
  YES       85      112      103       99
[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 57  3  0  3
  subtype2 80  4  0  5
  subtype3 77  2  0  7
  subtype4 62  1  1  3
D4V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       57       80       77       62
  R1        3        4        2        1
  R2        0        0        0        1
  RX        3        5        7        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         6    69
  subtype2     0                         8    97
  subtype3     4                         8    76
  subtype4     0                         9    89
D4V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        0        4        0
  BLACK OR AFRICAN AMERICAN        6        8        8        9
  WHITE                           69       97       76       89
[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 66
  subtype2  3 83
  subtype3  0 74
  subtype4  3 80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   66
  subtype2    3   83
  subtype3    0   74
  subtype4    3   80
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        3        0        3
  NOT HISPANIC OR LATINO       66       83       74       80
[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 29 12
  subtype2 45 12
  subtype3 38 19
subtype1 subtype2 subtype3 
      41       57       57 
subtype1 subtype2 subtype3 
      12       12       19 
$subtype1
TCGA-05-4249 TCGA-05-4384 TCGA-05-4426 TCGA-35-3615 TCGA-38-4626 TCGA-44-2657 
        1523          426          791           14         1962          400 
TCGA-44-7659 TCGA-44-7671 TCGA-49-4486 TCGA-49-4510 TCGA-49-6742 TCGA-49-6744 
         444          535         1932          896          445          890 
TCGA-50-5051 TCGA-50-5932 TCGA-53-7626 TCGA-64-1680 TCGA-69-7761 TCGA-69-7763 
         455         1091         1971         1126          186          690 
TCGA-69-7764 TCGA-73-4659 TCGA-73-4676 TCGA-73-7498 TCGA-78-7147 TCGA-78-7156 
         414          711          164          621         1950         1961 
TCGA-78-7158 TCGA-78-7161 TCGA-78-7162 TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 
        1963          215         1940         1937         1944          327 
TCGA-78-7633 TCGA-80-5607 TCGA-86-7713 TCGA-91-6849 TCGA-91-7771 TCGA-95-7947 
         994         1965          422           35          492          477 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7937 TCGA-97-7941 TCGA-99-7458 
         964         1332          181           22          392 

$subtype2
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-05-5420 TCGA-05-5423 TCGA-05-5429 TCGA-38-6178 TCGA-44-2656 
         761          457          151           30          448         1429 
TCGA-44-2661 TCGA-44-2665 TCGA-44-3919 TCGA-44-5645 TCGA-44-6146 TCGA-44-6147 
         741         1301          190          383          302          845 
TCGA-44-6775 TCGA-44-6776 TCGA-44-6777 TCGA-49-4501 TCGA-49-4505 TCGA-49-4512 
         705         1938         1942         1421          428          157 
TCGA-49-6745 TCGA-50-5049 TCGA-50-5068 TCGA-50-5941 TCGA-50-5942 TCGA-50-5944 
         522         2146         1499          567          883          764 
TCGA-50-6597 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-6712 TCGA-55-7573 
        1015          701         1178         1375           24            4 
TCGA-55-7911 TCGA-64-1679 TCGA-64-1681 TCGA-64-5778 TCGA-64-5781 TCGA-67-6215 
          21         1686         1968         1305         1559          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-78-7535 TCGA-86-6851 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 
        1973         1972         1959          323         1940           79 
TCGA-91-6840 TCGA-95-7039 TCGA-95-7948 
         372           34          476 

$subtype3
TCGA-05-4420 TCGA-05-5715 TCGA-38-4627 TCGA-44-3396 TCGA-44-4112 TCGA-44-6145 
         912           62         1147         1130          722          328 
TCGA-44-6774 TCGA-44-6779 TCGA-44-7662 TCGA-44-7670 TCGA-44-7672 TCGA-49-4494 
         658         1978          218          882          719         1081 
TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6761 TCGA-50-5072 TCGA-50-5931 
         999          268         1700          354          246          267 
TCGA-50-5933 TCGA-50-7109 TCGA-53-7813 TCGA-55-6543 TCGA-55-6971 TCGA-55-7574 
        2370          255          424            2           25           95 
TCGA-55-7728 TCGA-55-7815 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 
          24           54         1728          628         1189         1959 
TCGA-67-3771 TCGA-69-7765 TCGA-73-4658 TCGA-73-7499 TCGA-75-6214 TCGA-75-7027 
         610          165         1600          519         1970         1956 
TCGA-78-7148 TCGA-78-7149 TCGA-78-7150 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1944         1093         1963         1202          760         1948 
TCGA-78-7155 TCGA-78-7159 TCGA-78-7160 TCGA-78-7163 TCGA-78-7166 TCGA-78-7536 
        1957         1221          678         1950         1934         1949 
TCGA-78-7540 TCGA-78-7542 TCGA-80-5608 TCGA-91-6847 TCGA-93-7348 TCGA-95-7043 
         881         1952         1972          842          127            2 
TCGA-95-7567 TCGA-97-7552 TCGA-97-7554 
         568         1932          775 

subtype1 subtype2 subtype3 
      14        4        2 
subtype1 subtype2 subtype3 
    1971     2146     2370 
subtype1 subtype2 subtype3 
     690      701      881 
[1] "14.0 - 1971.0 (690.0)" "4.0 - 2146.0 (701.0)"  "2.0 - 2370.0 (881.0)" 
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       0       12        9         6         7          6          1
  subtype2       0       18       20         5        12         14          2
  subtype3       1       11       23         4         6         13          4
          vv
clus       STAGE IV
  subtype1        3
  subtype2        2
  subtype3        2
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        1
  STAGE IA         12       18       11
  STAGE IB          9       20       23
  STAGE IIA         6        5        4
  STAGE IIB         7       12        6
  STAGE IIIA        6       14       13
  STAGE IIIB        1        2        4
  STAGE IV          3        2        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 12 27  2  3
  subtype2 20 43  7  3
  subtype3 15 38  4  6
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       12       20       15
  T2       27       43       38
  T3        2        7        4
  T4        3        3        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2+N3
  subtype1 27  9     7
  subtype2 40 15    14
  subtype3 39 10    14
D5V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          27       40       39
  N1           9       15       10
  N2+N3        7       14       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 30  3 11
  subtype2 57  2 12
  subtype3 49  1 14
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       30       57       49
  M1        3        2        1
  MX       11       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"
D5V7, binary
          cls
clus        0  1
  subtype1 20 24
  subtype2 48 25
  subtype3 37 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   24
  subtype2   48   25
  subtype3   37   27
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       48       37
  MALE         24       25       27
[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                          3                                15
  subtype2                          2                                14
  subtype3                          0                                14
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 17
  subtype2                                                 51
  subtype3                                                 43
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          0
  subtype3                                          3
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             5
  subtype2                                             2
  subtype3                                             1
          vv
clus       LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  subtype1                                  1                            0
  subtype2                                  1                            1
  subtype3                                  0                            0
          vv
clus       LUNG PAPILLARY ADENOCARCINOMA MUCINOUS (COLLOID) CARCINOMA
  subtype1                             2                            1
  subtype2                             1                            1
  subtype3                             2                            1
D5V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                3        2        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        15       14       14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       17       51       43
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        0        3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             5        2        1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        1        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        1        0
  LUNG PAPILLARY ADENOCARCINOMA                             2        1        2
  MUCINOUS (COLLOID) CARCINOMA                              1        1        1
[1] 9 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  2 42
  subtype2  3 70
  subtype3  7 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   42
  subtype2    3   70
  subtype3    7   57
     clus
vv    subtype1 subtype2 subtype3
  NO         2        3        7
  YES       42       70       57
[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 30  3  0  1
  subtype2 47  3  1  4
  subtype3 42  2  0  0
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       30       47       42
  R1        3        3        2
  R2        0        1        0
  RX        1        4        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         3    36
  subtype2     2                         1    52
  subtype3     0                         2    53
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        2        0
  BLACK OR AFRICAN AMERICAN        3        1        2
  WHITE                           36       52       53
[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  0 28
  subtype2  1 42
  subtype3  1 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   28
  subtype2    1   42
  subtype3    1   36
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        1        1
  NOT HISPANIC OR LATINO       28       42       36
[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 27  6
  subtype2 20 11
  subtype3 23 10
  subtype4 17 11
  subtype5 25  5
subtype1 subtype2 subtype3 subtype4 subtype5 
      33       31       33       28       30 
subtype1 subtype2 subtype3 subtype4 subtype5 
       6       11       10       11        5 
$subtype1
TCGA-05-4249 TCGA-05-4405 TCGA-05-4410 TCGA-05-4430 TCGA-05-5423 TCGA-44-2656 
        1523          610         1958          761          151         1429 
TCGA-44-2661 TCGA-44-3919 TCGA-44-5645 TCGA-44-6147 TCGA-44-6776 TCGA-49-4501 
         741          190          383          845         1938         1421 
TCGA-49-4505 TCGA-49-4512 TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-55-1592 
         428          157          883          764         1015          701 
TCGA-55-7573 TCGA-55-7815 TCGA-55-7911 TCGA-64-1680 TCGA-64-1681 TCGA-67-6215 
           4           54           21         1126         1968          174 
TCGA-67-6216 TCGA-67-6217 TCGA-71-6725 TCGA-73-4675 TCGA-78-7147 TCGA-91-6828 
         141          422           61           40         1950          323 
TCGA-91-6835 TCGA-91-6840 TCGA-95-7948 
          79          372          476 

$subtype2
TCGA-05-4384 TCGA-05-4396 TCGA-05-4417 TCGA-05-4420 TCGA-05-4422 TCGA-35-3615 
         426         1947          455          912          365           14 
TCGA-44-7671 TCGA-49-4486 TCGA-49-4494 TCGA-49-4510 TCGA-50-5051 TCGA-55-6543 
         535         1932         1081          896          455            2 
TCGA-55-6971 TCGA-64-5774 TCGA-67-3771 TCGA-69-7763 TCGA-73-7498 TCGA-78-7148 
          25         1959          610          690          621         1944 
TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7156 TCGA-78-7160 TCGA-78-7161 
        1093         1202          760         1961          678          215 
TCGA-78-7162 TCGA-78-7163 TCGA-78-7167 TCGA-78-7536 TCGA-78-7537 TCGA-78-7633 
        1940         1950         1937         1949         1944          994 
TCGA-86-7713 
         422 

$subtype3
TCGA-05-4398 TCGA-05-5715 TCGA-38-4627 TCGA-38-6178 TCGA-44-2665 TCGA-44-4112 
        1431           62         1147          448         1301          722 
TCGA-44-6145 TCGA-44-6775 TCGA-44-6777 TCGA-49-6745 TCGA-49-6761 TCGA-50-5049 
         328          705         1942          522          354         2146 
TCGA-50-5068 TCGA-50-5931 TCGA-50-5933 TCGA-50-5941 TCGA-55-1594 TCGA-55-1596 
        1499          267         2370          567         1178         1375 
TCGA-55-6712 TCGA-64-1676 TCGA-64-1679 TCGA-64-5778 TCGA-69-7760 TCGA-75-7031 
          24         1728         1686         1305          202         1965 
TCGA-78-7145 TCGA-78-7155 TCGA-78-7535 TCGA-86-6851 TCGA-91-6829 TCGA-91-6847 
        1973         1957         1972         1959         1940          842 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7567 
          34            2          568 

$subtype4
TCGA-05-5429 TCGA-44-3396 TCGA-44-6146 TCGA-44-6774 TCGA-44-6779 TCGA-44-7662 
          30         1130          302          658         1978          218 
TCGA-44-7670 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-50-5072 TCGA-50-7109 
         882          999          268         1700          246          255 
TCGA-53-7813 TCGA-55-7728 TCGA-64-1677 TCGA-64-1678 TCGA-64-5781 TCGA-69-7761 
         424           24          628         1189         1559          186 
TCGA-75-6214 TCGA-75-7027 TCGA-78-7150 TCGA-78-7154 TCGA-78-7159 TCGA-78-7166 
        1970         1956         1963         1948         1221         1934 
TCGA-78-7540 TCGA-78-7542 TCGA-95-7947 TCGA-97-7552 
         881         1952          477         1932 

$subtype5
TCGA-05-4426 TCGA-05-5420 TCGA-38-4626 TCGA-44-2657 TCGA-44-7659 TCGA-44-7672 
         791          457         1962          400          444          719 
TCGA-49-6742 TCGA-49-6744 TCGA-50-5932 TCGA-53-7626 TCGA-55-7574 TCGA-69-7764 
         445          890         1091         1971           95          414 
TCGA-69-7765 TCGA-73-4658 TCGA-73-4659 TCGA-73-4676 TCGA-73-7499 TCGA-78-7158 
         165         1600          711          164          519         1963 
TCGA-78-7539 TCGA-80-5607 TCGA-80-5608 TCGA-91-6849 TCGA-91-7771 TCGA-93-7348 
         327         1965         1972           35          492          127 
TCGA-97-7546 TCGA-97-7553 TCGA-97-7554 TCGA-97-7937 TCGA-97-7941 TCGA-99-7458 
         964         1332          775          181           22          392 

subtype1 subtype2 subtype3 subtype4 subtype5 
       4        2        2       24       22 
subtype1 subtype2 subtype3 subtype4 subtype5 
    1968     1961     2370     1978     1972 
subtype1 subtype2 subtype3 subtype4 subtype5 
   476.0    896.0   1178.0    940.5    505.5 
[1] "4.0 - 1968.0 (476.0)"  "2.0 - 1961.0 (896.0)"  "2.0 - 2370.0 (1178.0)"
[4] "24.0 - 1978.0 (940.5)" "22.0 - 1972.0 (505.5)"
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       0       17       12         3         3          3          0
  subtype2       0        7       12         1         3          5          2
  subtype3       0        5       14         4         9          9          3
  subtype4       1        3        8         2         6         10          1
  subtype5       0        9        6         5         4          6          1
          vv
clus       STAGE IV
  subtype1        2
  subtype2        3
  subtype3        1
  subtype4        0
  subtype5        1
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        0        0        1        0
  STAGE IA         17        7        5        3        9
  STAGE IB         12       12       14        8        6
  STAGE IIA         3        1        4        2        5
  STAGE IIB         3        3        9        6        4
  STAGE IIIA        3        5        9       10        6
  STAGE IIIB        0        2        3        1        1
  STAGE IV          2        3        1        0        1
[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 17 22  1  0
  subtype2  6 21  2  4
  subtype3  8 29  3  4
  subtype4  6 18  6  1
  subtype5 10 18  1  3
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       17        6        8        6       10
  T2       22       21       29       18       18
  T3        1        2        3        6        1
  T4        0        4        4        1        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       N0 N1 N2+N3
  subtype1 27  7     3
  subtype2 23  4     6
  subtype3 22 11    11
  subtype4 15  6     9
  subtype5 19  6     6
D6V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          27       23       22       15       19
  N1           7        4       11        6        6
  N2+N3        3        6       11        9        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 MX
  subtype1 31  2  6
  subtype2 28  3  2
  subtype3 32  1 11
  subtype4 25  0  6
  subtype5 20  0 12
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       31       28       32       25       20
  M1        2        3        1        0        0
  MX        6        2       11        6       12
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 30 10
  subtype2 11 22
  subtype3 27 18
  subtype4 16 15
  subtype5 21 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   10
  subtype2   11   22
  subtype3   27   18
  subtype4   16   15
  subtype5   21   11
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       30       11       27       16       21
  MALE         10       22       18       15       11
[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"
D6V8, continuous
[1] "Remove cluster labels:" "subtype2"               "subtype3"              
[4] "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 
       3        2        2        1        6 
[1] "subtype1" "subtype1" "subtype1" "subtype5" "subtype5" "subtype5" "subtype5"
[8] "subtype5" "subtype5"
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          1                                 7
  subtype2                          0                                17
  subtype3                          1                                 8
  subtype4                          1                                 4
  subtype5                          2                                 7
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 29
  subtype2                                                 13
  subtype3                                                 33
  subtype4                                                 20
  subtype5                                                 16
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          1
  subtype3                                          0
  subtype4                                          2
  subtype5                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             1
  subtype2                                             1
  subtype3                                             2
  subtype4                                             1
  subtype5                                             3
          vv
clus       LUNG MICROPAPILLARY ADENOCARCINOMA LUNG MUCINOUS ADENOCARCINOMA
  subtype1                                  1                            0
  subtype2                                  0                            0
  subtype3                                  0                            0
  subtype4                                  0                            1
  subtype5                                  1                            0
          vv
clus       LUNG PAPILLARY ADENOCARCINOMA MUCINOUS (COLLOID) CARCINOMA
  subtype1                             1                            0
  subtype2                             1                            0
  subtype3                             0                            1
  subtype4                             1                            1
  subtype5                             2                            1
D6V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                1        0        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         7       17        8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       29       13       33
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        1        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1        1        2
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             1        1        0
  MUCINOUS (COLLOID) CARCINOMA                              0        0        1
                                                    clus
vv                                                   subtype4 subtype5
  LUNG ACINAR ADENOCARCINOMA                                1        2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                         4        7
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       20       16
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                2        0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1        3
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              1        0
  LUNG PAPILLARY ADENOCARCINOMA                             1        2
  MUCINOUS (COLLOID) CARCINOMA                              1        1
[1] 9 5
[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  2 38
  subtype2  1 32
  subtype3  3 42
  subtype4  4 27
  subtype5  2 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   38
  subtype2    1   32
  subtype3    3   42
  subtype4    4   27
  subtype5    2   30
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         2        1        3        4        2
  YES       38       32       42       27       30
[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"
D6V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 30  1  1  3
  subtype2 28  1  0  1
  subtype3 22  2  0  1
  subtype4 19  1  0  0
  subtype5 20  3  0  0
D6V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       30       28       22       19       20
  R1        1        1        2        1        3
  R2        1        0        0        0        0
  RX        3        1        1        0        0
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    30
  subtype2     0                         3    22
  subtype3     1                         0    38
  subtype4     0                         0    25
  subtype5     0                         2    26
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            1        0        1        0        0
  BLACK OR AFRICAN AMERICAN        1        3        0        0        2
  WHITE                           30       22       38       25       26
[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"
D6V14, binary
          cls
clus        0  1
  subtype1  0 27
  subtype2  0 11
  subtype3  1 28
  subtype4  1 16
  subtype5  0 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   27
  subtype2    0   11
  subtype3    1   28
  subtype4    1   16
  subtype5    0   24
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        0        1        1        0
  NOT HISPANIC OR LATINO       27       11       28       16       24
[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(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 84 30
  subtype2 79 17
  subtype3 40 20
  subtype4 77 14
  subtype5 41  3
subtype1 subtype2 subtype3 subtype4 subtype5 
     114       96       60       91       44 
subtype1 subtype2 subtype3 subtype4 subtype5 
      30       17       20       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-95-7562 TCGA-95-7567 TCGA-95-7948 
         417          224           34         1973          568          476 
TCGA-95-8494 TCGA-97-7554 TCGA-97-7937 TCGA-97-8547 TCGA-99-8028 TCGA-J2-8192 
          84          775          181          148          459          154 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N1 TCGA-MN-A4N4 TCGA-MN-A4N5 
         287          578            6          827         1175           84 
TCGA-MP-A4SV TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TI TCGA-MP-A4TK 
        1946         1954         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          462 
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          505 
TCGA-91-8497 TCGA-91-A4BD TCGA-93-7347 TCGA-95-8039 TCGA-97-7546 TCGA-97-7547 
         174          218          297          830          964         1965 
TCGA-97-7553 TCGA-97-8172 TCGA-97-8174 TCGA-97-8177 TCGA-97-8179 TCGA-97-A4M2 
        1332          182         1965          147           15          197 
TCGA-99-7458 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4SW TCGA-MP-A4TH 
         392          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 
         705           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-95-A4VP TCGA-97-8171 TCGA-99-8032 TCGA-J2-8194 TCGA-MP-A4T8 
           2          605          107           44          114         1957 
TCGA-MP-A5C7 
        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-55-8208 
        1499         1826         1233            4          600          674 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8616 TCGA-55-8621 TCGA-55-A48X 
           3          146          536           48          106           33 
TCGA-64-1680 TCGA-64-1681 TCGA-69-7974 TCGA-69-8254 TCGA-73-4675 TCGA-73-7499 
        1126         1968          184           77           40          519 
TCGA-75-7025 TCGA-78-7147 TCGA-86-8076 TCGA-86-8280 TCGA-91-6835 TCGA-93-7348 
        1967         1950          489           16           79          127 
TCGA-95-7947 TCGA-95-A4VN TCGA-97-7552 TCGA-97-7941 TCGA-97-8552 TCGA-97-A4M7 
         477          553         1932           22          115          271 
TCGA-99-8025 TCGA-L9-A443 
         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 
   544.5    424.0    451.0    508.0    483.0 
[1] "3.0 - 2370.0 (544.5)"  "1.0 - 2696.0 (424.0)"  "15.0 - 1997.0 (451.0)"
[4] "2.0 - 1972.0 (508.0)"  "3.0 - 1968.0 (483.0)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       2       21       39        17        26         21          4
  subtype2       0       41       29         9         9         12          1
  subtype3       0       11       17         2        17         17          3
  subtype4       1       22       35        10        11         13          3
  subtype5       1       18       12         5         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       41       11       22       18
  STAGE IB         39       29       17       35       12
  STAGE IIA        17        9        2       10        5
  STAGE IIB        26        9       17       11        5
  STAGE IIIA       21       12       17       13        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 87 12  6
  subtype2 48 45  6  4
  subtype3 14 43 10  4
  subtype4 26 64  8  3
  subtype5 24 21  5  1
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       31       48       14       26       24
  T2       87       45       43       64       21
  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 36    25
  subtype2 76 14    10
  subtype3 38 15    18
  subtype4 74 13    14
  subtype5 32 10     6
D7V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  N0          73       76       38       74       32
  N1          36       14       15       13       10
  N2+N3       25       10       18       14        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 94  5   0   0 36
  subtype2 71  2   0   0 30
  subtype3 53  5   0   0 14
  subtype4 70  4   1   2 24
  subtype5 31  2   0   1 15
D7V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        94       71       53       70       31
  M1         5        2        5        4        2
  M1A        0        0        0        1        0
  M1B        0        0        0        2        1
  MX        36       30       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 58
  subtype2 67 36
  subtype3 35 37
  subtype4 39 63
  subtype5 33 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78   58
  subtype2   67   36
  subtype3   35   37
  subtype4   39   63
  subtype5   33   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       78       67       35       39       33
  MALE         58       36       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                          6                                22
  subtype3                          1                                15
  subtype4                          5                                19
  subtype5                          1                                14
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                100
  subtype2                                                 58
  subtype3                                                 44
  subtype4                                                 66
  subtype5                                                 25
          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                                             1
          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        6        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        23       22       15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      100       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                                5        1
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        19       14
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       66       25
  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        1
  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   6 130
  subtype2   4  99
  subtype3   6  66
  subtype4   3  99
  subtype5   2  49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  130
  subtype2    4   99
  subtype3    6   66
  subtype4    3   99
  subtype5    2   49
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         6        4        6        3        2
  YES      130       99       66       99       49
[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  6
  subtype2 73  3  0  4
  subtype3 49  2  1  2
  subtype4 71  3  0  4
  subtype5 34  0  2  3
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       91       73       49       71       34
  R1        3        3        2        3        0
  R2        1        0        1        0        2
  RX        6        4        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                        10
  subtype2                                0     1                         5
  subtype3                                0     1                         1
  subtype4                                0     2                         8
  subtype5                                0     0                         3
          vv
clus       WHITE
  subtype1   105
  subtype2    86
  subtype3    56
  subtype4    74
  subtype5    41
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              10        5        1        8        3
  WHITE                                 105       86       56       74       41
[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   2 102
  subtype2   1  79
  subtype3   1  44
  subtype4   2  67
  subtype5   1  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  102
  subtype2    1   79
  subtype3    1   44
  subtype4    2   67
  subtype5    1   41
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        1        1        2        1
  NOT HISPANIC OR LATINO      102       79       44       67       41
[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 60 14
  subtype2 41  7
  subtype3 24  8
  subtype4 52 15
  subtype5 28 11
  subtype6 40  5
  subtype7 22 17
  subtype8 12  2
  subtype9 42  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      74       48       32       67       39       45       39       14 
subtype9 
      47 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      14        7        8       15       11        5       17        2 
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-95-8039 TCGA-97-7554 TCGA-97-7937 TCGA-97-8175 TCGA-97-8547 
         476          830          775          181           87          148 
TCGA-99-7458 TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L9-A444 TCGA-MN-A4N5 TCGA-MP-A4SV 
         392          238          578            6           84         1946 
TCGA-MP-A4T9 TCGA-MP-A4TK 
        1980         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          462           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          505          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-95-8494 
        1988         1952         1954          824          417           84 
TCGA-MP-A4TC TCGA-MP-A4TI 
        1944         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          705            5 
TCGA-55-8091 TCGA-55-8096 TCGA-55-8208 TCGA-55-8614 TCGA-55-8620 TCGA-55-A48Z 
         600           47          674          536           66           29 
TCGA-55-A491 TCGA-55-A4DF TCGA-64-1677 TCGA-64-1679 TCGA-64-5775 TCGA-67-3771 
        1952           47          628         1686           62          610 
TCGA-69-7979 TCGA-69-7980 TCGA-73-7499 TCGA-75-6214 TCGA-78-7147 TCGA-78-7155 
          89          382          519         1970         1950         1957 
TCGA-78-7163 TCGA-78-8640 TCGA-78-8662 TCGA-86-6851 TCGA-86-7711 TCGA-86-7953 
        1950         1949         1964         1959          630          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8055 TCGA-86-8074 TCGA-86-8075 TCGA-86-8358 
        1963          508           10           24          479           19 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6840 TCGA-91-6847 TCGA-91-6848 TCGA-91-8499 
        1940           60          372          842          224           36 
TCGA-95-7043 TCGA-95-7562 TCGA-95-7947 TCGA-J2-8192 TCGA-J2-A4AD TCGA-MN-A4N1 
           2         1973          477          154          287          827 
TCGA-MN-A4N4 
        1175 

$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-95-A4VP TCGA-99-8032 TCGA-MP-A4T8 
         605           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-95-A4VN TCGA-97-7553 TCGA-97-8552 TCGA-97-A4M2 TCGA-97-A4M7 TCGA-99-8025 
         553         1332          115          197          271          427 
TCGA-99-8028 TCGA-J2-A4AE TCGA-L9-A443 TCGA-MP-A4SW TCGA-MP-A4T4 
         459          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     1973     1965     1972     1997     1932 
subtype9 
    2174 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
   441.5    431.0    661.0    592.0    690.0    455.0    678.0    139.5 
subtype9 
   459.0 
[1] "3.0 - 2696.0 (441.5)"  "3.0 - 2151.0 (431.0)"  "23.0 - 2370.0 (661.0)"
[4] "2.0 - 1973.0 (592.0)"  "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 (459.0)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       18       28         3        17         11          0
  subtype2       0       15       16         7         6          5          1
  subtype3       0        6       12         5         7         10          3
  subtype4       1       21       23        13         5         10          2
  subtype5       0       15       13         2         6          3          2
  subtype6       1        6       15         6         5         12          1
  subtype7       0        7        8         1        12         12          2
  subtype8       0        1        7         0         6          1          0
  subtype9       1       24       10         6         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         18       15        6       21       15        6        7
  STAGE IB         28       16       12       23       13       15        8
  STAGE IIA         3        7        5       13        2        6        1
  STAGE IIB        17        6        7        5        6        5       12
  STAGE IIIA       11        5       10       10        3       12       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        6
  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 22 48  9  3
  subtype2 21 28  2  1
  subtype3  9 26  6  3
  subtype4 32 42  2  3
  subtype5 14 22  4  3
  subtype6  8 34  5  1
  subtype7  8 30  5  3
  subtype8  1  9  6  0
  subtype9 28 21  2  1
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1       22       21        9       32       14        8        8        1
  T2       48       28       26       42       22       34       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       21
  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 55 16    10
  subtype2 34 10     7
  subtype3 24  9    11
  subtype4 48 20    11
  subtype5 33  7     2
  subtype6 32  3    12
  subtype7 21 11    14
  subtype8 13  1     1
  subtype9 33 11     5
D8V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0          55       34       24       48       33       32       21       13
  N1          16       10        9       20        7        3       11        1
  N2+N3       10        7       11       11        2       12       14        1
       clus
vv      subtype9
  N0          33
  N1          11
  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 24
  subtype2 35  1   1   0 15
  subtype3 33  1   0   0 10
  subtype4 47  4   0   1 27
  subtype5 34  2   0   0  7
  subtype6 34  1   0   1 11
  subtype7 37  5   0   0  5
  subtype8  8  0   0   0  7
  subtype9 36  1   0   1 13
D8V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  M0        55       35       33       47       34       34       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        24       15       10       27        7       11        5        7
     clus
vv    subtype9
  M0        36
  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 32
  subtype2 45  7
  subtype3 20 24
  subtype4 45 35
  subtype5 14 29
  subtype6 20 28
  subtype7 18 29
  subtype8  6 10
  subtype9 34 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50   32
  subtype2   45    7
  subtype3   20   24
  subtype4   45   35
  subtype5   14   29
  subtype6   20   28
  subtype7   18   29
  subtype8    6   10
  subtype9   34   18
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       50       45       20       45       14       20       18
  MALE         32        7       24       35       29       28       29
        clus
vv       subtype8 subtype9
  FEMALE        6       34
  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       18        6       12        5        2 
subtype9 
      10 
 [1] "subtype3" "subtype3" "subtype4" "subtype4" "subtype2" "subtype9"
 [7] "subtype2" "subtype6" "subtype2" "subtype7" "subtype4" "subtype3"
[13] "subtype4" "subtype6" "subtype6" "subtype9" "subtype9" "subtype4"
[19] "subtype4" "subtype6" "subtype4" "subtype5" "subtype2" "subtype7"
[25] "subtype1" "subtype6" "subtype7" "subtype5" "subtype9" "subtype5"
[31] "subtype1" "subtype1" "subtype9" "subtype6" "subtype7" "subtype1"
[37] "subtype4" "subtype9" "subtype9" "subtype9" "subtype1" "subtype1"
[43] "subtype6" "subtype1" "subtype3" "subtype1" "subtype3" "subtype5"
[49] "subtype4" "subtype3" "subtype3" "subtype6" "subtype4" "subtype6"
[55] "subtype2" "subtype4" "subtype4" "subtype4" "subtype9" "subtype4"
[61] "subtype4" "subtype9" "subtype2" "subtype1" "subtype5" "subtype4"
[67] "subtype6" "subtype2" "subtype6" "subtype2" "subtype6" "subtype1"
[73] "subtype2" "subtype5" "subtype2" "subtype7" "subtype1" "subtype4"
[79] "subtype4" "subtype1"
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          3                                14
  subtype2                          3                                 9
  subtype3                          0                                 4
  subtype4                          2                                13
  subtype5                          1                                17
  subtype6                          4                                 8
  subtype7                          0                                13
  subtype8                          2                                 4
  subtype9                          0                                11
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 52
  subtype2                                                 30
  subtype3                                                 39
  subtype4                                                 59
  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                                             1
          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                                3        3        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        14        9        4
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       52       30       39
  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        4
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        13       17        8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       59       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        1
  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 80
  subtype2  2 50
  subtype3  3 41
  subtype4  1 79
  subtype5  0 43
  subtype6  3 45
  subtype7  5 42
  subtype8  0 16
  subtype9  5 47
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   80
  subtype2    2   50
  subtype3    3   41
  subtype4    1   79
  subtype5    0   43
  subtype6    3   45
  subtype7    5   42
  subtype8    0   16
  subtype9    5   47
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  NO         2        2        3        1        0        3        5        0
  YES       80       50       41       79       43       45       42       16
     clus
vv    subtype9
  NO         5
  YES       47
[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  4
  subtype2 40  2  0  0
  subtype3 30  0  2  0
  subtype4 47  3  2  6
  subtype5 27  0  0  3
  subtype6 35  1  0  1
  subtype7 33  2  0  2
  subtype8 11  0  0  0
  subtype9 38  0  0  3
D8V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  R0       57       40       30       47       27       35       33       11
  R1        3        2        0        3        0        1        2        0
  R2        0        0        2        2        0        0        0        0
  RX        4        0        0        6        3        1        2        0
    clus
vv   subtype9
  R0       38
  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                         7
  subtype5                                0     0                         4
  subtype6                                0     0                         3
  subtype7                                0     2                         0
  subtype8                                0     0                         0
  subtype9                                0     0                         4
          vv
clus       WHITE
  subtype1    62
  subtype2    42
  subtype3    34
  subtype4    62
  subtype5    33
  subtype6    36
  subtype7    38
  subtype8    11
  subtype9    44
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        7        4
  WHITE                                  62       42       34       62       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                                  36       38       11       44
[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 63
  subtype2  1 39
  subtype3  0 30
  subtype4  4 56
  subtype5  0 29
  subtype6  0 32
  subtype7  2 29
  subtype8  0 10
  subtype9  0 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   63
  subtype2    1   39
  subtype3    0   30
  subtype4    4   56
  subtype5    0   29
  subtype6    0   32
  subtype7    2   29
  subtype8    0   10
  subtype9    0   45
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        4        0        0
  NOT HISPANIC OR LATINO       63       39       30       56       29       32
                        clus
vv                       subtype7 subtype8 subtype9
  HISPANIC OR LATINO            2        0        0
  NOT HISPANIC OR LATINO       29       10       45
[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 124  30
  subtype2 152  37
  subtype3  53  19
subtype1 subtype2 subtype3 
     154      189       72 
subtype1 subtype2 subtype3 
      30       37       19 
$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-55-1595 TCGA-55-6712 TCGA-55-6972 
         764          105         1971         1479           24         1475 
TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 TCGA-55-7573 TCGA-55-7576 
        2151           53           18           35            4           40 
TCGA-55-7724 TCGA-55-7725 TCGA-55-7727 TCGA-55-7903 TCGA-55-7911 TCGA-55-7914 
         705           39           34           19           21            3 
TCGA-55-8090 TCGA-55-8097 TCGA-55-8205 TCGA-55-8206 TCGA-55-8207 TCGA-55-8510 
           6           15           33           46           66          228 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X TCGA-55-A492 
           3          146           49          106           33            1 
TCGA-62-8395 TCGA-62-8397 TCGA-62-8399 TCGA-62-A46V TCGA-62-A472 TCGA-64-1680 
        1216         1289         2696         2199          910         1126 
TCGA-64-1681 TCGA-64-5778 TCGA-64-5815 TCGA-67-3770 TCGA-67-3773 TCGA-67-3774 
        1968         1305          866           31          427          385 
TCGA-67-6215 TCGA-67-6216 TCGA-67-6217 TCGA-69-7761 TCGA-69-7763 TCGA-69-7764 
         174          141          422          186          690          414 
TCGA-69-7765 TCGA-69-8253 TCGA-69-8254 TCGA-73-4662 TCGA-73-4676 TCGA-73-7498 
         165          100           77          912          164          621 
TCGA-78-7145 TCGA-78-7148 TCGA-78-7149 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 
        1973         1944         1093         1202          760         1948 
TCGA-78-7156 TCGA-78-7160 TCGA-78-7162 TCGA-78-7166 TCGA-78-7167 TCGA-78-7537 
        1961          678         1940         1934         1937         1944 
TCGA-78-7540 TCGA-78-7633 TCGA-78-8655 TCGA-78-8660 TCGA-80-5607 TCGA-86-7714 
         881          994         1981         1954         1965         1968 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8280 TCGA-86-8281 TCGA-86-8668 TCGA-86-A4P8 
         489          476           16         1955           45           39 
TCGA-91-6835 TCGA-91-6849 TCGA-91-7771 TCGA-91-8496 TCGA-91-8497 TCGA-91-A4BD 
          79           35          492          505          174          218 
TCGA-93-7347 TCGA-95-7567 TCGA-95-7947 TCGA-95-7948 TCGA-95-8039 TCGA-95-A4VK 
         297          568          477          476          830          121 
TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7546 TCGA-97-7552 TCGA-97-7553 TCGA-97-7941 
         553          605          964         1932         1332           22 
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-99-8028 TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 
         459          282          238          435          266          312 
TCGA-MP-A4T7 TCGA-MP-A4TH TCGA-MP-A4TK TCGA-S2-AA1A 
        1954          142         1971          121 

$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-44-3396 TCGA-44-3918 TCGA-44-5643 TCGA-44-5644 TCGA-44-7660 TCGA-44-7667 
        1130         1036         1013          863          592          557 
TCGA-44-7670 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47A TCGA-44-A4SS 
         882          385           99          486          466          415 
TCGA-49-4494 TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6743 
        1081         1421          999          268         1700          369 
TCGA-49-AARQ TCGA-50-5049 TCGA-50-5066 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 
        6443         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-55-1596 TCGA-55-5899 TCGA-55-6969 TCGA-55-6987 TCGA-55-7284 
        1178         1375           87         1239         1170          121 
TCGA-55-7570 TCGA-55-7728 TCGA-55-7815 TCGA-55-7907 TCGA-55-7910 TCGA-55-7994 
           6           24           54           16          197           31 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8092 TCGA-55-8094 
           5           33          462          100           26            4 
TCGA-55-8096 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 
          47          674           44           23           29           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8511 TCGA-55-8514 TCGA-55-8615 TCGA-55-8616 
           8           15            9          202           15           48 
TCGA-55-8620 TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A493 
          66           42           29           48         1952           28 
TCGA-55-A494 TCGA-55-A4DF TCGA-62-8398 TCGA-62-8402 TCGA-62-A46U TCGA-62-A471 
           5           47         1970         1445         2067         1246 
TCGA-64-1677 TCGA-64-1678 TCGA-64-5774 TCGA-64-5779 TCGA-67-3771 TCGA-67-3772 
         628         1189         1959          864          610          573 
TCGA-69-7760 TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 
         202          230          184           70           89          382 
TCGA-69-8255 TCGA-69-A59K TCGA-73-4659 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 
         129          214          711          519          305         1970 
TCGA-75-7031 TCGA-78-7146 TCGA-78-7147 TCGA-78-7150 TCGA-78-7155 TCGA-78-7158 
        1965         1988         1950         1963         1957         1963 
TCGA-78-7159 TCGA-78-7161 TCGA-78-7220 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 
        1221          215         1965         1972         1949          327 
TCGA-78-7542 TCGA-78-8640 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 
        1952         1949         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-86-8056 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         745         1963          482           19           26           35 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8673 TCGA-86-A456 TCGA-86-A4D0 TCGA-91-6828 
          34           18          455           10           30          323 
TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 TCGA-91-8499 TCGA-91-A4BC 
          60          310          417          372           36           44 
TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-97-7547 
         186           34            2         1973          377         1965 
TCGA-97-8171 TCGA-97-8172 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8194 
         107          182          427           44          170          114 
TCGA-J2-A4AD TCGA-L4-A4E5 TCGA-L9-A444 TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 
         287          578            6          111          102          827 
TCGA-MN-A4N4 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 
        1175           84         1946         1967         1954         1957 
TCGA-MP-A4TA TCGA-MP-A4TE TCGA-MP-A5C7 
        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-44-2668 TCGA-44-6144 TCGA-44-6147 TCGA-44-6774 TCGA-44-6775 TCGA-44-6778 
         246          723          845          658          705         1864 
TCGA-44-6779 TCGA-44-7662 TCGA-44-7669 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4512 
        1978          218         1970          260           76          157 
TCGA-49-6742 TCGA-49-6761 TCGA-50-5072 TCGA-50-5933 TCGA-50-7109 TCGA-55-6543 
         445          354          246         2370          255            2 
TCGA-55-6642 TCGA-55-6971 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-7574 
         993           25           67         1826         1233           95 
TCGA-55-7726 TCGA-55-7816 TCGA-55-8091 TCGA-55-8299 TCGA-55-8614 TCGA-55-A4DG 
          39           44          600          216          536          162 
TCGA-64-1676 TCGA-64-1679 TCGA-64-5775 TCGA-64-5781 TCGA-71-6725 TCGA-71-8520 
        1728         1686           62         1559           61            3 
TCGA-73-4658 TCGA-73-4675 TCGA-75-7025 TCGA-75-7027 TCGA-78-7163 TCGA-78-8648 
        1600           40         1967         1956         1950         1971 
TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 TCGA-86-8672 TCGA-86-8674 
          10           13           24          479           15          405 
TCGA-86-A4P7 TCGA-91-6829 TCGA-91-6847 TCGA-91-6848 TCGA-93-7348 TCGA-95-8494 
          14         1940          842          224          127           84 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8177 TCGA-97-8547 TCGA-97-A4M7 TCGA-J2-8192 
         775          181          147          148          271          154 
TCGA-L9-A443 TCGA-MP-A4T2 TCGA-MP-A4T9 TCGA-MP-A4TC TCGA-MP-A4TF TCGA-MP-A4TI 
         116         1951         1980         1944         1970         1955 

subtype1 subtype2 subtype3 
       1        2        2 
subtype1 subtype2 subtype3 
    2696     6443     2370 
subtype1 subtype2 subtype3 
   467.5    486.0    446.5 
[1] "1.0 - 2696.0 (467.5)" "2.0 - 6443.0 (486.0)" "2.0 - 2370.0 (446.5)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       61       36        17        25         21          1
  subtype2       3       40       68        22        33         29          8
  subtype3       1       14       29        10        10         19          2
          vv
clus       STAGE IV
  subtype1        9
  subtype2       12
  subtype3        2
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        3        1
  STAGE IA         61       40       14
  STAGE IB         36       68       29
  STAGE IIA        17       22       10
  STAGE IIB        25       33       10
  STAGE IIIA       21       29       19
  STAGE IIIB        1        8        2
  STAGE IV          9       12        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  71  81  14   6
  subtype2  51 131  22   9
  subtype3  24  52   7   3
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       71       51       24
  T2       81      131       52
  T3       14       22        7
  T4        6        9        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 108  37    21
  subtype2 139  38    35
  subtype3  52  15    18
D9V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0         108      139       52
  N1          37       38       15
  N2+N3       21       35       18
[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 118   7   0   1  44
  subtype2 152   8   1   3  50
  subtype3  54   1   0   0  31
D9V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       118      152       54
  M1         7        8        1
  M1A        0        1        0
  M1B        1        3        0
  MX        44       50       31
[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  98  74
  subtype2 110 105
  subtype3  46  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   98   74
  subtype2  110  105
  subtype3   46   41
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       98      110       46
  MALE         74      105       41
[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                          8                                37
  subtype2                          7                                50
  subtype3                          0                                 6
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 93
  subtype2                                                140
  subtype3                                                 70
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          4
  subtype2                                          0
  subtype3                                          1
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            12
  subtype2                                             4
  subtype3                                             3
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  1
  subtype2                              1                                  0
  subtype3                              0                                  2
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            2                             8
  subtype2                            0                             8
  subtype3                            0                             3
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             2
  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                                8        7        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        37       50        6
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       93      140       70
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                4        0        1
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            12        4        3
  LUNG CLEAR CELL ADENOCARCINOMA                            1        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        1        0        2
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             8        8        3
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             2        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   7 165
  subtype2   9 206
  subtype3   4  83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7  165
  subtype2    9  206
  subtype3    4   83
     clus
vv    subtype1 subtype2 subtype3
  NO         7        9        4
  YES      165      206       83
[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 117   2   2   8
  subtype2 155   7   2   7
  subtype3  52   3   0   6
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      117      155       52
  R1        2        7        3
  R2        2        2        0
  RX        8        7        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                        13   139
  subtype2     4                        18   154
  subtype3     2                         4    72
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        4        2
  BLACK OR AFRICAN AMERICAN       13       18        4
  WHITE                          139      154       72
[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   1 127
  subtype2   5 149
  subtype3   1  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  127
  subtype2    5  149
  subtype3    1   67
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        1
  NOT HISPANIC OR LATINO      127      149       67
[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  45  15
  subtype2 134  33
  subtype3  88  21
  subtype4  62  17
subtype1 subtype2 subtype3 subtype4 
      60      167      109       79 
subtype1 subtype2 subtype3 subtype4 
      15       33       21       17 
$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-50-8460 TCGA-55-1595 TCGA-55-6972 TCGA-55-6986 TCGA-55-7227 TCGA-55-7281 
         105         1479         1475         2151           53           18 
TCGA-55-7573 TCGA-55-7727 TCGA-55-7911 TCGA-55-A491 TCGA-55-A492 TCGA-62-8397 
           4           34           21         1952            1         1289 
TCGA-62-A472 TCGA-64-5815 TCGA-67-6215 TCGA-67-6217 TCGA-69-7763 TCGA-69-7765 
         910          866          174          422          690          165 
TCGA-69-8253 TCGA-73-7498 TCGA-78-7148 TCGA-78-7149 TCGA-78-7156 TCGA-78-7166 
         100          621         1944         1093         1961         1934 
TCGA-78-7537 TCGA-78-7633 TCGA-78-8660 TCGA-86-7714 TCGA-86-8281 TCGA-91-8496 
        1944          994         1954         1968         1955          505 
TCGA-93-7347 TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VP TCGA-97-8174 TCGA-97-8179 
         297          830          121          605         1965           15 
TCGA-99-7458 TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-MP-A4T7 TCGA-MP-A4TC TCGA-MP-A4TK 
         392          238          435         1954         1944         1971 

$subtype2
TCGA-05-4249 TCGA-05-4390 TCGA-05-4396 TCGA-05-4417 TCGA-05-4422 TCGA-05-4425 
        1523         1126         1947          455          365          669 
TCGA-05-5420 TCGA-05-5423 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 TCGA-35-4123 
         457          151          882          670           62          182 
TCGA-35-5375 TCGA-38-4625 TCGA-38-4626 TCGA-38-4627 TCGA-38-4628 TCGA-38-4629 
         264         1952         1962         1147         1492          864 
TCGA-38-4630 TCGA-38-4631 TCGA-38-4632 TCGA-38-6178 TCGA-44-2655 TCGA-44-2659 
        1073          354         1357          448         1324         1367 
TCGA-44-2662 TCGA-44-2665 TCGA-44-2668 TCGA-44-3918 TCGA-44-5643 TCGA-44-7662 
        1280         1301          246         1036         1013          218 
TCGA-44-8117 TCGA-44-8120 TCGA-44-A47A TCGA-44-A4SS TCGA-44-A4SU TCGA-49-4494 
         385          260          466          415           76         1081 
TCGA-49-4501 TCGA-49-4506 TCGA-49-4507 TCGA-49-4514 TCGA-49-6761 TCGA-49-AARQ 
        1421          999          268         1700          354         6443 
TCGA-50-5051 TCGA-50-5066 TCGA-50-5930 TCGA-50-5933 TCGA-50-5935 TCGA-50-5941 
         455          944          282         2370          653          567 
TCGA-50-7109 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-6543 TCGA-55-6642 
         255         1986          424          280            2          993 
TCGA-55-6971 TCGA-55-7576 TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 
          25           40           54           19           16          197 
TCGA-55-7995 TCGA-55-8085 TCGA-55-8089 TCGA-55-8091 TCGA-55-8299 TCGA-55-8301 
           5           33          100          600          216           44 
TCGA-55-8302 TCGA-55-8506 TCGA-55-8510 TCGA-55-8511 TCGA-55-8615 TCGA-55-8616 
          23           11          228            9           15           48 
TCGA-55-A48Y TCGA-55-A48Z TCGA-55-A494 TCGA-62-8395 TCGA-62-8398 TCGA-62-8402 
          42           29            5         1216         1970         1445 
TCGA-62-A46U TCGA-62-A46V TCGA-62-A471 TCGA-64-1676 TCGA-64-1677 TCGA-64-1678 
        2067         2199         1246         1728          628         1189 
TCGA-64-5781 TCGA-67-3772 TCGA-67-3773 TCGA-67-3774 TCGA-67-6216 TCGA-69-7760 
        1559          573          427          385          141          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-71-8520 TCGA-73-4658 TCGA-73-4659 TCGA-73-4662 
         214           61            3         1600          711          912 
TCGA-73-4675 TCGA-73-A9RS TCGA-75-7027 TCGA-78-7145 TCGA-78-7155 TCGA-78-7159 
          40          305         1956         1973         1957         1221 
TCGA-78-7161 TCGA-78-7163 TCGA-78-7535 TCGA-78-7536 TCGA-78-7539 TCGA-78-8655 
         215         1950         1972         1949          327         1981 
TCGA-78-8662 TCGA-80-5607 TCGA-80-5608 TCGA-83-5908 TCGA-86-7701 TCGA-86-7713 
        1964         1965         1972          824           11          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-8054 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
         591         1963          745           13           24          479 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8359 TCGA-86-8668 TCGA-86-8669 TCGA-86-8672 
         476          482           26           45           34           15 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 TCGA-86-A4P7 TCGA-91-6828 TCGA-91-6836 
         455          405           30           14          323          417 
TCGA-91-6847 TCGA-93-7348 TCGA-93-8067 TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 
         842          127          186           34            2         1973 
TCGA-95-7567 TCGA-95-7944 TCGA-97-7554 TCGA-97-7937 TCGA-97-8171 TCGA-97-8547 
         568          377          775          181          107          148 
TCGA-97-A4M7 TCGA-99-8025 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 TCGA-J2-8194 
         271          427           44          170          154          114 
TCGA-L4-A4E5 TCGA-L9-A443 TCGA-L9-A444 TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 
         578          116            6          102          827           84 
TCGA-MP-A4SW TCGA-MP-A4T2 TCGA-MP-A4T8 TCGA-MP-A4TF TCGA-MP-A5C7 
        1967         1951         1957         1970         1490 

$subtype3
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-38-7271 TCGA-38-A44F TCGA-44-2657 TCGA-44-2661 TCGA-44-2666 
         225         1971          133          400          741           97 
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-A47G TCGA-49-4505 TCGA-49-4510 
         705         1978          366          351          428          896 
TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 TCGA-50-5055 TCGA-50-5068 TCGA-50-6597 
         157          890          522          785         1499         1015 
TCGA-53-7626 TCGA-55-6712 TCGA-55-6980 TCGA-55-6983 TCGA-55-6985 TCGA-55-7283 
        1971           24           67         1826         1233           35 
TCGA-55-7284 TCGA-55-7574 TCGA-55-7724 TCGA-55-7725 TCGA-55-7726 TCGA-55-7728 
         121           95          705           39           39           24 
TCGA-55-7816 TCGA-55-7914 TCGA-55-8087 TCGA-55-8090 TCGA-55-8097 TCGA-55-8205 
          44            3          462            6           15           33 
TCGA-55-8206 TCGA-55-8207 TCGA-55-8512 TCGA-55-8513 TCGA-55-8614 TCGA-55-8619 
          46           66            3          146          536           49 
TCGA-55-8621 TCGA-55-A48X TCGA-55-A4DG TCGA-64-1680 TCGA-64-1681 TCGA-64-5778 
         106           33          162         1126         1968         1305 
TCGA-67-3770 TCGA-69-7761 TCGA-69-7764 TCGA-69-8254 TCGA-73-4676 TCGA-75-7025 
          31          186          414           77          164         1967 
TCGA-78-7147 TCGA-78-7152 TCGA-78-7153 TCGA-78-7154 TCGA-78-7158 TCGA-78-7160 
        1950         1202          760         1948         1963          678 
TCGA-78-7162 TCGA-78-7167 TCGA-78-7540 TCGA-86-8056 TCGA-86-8076 TCGA-86-8280 
        1940         1937          881         1963          489           16 
TCGA-86-8671 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-6835 TCGA-91-6849 TCGA-91-7771 
          18           10           39           79           35          492 
TCGA-91-8497 TCGA-91-A4BD TCGA-95-7947 TCGA-95-7948 TCGA-95-8494 TCGA-95-A4VN 
         174          218          477          476           84          553 
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-97-8175 TCGA-97-8177 TCGA-97-8552 TCGA-97-A4M2 TCGA-99-8028 TCGA-J2-A4AE 
          87          147          115          197          459          282 
TCGA-L9-A50W TCGA-L9-A743 TCGA-MP-A4T4 TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A4TI 
         266          312         1954         1980          142         1955 
TCGA-S2-AA1A 
         121 

$subtype4
TCGA-05-4382 TCGA-05-4389 TCGA-05-4398 TCGA-05-4415 TCGA-05-4420 TCGA-05-4424 
         607         1369         1431         1997          912          913 
TCGA-05-4427 TCGA-05-4430 TCGA-05-4432 TCGA-44-3396 TCGA-44-5644 TCGA-44-6144 
         791          761          761         1130          863          723 
TCGA-44-6778 TCGA-44-7660 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8119 
        1864          592          557         1970          882           99 
TCGA-44-A479 TCGA-49-6742 TCGA-49-6743 TCGA-50-5049 TCGA-50-5072 TCGA-50-5931 
         486          445          369         2146          246          267 
TCGA-50-5946 TCGA-55-1592 TCGA-55-1594 TCGA-55-1596 TCGA-55-5899 TCGA-55-6969 
         686          701         1178         1375           87         1239 
TCGA-55-6987 TCGA-55-7570 TCGA-55-7994 TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 
        1170            6           31           26            4           47 
TCGA-55-8208 TCGA-55-8505 TCGA-55-8507 TCGA-55-8508 TCGA-55-8514 TCGA-55-8620 
         674           29            8           15          202           66 
TCGA-55-A490 TCGA-55-A493 TCGA-55-A4DF TCGA-62-8399 TCGA-64-1679 TCGA-64-5774 
          48           28           47         2696         1686         1959 
TCGA-64-5775 TCGA-64-5779 TCGA-67-3771 TCGA-73-7499 TCGA-75-6214 TCGA-75-7031 
          62          864          610          519         1970         1965 
TCGA-78-7146 TCGA-78-7150 TCGA-78-7220 TCGA-78-7542 TCGA-78-8640 TCGA-78-8648 
        1988         1963         1965         1952         1949         1971 
TCGA-86-6851 TCGA-86-7711 TCGA-86-7955 TCGA-86-8055 TCGA-86-8358 TCGA-86-8585 
        1959          630          508           10           19           35 
TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6840 TCGA-91-6848 TCGA-91-8499 
        1940           60          310          372          224           36 
TCGA-91-A4BC TCGA-J2-A4AD TCGA-L9-A7SV TCGA-MN-A4N4 TCGA-MP-A4SV TCGA-MP-A4TA 
          44          287          111         1175         1946         1951 
TCGA-MP-A4TE 
        1970 

subtype1 subtype2 subtype3 subtype4 
       1        2        3        4 
subtype1 subtype2 subtype3 subtype4 
    2174     6443     1980     2696 
subtype1 subtype2 subtype3 subtype4 
     743      422      383      674 
[1] "1.0 - 2174.0 (743.0)" "2.0 - 6443.0 (422.0)" "3.0 - 1980.0 (383.0)"
[4] "4.0 - 2696.0 (674.0)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       0       25       13         2        11          9          1
  subtype2       4       35       59        20        29         28          6
  subtype3       1       36       35        15        17         16          2
  subtype4       0       19       26        12        11         16          2
          vv
clus       STAGE IV
  subtype1        3
  subtype2        9
  subtype3        6
  subtype4        5
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        4        1        0
  STAGE IA         25       35       36       19
  STAGE IB         13       59       35       26
  STAGE IIA         2       20       15       12
  STAGE IIB        11       29       17       11
  STAGE IIIA        9       28       16       16
  STAGE IIIB        1        6        2        2
  STAGE IV          3        9        6        5
[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  27  30   3   4
  subtype2  45 117  19   7
  subtype3  47  65  12   4
  subtype4  27  52   9   3
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       27       45       47       27
  T2       30      117       65       52
  T3        3       19       12        9
  T4        4        7        4        3
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1 N2+N3
  subtype1  41  13     7
  subtype2 123  34    31
  subtype3  79  27    18
  subtype4  56  16    18
D10V5, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  N0          41      123       79       56
  N1          13       34       27       16
  N2+N3        7       31       18       18
[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  45   2   0   0  17
  subtype2 137   8   1   0  43
  subtype3  82   4   0   1  40
  subtype4  60   2   0   3  25
D10V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        45      137       82       60
  M1         2        8        4        2
  M1A        0        1        0        0
  M1B        0        0        1        3
  MX        17       43       40       25
[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"
D10V7, binary
          cls
clus         0   1
  subtype1  31  33
  subtype2 108  82
  subtype3  80  49
  subtype4  35  56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   33
  subtype2  108   82
  subtype3   80   49
  subtype4   35   56
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       31      108       80       35
  MALE         33       82       49       56
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
          vv
clus       LUNG ACINAR ADENOCARCINOMA LUNG ADENOCARCINOMA MIXED SUBTYPE
  subtype1                          4                                15
  subtype2                          4                                36
  subtype3                          5                                25
  subtype4                          2                                17
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 36
  subtype2                                                132
  subtype3                                                 70
  subtype4                                                 65
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          0
  subtype2                                          2
  subtype3                                          3
  subtype4                                          0
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             4
  subtype2                                             4
  subtype3                                            10
  subtype4                                             1
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  0
  subtype2                              0                                  3
  subtype3                              0                                  0
  subtype4                              1                                  0
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            0                             4
  subtype2                            0                             8
  subtype3                            2                             6
  subtype4                            0                             1
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               0
  subtype3                               1
  subtype4                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             1
  subtype3                                             2
  subtype4                                             2
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            0
  subtype2                            0
  subtype3                            5
  subtype4                            2
D10V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                4        4        5
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        15       36       25
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       36      132       70
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0        2        3
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             4        4       10
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        3        0
  LUNG MUCINOUS ADENOCARCINOMA                              0        0        2
  LUNG PAPILLARY ADENOCARCINOMA                             4        8        6
  LUNG SIGNET RING ADENOCARCINOMA                           0        0        1
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        1        2
  MUCINOUS (COLLOID) CARCINOMA                              0        0        5
                                                    clus
vv                                                   subtype4
  LUNG ACINAR ADENOCARCINOMA                                2
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        17
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       65
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                0
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             1
  LUNG CLEAR CELL ADENOCARCINOMA                            1
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0
  LUNG MUCINOUS ADENOCARCINOMA                              0
  LUNG PAPILLARY ADENOCARCINOMA                             1
  LUNG SIGNET RING ADENOCARCINOMA                           0
  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"
D10V10, binary
          cls
clus         0   1
  subtype1   4  60
  subtype2   7 183
  subtype3   5 124
  subtype4   4  87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   60
  subtype2    7  183
  subtype3    5  124
  subtype4    4   87
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         4        7        5        4
  YES       60      183      124       87
[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"
D10V11, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  39   1   0   3
  subtype2 137   6   1   8
  subtype3  87   3   2   6
  subtype4  61   2   1   4
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       39      137       87       61
  R1        1        6        3        2
  R2        0        1        2        1
  RX        3        8        6        4
[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     1                         5    51
  subtype2     4                        14   146
  subtype3     1                         7   106
  subtype4     1                         9    62
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        4        1        1
  BLACK OR AFRICAN AMERICAN        5       14        7        9
  WHITE                           51      146      106       62
[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"
D10V14, binary
          cls
clus         0   1
  subtype1   0  45
  subtype2   3 142
  subtype3   2  95
  subtype4   2  61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   45
  subtype2    3  142
  subtype3    2   95
  subtype4    2   61
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        3        2        2
  NOT HISPANIC OR LATINO       45      142       95       61
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(11) Variable = MIRSEQ_MATURE_CNMF
D11V1, survival
          sevent
clus2        0   1
  subtype1  89  33
  subtype2 135  20
  subtype3  56  14
subtype1 subtype2 subtype3 
     122      155       70 
subtype1 subtype2 subtype3 
      33       20       14 
$subtype1
TCGA-05-4384 TCGA-05-4396 TCGA-05-4405 TCGA-05-4410 TCGA-05-4424 TCGA-05-4425 
         426         1947          610         1958          913          669 
TCGA-05-4427 TCGA-05-4433 TCGA-05-5423 TCGA-05-5429 TCGA-35-5375 TCGA-38-4632 
         791          730          151           30          264         1357 
TCGA-38-7271 TCGA-38-A44F TCGA-44-5643 TCGA-44-5644 TCGA-44-5645 TCGA-44-6145 
        1971          133         1013          863          383          328 
TCGA-44-6146 TCGA-44-6147 TCGA-44-6775 TCGA-44-6776 TCGA-44-6778 TCGA-44-6779 
         302          845          705         1938         1864         1978 
TCGA-44-7659 TCGA-44-7661 TCGA-44-7669 TCGA-44-7670 TCGA-44-7671 TCGA-44-7672 
         444          366         1970          882          535          719 
TCGA-49-4514 TCGA-49-6742 TCGA-49-6743 TCGA-49-6744 TCGA-49-6745 TCGA-50-5051 
        1700          445          369          890          522          455 
TCGA-50-5055 TCGA-50-5068 TCGA-50-5930 TCGA-50-5932 TCGA-50-5935 TCGA-50-5941 
         785         1499          282         1091          653          567 
TCGA-50-5942 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-50-8460 TCGA-53-7624 
         883          764         1015          255          105         1986 
TCGA-53-7626 TCGA-53-7813 TCGA-55-6712 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
        1971          424           24           53           18           35 
TCGA-55-7284 TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7727 
         121            4           95           40          705           34 
TCGA-55-7815 TCGA-55-7903 TCGA-55-7907 TCGA-55-7910 TCGA-55-7911 TCGA-55-7914 
          54           19           16          197           21            3 
TCGA-55-8206 TCGA-55-8512 TCGA-55-8621 TCGA-62-8397 TCGA-64-1681 TCGA-67-6215 
          46            3          106         1289         1968          174 
TCGA-67-6216 TCGA-67-6217 TCGA-69-7760 TCGA-69-7765 TCGA-69-8254 TCGA-71-6725 
         141          422          202          165           77           61 
TCGA-73-4676 TCGA-78-7145 TCGA-78-7146 TCGA-78-7147 TCGA-78-7148 TCGA-78-7149 
         164         1973         1988         1950         1944         1093 
TCGA-78-7152 TCGA-78-7154 TCGA-78-7156 TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 
        1202         1948         1961         1221          678          215 
TCGA-78-7166 TCGA-78-7167 TCGA-78-7220 TCGA-78-7535 TCGA-78-7537 TCGA-78-7539 
        1934         1937         1965         1972         1944          327 
TCGA-78-7540 TCGA-78-7542 TCGA-78-7633 TCGA-86-7701 TCGA-86-7711 TCGA-86-7714 
         881         1952          994           11          630         1968 
TCGA-86-8056 TCGA-91-6828 TCGA-91-6829 TCGA-91-6835 TCGA-91-6836 TCGA-91-7771 
        1963          323         1940           79          417          492 
TCGA-91-8496 TCGA-91-8497 TCGA-95-7567 TCGA-97-7546 TCGA-97-7547 TCGA-97-7552 
         505          174          568          964         1965         1932 
TCGA-97-7553 TCGA-97-7937 TCGA-97-8172 TCGA-97-8174 TCGA-97-8552 TCGA-99-7458 
        1332          181          182         1965          115          392 
TCGA-L9-A50W TCGA-S2-AA1A 
         266          121 

$subtype2
TCGA-05-4390 TCGA-05-4415 TCGA-05-5420 TCGA-05-5425 TCGA-05-5428 TCGA-05-5715 
        1126         1997          457          882          670           62 
TCGA-44-7660 TCGA-44-8117 TCGA-44-8119 TCGA-44-A479 TCGA-44-A47B TCGA-44-A47F 
         592          385           99          486          287          337 
TCGA-44-A47G TCGA-44-A4SS TCGA-49-AARQ TCGA-50-5931 TCGA-50-5946 TCGA-53-A4EZ 
         351          415         6443          267          686          280 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6972 TCGA-55-6980 TCGA-55-6986 TCGA-55-6987 
        1239           25         1475           67         2151         1170 
TCGA-55-7728 TCGA-55-7994 TCGA-55-8085 TCGA-55-8087 TCGA-55-8089 TCGA-55-8090 
          24           31           33          462          100            6 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8208 TCGA-55-8301 TCGA-55-8302 TCGA-55-8506 
          26            4          674           44           23           11 
TCGA-55-8507 TCGA-55-8508 TCGA-55-8510 TCGA-55-8511 TCGA-55-8513 TCGA-55-8514 
           8           15          228            9          146          202 
TCGA-55-8615 TCGA-55-8616 TCGA-55-8619 TCGA-55-8620 TCGA-55-A48X TCGA-55-A48Y 
          15           48           49           66           33           42 
TCGA-55-A48Z TCGA-55-A490 TCGA-55-A491 TCGA-55-A492 TCGA-55-A493 TCGA-55-A494 
          29           48         1952            1           28            5 
TCGA-55-A4DF TCGA-55-A4DG TCGA-62-8395 TCGA-62-8398 TCGA-62-8399 TCGA-62-8402 
          47          162         1216         1970         2696         1445 
TCGA-62-A46U TCGA-62-A471 TCGA-62-A472 TCGA-64-5774 TCGA-64-5778 TCGA-64-5779 
        2067         1246          910         1959         1305          864 
TCGA-69-7973 TCGA-69-7974 TCGA-69-7978 TCGA-69-7979 TCGA-69-7980 TCGA-69-8253 
         230          184           70           89          382          100 
TCGA-69-8255 TCGA-69-A59K TCGA-73-7498 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 
         129          214          621          519          305         1970 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7155 TCGA-78-7536 TCGA-78-8640 TCGA-78-8655 
        1956         1965         1957         1949         1949         1981 
TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 TCGA-83-5908 TCGA-86-6851 TCGA-86-7713 
        1954         1964         1972          824         1959          422 
TCGA-86-7953 TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8076 TCGA-86-8280 
         591         1963          508          745          489           16 
TCGA-86-8281 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 TCGA-86-8669 TCGA-86-8671 
        1955           19           26           35           34           18 
TCGA-86-8673 TCGA-86-8674 TCGA-86-A456 TCGA-86-A4D0 TCGA-86-A4P8 TCGA-91-6830 
         455          405           10           30           39           60 
TCGA-91-6840 TCGA-91-6847 TCGA-91-6849 TCGA-91-8499 TCGA-91-A4BC TCGA-91-A4BD 
         372          842           35           36           44          218 
TCGA-93-7347 TCGA-95-7043 TCGA-95-7562 TCGA-95-7944 TCGA-95-7947 TCGA-95-7948 
         297            2         1973          377          477          476 
TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP TCGA-97-7941 TCGA-97-8171 
         830          121          553          605           22          107 
TCGA-97-8175 TCGA-97-8179 TCGA-97-A4M2 TCGA-99-8025 TCGA-J2-8194 TCGA-J2-A4AD 
          87           15          197          427          114          287 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E5 TCGA-L4-A4E6 TCGA-L9-A444 TCGA-L9-A743 
         282          238          578          435            6          312 
TCGA-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW 
         111          102          827           84         1946         1967 
TCGA-MP-A4T2 TCGA-MP-A4T4 TCGA-MP-A4T7 TCGA-MP-A4T8 TCGA-MP-A4T9 TCGA-MP-A4TA 
        1951         1954         1954         1957         1980         1951 
TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TH TCGA-MP-A4TK TCGA-MP-A5C7 
        1970         1970          142         1971         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-44-6777 TCGA-44-7662 TCGA-44-7667 TCGA-44-8120 TCGA-44-A4SU TCGA-49-4512 
        1942          218          557          260           76          157 
TCGA-49-6761 TCGA-50-5045 TCGA-50-5049 TCGA-50-5066 TCGA-50-5072 TCGA-50-5933 
         354         2174         2146          944          246         2370 
TCGA-55-5899 TCGA-55-6543 TCGA-55-6642 TCGA-55-6983 TCGA-55-6985 TCGA-55-7570 
          87            2          993         1826         1233            6 
TCGA-55-7726 TCGA-55-7816 TCGA-55-8091 TCGA-55-8096 TCGA-55-8205 TCGA-55-8299 
          39           44          600           47           33          216 
TCGA-55-8505 TCGA-55-8614 TCGA-62-A46V TCGA-64-1679 TCGA-64-5775 TCGA-64-5781 
          29          536         2199         1686           62         1559 
TCGA-64-5815 TCGA-71-8520 TCGA-73-4658 TCGA-75-7025 TCGA-78-7150 TCGA-78-7163 
         866            3         1600         1967         1963         1950 
TCGA-78-8648 TCGA-80-5607 TCGA-86-8055 TCGA-86-8073 TCGA-86-8074 TCGA-86-8075 
        1971         1965           10           13           24          479 
TCGA-86-8278 TCGA-86-8279 TCGA-86-8668 TCGA-86-8672 TCGA-86-A4P7 TCGA-91-6831 
         476          482           45           15           14          310 
TCGA-91-6848 TCGA-93-7348 TCGA-95-7039 TCGA-95-8494 TCGA-97-7554 TCGA-97-8177 
         224          127           34           84          775          147 
TCGA-97-8547 TCGA-97-A4M7 TCGA-99-8028 TCGA-99-8032 TCGA-99-8033 TCGA-J2-8192 
         148          271          459           44          170          154 
TCGA-L9-A443 TCGA-MN-A4N4 TCGA-MP-A4TC TCGA-MP-A4TI 
         116         1175         1944         1955 

subtype1 subtype2 subtype3 
       3        1        2 
subtype1 subtype2 subtype3 
    1988     6443     2370 
subtype1 subtype2 subtype3 
   567.5    351.0    354.0 
[1] "3.0 - 1988.0 (567.5)" "1.0 - 6443.0 (351.0)" "2.0 - 2370.0 (354.0)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       2       31       33        17        18         23          4
  subtype2       3       46       48        22        26         21          3
  subtype3       0       17       26         7        14         16          1
          vv
clus       STAGE IV
  subtype1       10
  subtype2        6
  subtype3        3
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           2        3        0
  STAGE IA         31       46       17
  STAGE IB         33       48       26
  STAGE IIA        17       22        7
  STAGE IIB        18       26       14
  STAGE IIIA       23       21       16
  STAGE IIIB        4        3        1
  STAGE IV         10        6        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 43 73 13 10
  subtype2 60 96 16  2
  subtype3 21 52  7  2
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       43       60       21
  T2       73       96       52
  T3       13       16        7
  T4       10        2        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1 N2+N3
  subtype1  81  32    21
  subtype2 119  29    26
  subtype3  50  15    16
D11V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          81      119       50
  N1          32       29       15
  N2+N3       21       26       16
[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  90   8   0   1  37
  subtype2 114   2   1   3  55
  subtype3  54   2   0   0  27
D11V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        90      114       54
  M1         8        2        2
  M1A        0        1        0
  M1B        1        3        0
  MX        37       55       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"
D11V7, binary
          cls
clus        0  1
  subtype1 73 66
  subtype2 93 82
  subtype3 48 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   73   66
  subtype2   93   82
  subtype3   48   36
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       73       93       48
  MALE         66       82       36
[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                          4                                35
  subtype2                          9                                30
  subtype3                          0                                 8
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 73
  subtype2                                                109
  subtype3                                                 69
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          3
  subtype2                                          0
  subtype3                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                            11
  subtype2                                             7
  subtype3                                             1
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              1                                  2
  subtype2                              0                                  0
  subtype3                              0                                  1
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            1                             7
  subtype2                            0                            10
  subtype3                            1                             1
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               0
  subtype2                               1
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             0
  subtype2                                             5
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            2
  subtype2                            4
  subtype3                            1
D11V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                4        9        0
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        35       30        8
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       73      109       69
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS            11        7        1
  LUNG CLEAR CELL ADENOCARCINOMA                            1        0        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        2        0        1
  LUNG MUCINOUS ADENOCARCINOMA                              1        0        1
  LUNG PAPILLARY ADENOCARCINOMA                             7       10        1
  LUNG SIGNET RING ADENOCARCINOMA                           0        1        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             0        5        0
  MUCINOUS (COLLOID) CARCINOMA                              2        4        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"
D11V10, binary
          cls
clus         0   1
  subtype1   9 130
  subtype2   3 172
  subtype3   6  78
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9  130
  subtype2    3  172
  subtype3    6   78
     clus
vv    subtype1 subtype2 subtype3
  NO         9        3        6
  YES      130      172       78
[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  82   5   1   4
  subtype2 129   2   0  10
  subtype3  53   2   0   3
D11V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       82      129       53
  R1        5        2        2
  R2        1        0        0
  RX        4       10        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     1                        12   106
  subtype2     2                        15   136
  subtype3     1                         6    69
D11V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        2        1
  BLACK OR AFRICAN AMERICAN       12       15        6
  WHITE                          106      136       69
[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   4  84
  subtype2   2 137
  subtype3   0  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   84
  subtype2    2  137
  subtype3    0   67
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        0
  NOT HISPANIC OR LATINO       84      137       67
[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  64  12
  subtype2 160  37
  subtype3  56  18
subtype1 subtype2 subtype3 
      76      197       74 
subtype1 subtype2 subtype3 
      12       37       18 
$subtype1
TCGA-05-4384 TCGA-05-4396 TCGA-05-4433 TCGA-05-5429 TCGA-38-A44F TCGA-44-5645 
         426         1947          730           30          133          383 
TCGA-44-6146 TCGA-44-6148 TCGA-44-6776 TCGA-44-A47B TCGA-44-A47F TCGA-44-A47G 
         302          704         1938          287          337          351 
TCGA-50-5932 TCGA-50-5942 TCGA-50-8460 TCGA-55-6972 TCGA-55-6983 TCGA-55-7284 
        1091          883          105         1475         1826          121 
TCGA-55-7727 TCGA-55-7728 TCGA-55-7911 TCGA-55-8085 TCGA-55-8087 TCGA-55-8206 
          34           24           21           33          462           46 
TCGA-55-8512 TCGA-55-8513 TCGA-55-8616 TCGA-55-8619 TCGA-55-8621 TCGA-55-A48X 
           3          146           48           49          106           33 
TCGA-55-A492 TCGA-55-A4DG TCGA-62-8395 TCGA-62-8397 TCGA-62-A472 TCGA-67-6215 
           1          162         1216         1289          910          174 
TCGA-67-6217 TCGA-69-8254 TCGA-73-7498 TCGA-78-7149 TCGA-78-7152 TCGA-78-7156 
         422           77          621         1093         1202         1961 
TCGA-78-7167 TCGA-78-7537 TCGA-78-7539 TCGA-78-7540 TCGA-78-7633 TCGA-86-8056 
        1937         1944          327          881          994         1963 
TCGA-86-8280 TCGA-86-8281 TCGA-86-A456 TCGA-86-A4P8 TCGA-91-7771 TCGA-91-8496 
          16         1955           10           39          492          505 
TCGA-91-8497 TCGA-91-A4BD TCGA-95-8039 TCGA-95-A4VK TCGA-95-A4VN TCGA-95-A4VP 
         174          218          830          121          553          605 
TCGA-97-7552 TCGA-97-7941 TCGA-97-8172 TCGA-97-8174 TCGA-97-8552 TCGA-97-A4M2 
        1932           22          182         1965          115          197 
TCGA-J2-A4AE TCGA-J2-A4AG TCGA-L4-A4E6 TCGA-L9-A50W TCGA-L9-A743 TCGA-MP-A4T7 
         282          238          435          266          312         1954 
TCGA-MP-A4T9 TCGA-MP-A4TH TCGA-MP-A5C7 TCGA-S2-AA1A 
        1980          142         1490          121 

$subtype2
TCGA-05-4390 TCGA-05-4415 TCGA-05-4424 TCGA-05-4425 TCGA-05-5420 TCGA-05-5423 
        1126         1997          913          669          457          151 
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-44-6145 TCGA-44-6147 TCGA-44-6778 
        1013          863          723          328          845         1864 
TCGA-44-7660 TCGA-44-7662 TCGA-44-7667 TCGA-44-7669 TCGA-44-7670 TCGA-44-8117 
         592          218          557         1970          882          385 
TCGA-44-8119 TCGA-44-8120 TCGA-44-A479 TCGA-44-A4SS TCGA-49-4514 TCGA-49-6742 
          99          260          486          415         1700          445 
TCGA-49-6743 TCGA-49-6761 TCGA-49-AARQ TCGA-50-5049 TCGA-50-5051 TCGA-50-5055 
         369          354         6443         2146          455          785 
TCGA-50-5066 TCGA-50-5068 TCGA-50-5072 TCGA-50-5930 TCGA-50-5931 TCGA-50-5935 
         944         1499          246          282          267          653 
TCGA-50-5941 TCGA-50-5946 TCGA-53-7624 TCGA-53-7813 TCGA-53-A4EZ TCGA-55-5899 
         567          686         1986          424          280           87 
TCGA-55-6969 TCGA-55-6971 TCGA-55-6980 TCGA-55-6985 TCGA-55-6986 TCGA-55-6987 
        1239           25           67         1233         2151         1170 
TCGA-55-7570 TCGA-55-7910 TCGA-55-7994 TCGA-55-8089 TCGA-55-8090 TCGA-55-8091 
           6          197           31          100            6          600 
TCGA-55-8092 TCGA-55-8094 TCGA-55-8096 TCGA-55-8205 TCGA-55-8208 TCGA-55-8299 
          26            4           47           33          674          216 
TCGA-55-8301 TCGA-55-8302 TCGA-55-8505 TCGA-55-8506 TCGA-55-8507 TCGA-55-8508 
          44           23           29           11            8           15 
TCGA-55-8510 TCGA-55-8511 TCGA-55-8514 TCGA-55-8614 TCGA-55-8615 TCGA-55-8620 
         228            9          202          536           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-62-8398 TCGA-62-8399 TCGA-62-A46U TCGA-62-A471 TCGA-64-1679 
          47         1970         2696         2067         1246         1686 
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-69-8253 TCGA-69-8255 
         184           70           89          382          100          129 
TCGA-69-A59K TCGA-73-4676 TCGA-73-7499 TCGA-73-A9RS TCGA-75-6214 TCGA-75-7025 
         214          164          519          305         1970         1967 
TCGA-75-7027 TCGA-75-7031 TCGA-78-7146 TCGA-78-7150 TCGA-78-7154 TCGA-78-7155 
        1956         1965         1988         1963         1948         1957 
TCGA-78-7159 TCGA-78-7160 TCGA-78-7161 TCGA-78-7220 TCGA-78-7536 TCGA-78-7542 
        1221          678          215         1965         1949         1952 
TCGA-78-8640 TCGA-78-8648 TCGA-78-8655 TCGA-78-8660 TCGA-78-8662 TCGA-80-5608 
        1949         1971         1981         1954         1964         1972 
TCGA-83-5908 TCGA-86-6851 TCGA-86-7701 TCGA-86-7711 TCGA-86-7713 TCGA-86-7953 
         824         1959           11          630          422          591 
TCGA-86-7954 TCGA-86-7955 TCGA-86-8054 TCGA-86-8055 TCGA-86-8073 TCGA-86-8075 
        1963          508          745           10           13          479 
TCGA-86-8076 TCGA-86-8278 TCGA-86-8279 TCGA-86-8358 TCGA-86-8359 TCGA-86-8585 
         489          476          482           19           26           35 
TCGA-86-8669 TCGA-86-8671 TCGA-86-8672 TCGA-86-8673 TCGA-86-8674 TCGA-86-A4D0 
          34           18           15          455          405           30 
TCGA-91-6828 TCGA-91-6829 TCGA-91-6830 TCGA-91-6831 TCGA-91-6836 TCGA-91-6840 
         323         1940           60          310          417          372 
TCGA-91-6847 TCGA-91-6848 TCGA-91-6849 TCGA-91-8499 TCGA-91-A4BC TCGA-93-7347 
         842          224           35           36           44          297 
TCGA-95-7039 TCGA-95-7043 TCGA-95-7562 TCGA-95-7567 TCGA-95-7944 TCGA-95-7947 
          34            2         1973          568          377          477 
TCGA-95-7948 TCGA-95-8494 TCGA-97-8171 TCGA-97-8175 TCGA-97-8179 TCGA-97-8547 
         476           84          107           87           15          148 
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-L9-A7SV TCGA-L9-A8F4 TCGA-MN-A4N1 TCGA-MN-A4N4 
         578            6          111          102          827         1175 
TCGA-MN-A4N5 TCGA-MP-A4SV TCGA-MP-A4SW TCGA-MP-A4T4 TCGA-MP-A4T8 TCGA-MP-A4TA 
          84         1946         1967         1954         1957         1951 
TCGA-MP-A4TC TCGA-MP-A4TE TCGA-MP-A4TF TCGA-MP-A4TI TCGA-MP-A4TK 
        1944         1970         1970         1955         1971 

$subtype3
TCGA-05-4405 TCGA-05-4410 TCGA-05-4417 TCGA-05-4427 TCGA-38-6178 TCGA-38-7271 
         610         1958          455          791          448         1971 
TCGA-44-6774 TCGA-44-6775 TCGA-44-6777 TCGA-44-6779 TCGA-44-7659 TCGA-44-7661 
         658          705         1942         1978          444          366 
TCGA-44-7671 TCGA-44-7672 TCGA-44-A4SU TCGA-49-4512 TCGA-49-6744 TCGA-49-6745 
         535          719           76          157          890          522 
TCGA-50-5045 TCGA-50-5933 TCGA-50-5944 TCGA-50-6597 TCGA-50-7109 TCGA-53-7626 
        2174         2370          764         1015          255         1971 
TCGA-55-6543 TCGA-55-6642 TCGA-55-6712 TCGA-55-7227 TCGA-55-7281 TCGA-55-7283 
           2          993           24           53           18           35 
TCGA-55-7573 TCGA-55-7574 TCGA-55-7576 TCGA-55-7724 TCGA-55-7726 TCGA-55-7815 
           4           95           40          705           39           54 
TCGA-55-7816 TCGA-55-7903 TCGA-55-7907 TCGA-55-7914 TCGA-62-8402 TCGA-62-A46V 
          44           19           16            3         1445         2199 
TCGA-64-1681 TCGA-64-5815 TCGA-67-6216 TCGA-69-7760 TCGA-69-7765 TCGA-71-6725 
        1968          866          141          202          165           61 
TCGA-71-8520 TCGA-73-4658 TCGA-78-7145 TCGA-78-7147 TCGA-78-7148 TCGA-78-7163 
           3         1600         1973         1950         1944         1950 
TCGA-78-7166 TCGA-78-7535 TCGA-80-5607 TCGA-86-7714 TCGA-86-8074 TCGA-86-8668 
        1934         1972         1965         1968           24           45 
TCGA-86-A4P7 TCGA-91-6835 TCGA-93-7348 TCGA-97-7546 TCGA-97-7547 TCGA-97-7553 
          14           79          127          964         1965         1332 
TCGA-97-7554 TCGA-97-7937 TCGA-97-8177 TCGA-97-A4M7 TCGA-99-7458 TCGA-J2-8192 
         775          181          147          271          392          154 
TCGA-L9-A443 TCGA-MP-A4T2 
         116         1951 

subtype1 subtype2 subtype3 
       1        2        2 
subtype1 subtype2 subtype3 
    1980     6443     2370 
subtype1 subtype2 subtype3 
   332.0    445.0    488.5 
[1] "1.0 - 1980.0 (332.0)" "2.0 - 6443.0 (445.0)" "2.0 - 2370.0 (488.5)"
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB
  subtype1       1       26       18         9        14          9          2
  subtype2       3       45       65        29        36         37          4
  subtype3       1       23       24         8         8         14          2
          vv
clus       STAGE IV
  subtype1        4
  subtype2       11
  subtype3        4
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        3        1
  STAGE IA         26       45       23
  STAGE IB         18       65       24
  STAGE IIA         9       29        8
  STAGE IIB        14       36        8
  STAGE IIIA        9       37       14
  STAGE IIIB        2        4        2
  STAGE IV          4       11        4
[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  32  37  11   4
  subtype2  62 139  22   5
  subtype3  30  45   3   5
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       32       62       30
  T2       37      139       45
  T3       11       22        3
  T4        4        5        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        N0  N1 N2+N3
  subtype1  59  13     8
  subtype2 141  44    42
  subtype3  50  19    13
D12V5, multiclass
       clus
vv      subtype1 subtype2 subtype3
  N0          59      141       50
  N1          13       44       19
  N2+N3        8       42       13
[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  54   3   0   1  24
  subtype2 154   7   1   3  64
  subtype3  50   2   0   0  31
D12V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        54      154       50
  M1         3        7        2
  M1A        0        1        0
  M1B        1        3        0
  MX        24       64       31
[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  42  42
  subtype2 111 119
  subtype3  61  23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   42
  subtype2  111  119
  subtype3   61   23
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       42      111       61
  MALE         42      119       23
[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                          4                                18
  subtype2                          6                                40
  subtype3                          3                                15
          vv
clus       LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                 38
  subtype2                                                159
  subtype3                                                 54
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS
  subtype1                                          3
  subtype2                                          0
  subtype3                                          2
          vv
clus       LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS
  subtype1                                             6
  subtype2                                             8
  subtype3                                             5
          vv
clus       LUNG CLEAR CELL ADENOCARCINOMA LUNG MICROPAPILLARY ADENOCARCINOMA
  subtype1                              0                                  0
  subtype2                              1                                  1
  subtype3                              0                                  2
          vv
clus       LUNG MUCINOUS ADENOCARCINOMA LUNG PAPILLARY ADENOCARCINOMA
  subtype1                            2                             7
  subtype2                            0                             8
  subtype3                            0                             3
          vv
clus       LUNG SIGNET RING ADENOCARCINOMA
  subtype1                               1
  subtype2                               0
  subtype3                               0
          vv
clus       LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA
  subtype1                                             1
  subtype2                                             4
  subtype3                                             0
          vv
clus       MUCINOUS (COLLOID) CARCINOMA
  subtype1                            4
  subtype2                            3
  subtype3                            0
D12V9, multiclass
                                                    clus
vv                                                   subtype1 subtype2 subtype3
  LUNG ACINAR ADENOCARCINOMA                                4        6        3
  LUNG ADENOCARCINOMA MIXED SUBTYPE                        18       40       15
  LUNG ADENOCARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       38      159       54
  LUNG BRONCHIOLOALVEOLAR CARCINOMA MUCINOUS                3        0        2
  LUNG BRONCHIOLOALVEOLAR CARCINOMA NONMUCINOUS             6        8        5
  LUNG CLEAR CELL ADENOCARCINOMA                            0        1        0
  LUNG MICROPAPILLARY ADENOCARCINOMA                        0        1        2
  LUNG MUCINOUS ADENOCARCINOMA                              2        0        0
  LUNG PAPILLARY ADENOCARCINOMA                             7        8        3
  LUNG SIGNET RING ADENOCARCINOMA                           1        0        0
  LUNG SOLID PATTERN PREDOMINANT ADENOCARCINOMA             1        4        0
  MUCINOUS (COLLOID) CARCINOMA                              4        3        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   1  83
  subtype2  10 220
  subtype3   7  77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   83
  subtype2   10  220
  subtype3    7   77
     clus
vv    subtype1 subtype2 subtype3
  NO         1       10        7
  YES       83      220       77
[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  61   0   0   6
  subtype2 153   5   1   8
  subtype3  50   4   0   3
D12V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       61      153       50
  R1        0        5        4
  R2        0        1        0
  RX        6        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     1                         4    68
  subtype2     1                        24   174
  subtype3     2                         5    69
D12V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        2
  BLACK OR AFRICAN AMERICAN        4       24        5
  WHITE                           68      174       69
[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   0  64
  subtype2   5 165
  subtype3   1  59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   64
  subtype2    5  165
  subtype3    1   59
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        5        1
  NOT HISPANIC OR LATINO       64      165       59
[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"
