[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"        "-oTLUSC-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/LUSC-TP/11541613/LUSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LUSC-TP/11590164/LUSC-TP.mergedcluster.txt"

nPatients in clinical file=422, in cluster file=504, common to both=422
[1]  12 422
[1] "MRNA_CNMF"
[1] 3
 1  2  3  4 
42 52 32 28 
 1  2  3  4 
42 52 32 28 
[1] "MRNA_CHIERARCHICAL"
[1] 3
 1  2  3 
47 56 51 
 1  2  3 
47 56 51 
[1] "CN_CNMF"
[1] 3
  1   2   3 
158 138 124 
  1   2   3 
158 138 124 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
118  91  79 
  1   2   3 
118  91  79 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
60 73 62 
 1  2  3 
60 73 62 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
54 41 52 48 
 1  2  3  4 
54 41 52 48 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3   4 
 96 128 124  71 
  1   2   3   4 
 96 128 124  71 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
156 157 106 
  1   2   3 
156 157 106 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
121  94  99  53  29 
  1   2   3   4   5 
121  94  99  53  29 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
 75 105 156  60 
  1   2   3   4 
 75 105 156  60 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 65 118  72 
  1   2   3 
 65 118  72 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
 26 107 122 
  1   2   3 
 26 107 122 
[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 422 columns.

[1] "Batch" "23"   
[1] "Last Follow UP"
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3409 TCGA-18-3410 TCGA-18-3411 
         370          136         2464         2417          146         1415 
TCGA-18-3412 TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 
         345          396         1810          862          758           50 
TCGA-18-3421 TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 
        1331          187           85         2754           92          827 
TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
        3636         1426         3016         2134         1852         1058 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-1083 
         474          965         3724          284         3644          267 
TCGA-21-5782 TCGA-21-5783 TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         962           NA         1268         1032          329          979 
TCGA-22-0940 TCGA-22-0944 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1011 
         608          223           NA          131         1953           53 
TCGA-22-1012 TCGA-22-1016 TCGA-22-1017 TCGA-22-4591 TCGA-22-4593 TCGA-22-4594 
         429          822         1485          623         1067         1470 
TCGA-22-4595 TCGA-22-4596 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4605 
         734           17         1161         1057          399           NA 
TCGA-22-4607 TCGA-22-4609 TCGA-22-4613 TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 
         587           NA          358          965         1975         1933 
TCGA-22-5474 TCGA-22-5477 TCGA-22-5478 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
         445         1346           24         1651         2170           NA 
TCGA-22-5482 TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 
         357          573          916         1912         1713          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 TCGA-33-4566 
          29         2524         3469         2979         1311         5287 
TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-4587 TCGA-33-4589 TCGA-33-6737 
        3149         4299          428           NA           NA           NA 
TCGA-33-6738 TCGA-34-2596 TCGA-34-2600 TCGA-34-2604 TCGA-34-2605 TCGA-34-2608 
         822           80         1874          958          881         1000 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5232 TCGA-34-5234 TCGA-34-5236 TCGA-34-5239 
         951         1528         2062         1715           NA          707 
TCGA-34-5240 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 TCGA-34-5929 TCGA-34-7107 
         365          428          941          552           NA           NA 
TCGA-34-8454 TCGA-34-8455 TCGA-37-3783 TCGA-37-3789 TCGA-37-3792 TCGA-37-4129 
         166           NA          120           13           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         247          227          238          207           12          103 
TCGA-39-5011 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5024 
        1454         2253         1361         2086           NA         2130 
TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 TCGA-39-5034 
        1849           52          740           59          833         1107 
TCGA-39-5035 TCGA-39-5036 TCGA-39-5037 TCGA-39-5039 TCGA-39-5040 TCGA-43-2576 
         474         1084         1086          544           NA         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-43-5670 
         684         1176          822         1007          349          849 
TCGA-43-6143 TCGA-43-6647 TCGA-43-6770 TCGA-43-6771 TCGA-43-6773 TCGA-43-7656 
         376          757          310           NA           NA          212 
TCGA-43-7657 TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-8118 TCGA-43-A474 
         236         2023          407          358           NA          353 
TCGA-43-A475 TCGA-43-A56U TCGA-43-A56V TCGA-46-3765 TCGA-46-3766 TCGA-46-3767 
         296          432          366           NA           NA           NA 
TCGA-46-3768 TCGA-46-3769 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
          NA           NA          324          423           12           12 
TCGA-51-4081 TCGA-51-6867 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 
         911           NA          541           NA          923           NA 
TCGA-52-7812 TCGA-56-1622 TCGA-56-5897 TCGA-56-5898 TCGA-56-6545 TCGA-56-6546 
          NA          881            3          555           62           26 
TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 
          30           13           30           44           40           26 
TCGA-56-7730 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8504 TCGA-56-8622 
           6           NA            1           41          178           55 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 TCGA-56-A49D 
          36           63           17           16           34           38 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZJ TCGA-56-A4ZK TCGA-56-A5DR 
           2           46           30           25            4            4 
TCGA-56-A5DS TCGA-58-8386 TCGA-58-8387 TCGA-58-8388 TCGA-58-8390 TCGA-58-8391 
           8           NA           NA          378          911         2167 
TCGA-58-8392 TCGA-58-8393 TCGA-58-A46J TCGA-58-A46K TCGA-58-A46L TCGA-58-A46M 
          NA         1058         2589           NA         1723         1072 
TCGA-58-A46N TCGA-60-2695 TCGA-60-2696 TCGA-60-2697 TCGA-60-2698 TCGA-60-2703 
         910          642          109           NA          311           NA 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2707 TCGA-60-2708 TCGA-60-2709 TCGA-60-2710 
          NA         2820          661         2447         1505         2024 
TCGA-60-2711 TCGA-60-2712 TCGA-60-2713 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 
        1260          274         1731         1531         1075         1475 
TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2722 TCGA-60-2723 TCGA-60-2724 
        1297           97          983          908         1092          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-5128 TCGA-63-5131 TCGA-63-6202 TCGA-63-7020 
         816          358           NA           NA           NA           NA 
TCGA-63-7021 TCGA-63-7022 TCGA-63-7023 TCGA-66-2727 TCGA-66-2734 TCGA-66-2737 
          NA           NA           NA           NA         1311           61 
TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         641           30           31           61           28           30 
TCGA-66-2757 TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 
          30          639          762           30           61           31 
TCGA-66-2767 TCGA-66-2768 TCGA-66-2769 TCGA-66-2770 TCGA-66-2771 TCGA-66-2773 
          61           61           NA          700          578           NA 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 
          61          578           NA          121           NA          759 
TCGA-66-2785 TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 
          60          790         1217          699           NA          699 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2793 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
          NA          913           NA         1645          122         1492 
TCGA-68-7755 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-8251 TCGA-68-A59I 
          83          202          211          244           96          121 
TCGA-68-A59J TCGA-70-6722 TCGA-70-6723 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
         104           NA           NA           NA           NA           NA 
TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7140 TCGA-77-7141 TCGA-77-7142 
          NA           NA         2737           NA           15         1286 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 TCGA-77-8007 
          NA           NA           NA           NA          479           NA 
TCGA-77-8008 TCGA-77-8009 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 TCGA-77-8133 
          NA         1641           NA         2522           NA           NA 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 TCGA-77-8143 TCGA-77-8144 
          NA           NA         3166           NA           NA          833 
TCGA-77-8145 TCGA-77-8146 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
          NA         2183          293           NA         1684         1092 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 
          10           NA         4026         3576           NA           NA 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GB TCGA-77-A5GF TCGA-77-A5GH TCGA-79-5596 
        1290         1280           NA          839          713           NA 
TCGA-85-6175 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7697 
          NA          364          395           34           18           10 
TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 TCGA-85-7844 TCGA-85-7950 
          49            1           NA           35          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8052 TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 
          26           60           16          960          428          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
          13           11           13           54           60           55 
TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 TCGA-85-8355 TCGA-85-8479 TCGA-85-8481 
          67           54           61           61           22           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8584 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL 
         445          424           NA            3          475           15 
TCGA-85-A4CN TCGA-85-A4JB TCGA-85-A4JC TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A4QR 
          NA           NA           NA           NA           NA           25 
TCGA-85-A50M TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A513 
          19           NA           NA           NA           NA           24 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 
          13          111          758          289           89          358 
TCGA-90-7964 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-7340 TCGA-92-7341 
         428          244          331          269           82          106 
TCGA-92-8063 TCGA-92-8064 TCGA-92-8065 TCGA-94-7033 TCGA-94-7557 TCGA-94-7943 
         122          160           70           87           NA          356 
TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JK 
         430         1213         1344          189          211          273 
TCGA-96-A4JL TCGA-98-7454 TCGA-98-8020 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         183          256           NA          413          224          308 
TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         222           35          449           36           83         1722 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 
Variable 1:'AGE':	nDistinctValues=45,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=139,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=270,	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=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=8,	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=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=123,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=97,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=55,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 23:'BATCH.NUMBER':	nDistinctValues=30,	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 422 columns, 1 survival variables, and 13 non-survival variables.
AGE, nv=45, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
100 254  48  20 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
100 254  48  20 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
100 254  48  20 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
100 254  48  20 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
263 113  35   5 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
263 113  35   5 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
263 113  35   5 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
263 113  35   5 
PATHOLOGY.M.STAGE, nv=4, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=8, binary=FALSE, numeric=TRUE
HISTOLOGICAL.TYPE, nv=4, binary=FALSE, numeric=FALSE
RADIATIONS.RADIATION.REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBERPACKYEARSSMOKED, nv=97, binary=FALSE, numeric=TRUE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = MRNA_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 24 17
  subtype2 31 18
  subtype3 13 17
  subtype4 16 11
subtype1 subtype2 subtype3 subtype4 
      41       49       30       27 
subtype1 subtype2 subtype3 subtype4 
      17       18       17       11 
$subtype1
TCGA-18-3406 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 TCGA-21-1079 
         370          396           50         1331         3636          965 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-22-0944 TCGA-22-1011 TCGA-22-4595 
        3724          284         3644          223           53          734 
TCGA-22-4607 TCGA-33-4547 TCGA-33-4589 TCGA-34-2600 TCGA-34-2609 TCGA-34-5241 
         587         1311         1948         1874          951          428 
TCGA-37-3783 TCGA-37-3789 TCGA-39-5029 TCGA-43-3920 TCGA-56-1622 TCGA-60-2707 
         120           13          740         1007          881          661 
TCGA-60-2708 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 TCGA-66-2734 
        1963         1297           97          983          717         1311 
TCGA-66-2742 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 
         641           30           61           61          578          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2789 
        1956          121         1954          699         1955 

$subtype2
TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
         136         2464         1415          345         1810          862 
TCGA-18-4086 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 
          85         1426         3016         2134         1852         1058 
TCGA-22-1012 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-33-4532 TCGA-33-4538 
         429         1161         1057          399         2524         2979 
TCGA-34-2596 TCGA-34-2605 TCGA-34-5240 TCGA-39-5016 TCGA-39-5021 TCGA-39-5036 
          80          881          365         2253         1947         1084 
TCGA-39-5037 TCGA-43-3394 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-60-2710 
        1086          822           12           12          911         1963 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2722 TCGA-60-2723 TCGA-66-2727 TCGA-66-2737 
        1260         1731          908         1092         1967           61 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 
         639          762           31          700         1946           61 
TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
         759         1217         1977          913         1645          122 
TCGA-66-2800 
        1492 

$subtype3
TCGA-18-3409 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 
        2417          608         1945          131         1952          822 
TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-33-4566 TCGA-34-2604 TCGA-34-2608 
        1485         1470           17         5287          958         1000 
TCGA-37-3792 TCGA-39-5030 TCGA-43-2576 TCGA-43-2581 TCGA-60-2696 TCGA-60-2698 
          12           59         1223         1176          109          311 
TCGA-60-2706 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2725 TCGA-66-2744 
        1958          274         1531         1075          816           30 
TCGA-66-2753 TCGA-66-2755 TCGA-66-2767 TCGA-66-2769 TCGA-66-2785 TCGA-66-2786 
          31           28           61         1947           60          790 

$subtype4
TCGA-18-3410 TCGA-18-3417 TCGA-18-4083 TCGA-21-1078 TCGA-21-1083 TCGA-22-4591 
         146          758          187          474          267          623 
TCGA-22-4613 TCGA-33-4533 TCGA-33-4582 TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 
         358         1940         1966          200          247          227 
TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5034 TCGA-39-5035 
         238          207           12         1454         1107          474 
TCGA-43-2578 TCGA-60-2695 TCGA-60-2716 TCGA-60-2726 TCGA-66-2754 TCGA-66-2756 
         684          642         1475          358           61           30 
TCGA-66-2757 TCGA-66-2790 TCGA-66-2793 
          30          699         1952 

subtype1 subtype2 subtype3 subtype4 
      13       12       12       12 
subtype1 subtype2 subtype3 subtype4 
    3724     3016     5287     1966 
subtype1 subtype2 subtype3 subtype4 
     717     1058      819      358 
[1] "13.0 - 3724.0 (717.0)"  "12.0 - 3016.0 (1058.0)" "12.0 - 5287.0 (819.0)" 
[4] "12.0 - 1966.0 (358.0)" 
D1V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  subtype1        2       21         0         9          6          2        2
  subtype2        2       24         4         9          6          7        0
  subtype3        8       11         2         4          4          2        0
  subtype4        8        5         1         5          3          4        2
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE IA          2        2        8        8
  STAGE IB         21       24       11        5
  STAGE IIA         0        4        2        1
  STAGE IIB         9        9        4        5
  STAGE IIIA        6        6        4        3
  STAGE IIIB        2        7        2        4
  STAGE IV          2        0        0        2
[1] 7 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  5 30  6  1
  subtype2  4 41  1  6
  subtype3 11 18  2  1
  subtype4 10 11  3  4
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        5        4       11       10
  T2       30       41       18       11
  T3        6        1        2        3
  T4        1        6        1        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       N0 N1 N2 N3
  subtype1 26 11  3  2
  subtype2 28 17  5  2
  subtype3 22  6  3  1
  subtype4 20  6  2  0
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       26       28       22       20
  N1       11       17        6        6
  N2        3        5        3        2
  N3        2        2        1        0
[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       M0 M1
  subtype1 38  2
  subtype2 50  0
  subtype3 32  0
  subtype4 26  2
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       38       50       32       26
  M1        2        0        0        2
[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  9 33
  subtype2 13 39
  subtype3 11 21
  subtype4 11 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   33
  subtype2   13   39
  subtype3   11   21
  subtype4   11   17
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        9       13       11       11
  MALE         33       39       21       17
[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
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     3
  subtype3                                     1
  subtype4                                     1
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      0
  subtype2                                      0
  subtype3                                      0
  subtype4                                      1
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          42
  subtype2                                                          49
  subtype3                                                          31
  subtype4                                                          26
D1V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       42       49
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       31       26
[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  1 41
  subtype2  0 52
  subtype3  1 31
  subtype4  0 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   41
  subtype2    0   52
  subtype3    1   31
  subtype4    0   28
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        0        1        0
  YES       41       52       31       28
[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
          vv
clus       R0 R1 R2 RX
  subtype1 38  0  1  1
  subtype2 47  1  1  1
  subtype3 27  1  0  3
  subtype4 27  1  0  0
D1V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       38       47       27       27
  R1        0        1        1        1
  R2        1        1        0        0
  RX        1        1        3        0
[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                         2    24
  subtype2     1                         3    27
  subtype3     1                         1    21
  subtype4     0                         1    19
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        1        0
  BLACK OR AFRICAN AMERICAN        2        3        1        1
  WHITE                           24       27       21       19
[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  3 23
  subtype2  1 26
  subtype3  0 20
  subtype4  0 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   23
  subtype2    1   26
  subtype3    0   20
  subtype4    0   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        1        0        0
  NOT HISPANIC OR LATINO       23       26       20       19
[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 25 21
  subtype2 33 20
  subtype3 26 22
subtype1 subtype2 subtype3 
      46       53       48 
subtype1 subtype2 subtype3 
      21       20       22 
$subtype1
TCGA-18-3406 TCGA-18-3414 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 
         370          396          758           50         1331         3636 
TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-22-1011 
         474          965         3724          284         3644           53 
TCGA-22-4591 TCGA-22-4595 TCGA-22-4607 TCGA-22-4613 TCGA-33-4547 TCGA-33-4582 
         623          734          587          358         1311         1966 
TCGA-33-4589 TCGA-34-2600 TCGA-34-5241 TCGA-37-3783 TCGA-37-3789 TCGA-39-5029 
        1948         1874          428          120           13          740 
TCGA-43-3920 TCGA-56-1622 TCGA-60-2696 TCGA-60-2707 TCGA-60-2708 TCGA-60-2716 
        1007          881          109          661         1963         1475 
TCGA-60-2719 TCGA-60-2721 TCGA-60-2724 TCGA-60-2726 TCGA-66-2734 TCGA-66-2742 
        1297          983          717          358         1311          641 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 TCGA-66-2778 TCGA-66-2780 
          30           61           61          578          578         1956 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2793 
         121         1954          699         1952 

$subtype2
TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
         136         2464         1415          345         1810          862 
TCGA-18-4083 TCGA-18-4086 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 
         187           85         1426         3016         2134         1852 
TCGA-21-1077 TCGA-22-0944 TCGA-22-1012 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 
        1058          223          429         1161         1057          399 
TCGA-33-4532 TCGA-33-4538 TCGA-34-2596 TCGA-34-2605 TCGA-34-5240 TCGA-37-4133 
        2524         2979           80          881          365          238 
TCGA-39-5016 TCGA-39-5021 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-51-4079 
        2253         1947         1084         1086          822           12 
TCGA-51-4080 TCGA-51-4081 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2722 
          12          911         1963         1260         1731          908 
TCGA-60-2723 TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 
        1092         1967           61          639          762           31 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2783 TCGA-66-2787 
          61          700         1946           61          759         1217 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 
        1977          913         1645          122         1492 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-21-1083 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
        2417          146          267          608         1945          131 
TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 TCGA-33-4533 
        1952          822         1485         1470           17         1940 
TCGA-33-4566 TCGA-34-2604 TCGA-34-2608 TCGA-34-2609 TCGA-37-3792 TCGA-37-4129 
        5287          958         1000          951           12          200 
TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-39-5011 TCGA-39-5030 
         247          227          207           12         1454           59 
TCGA-39-5034 TCGA-39-5035 TCGA-43-2576 TCGA-43-2578 TCGA-43-2581 TCGA-60-2695 
        1107          474         1223          684         1176          642 
TCGA-60-2698 TCGA-60-2706 TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2720 
         311         1958          274         1531         1075           97 
TCGA-60-2725 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 
         816           30           31           61           28           30 
TCGA-66-2757 TCGA-66-2769 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
          30         1947           60          790         1955          699 

subtype1 subtype2 subtype3 
      13       12       12 
subtype1 subtype2 subtype3 
    3724     3016     5287 
subtype1 subtype2 subtype3 
     708      913      663 
[1] "13.0 - 3724.0 (708.0)" "12.0 - 3016.0 (913.0)" "12.0 - 5287.0 (663.0)"
D2V2, continuous
          vv
clus       STAGE IA STAGE IB STAGE IIA STAGE IIB STAGE IIIA STAGE IIIB STAGE IV
  subtype1        4       20         2         9          7          2        3
  subtype2        2       25         4        10          6          9        0
  subtype3       14       16         1         8          6          4        1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE IA          4        2       14
  STAGE IB         20       25       16
  STAGE IIA         2        4        1
  STAGE IIB         9       10        8
  STAGE IIIA        7        6        6
  STAGE IIIB        2        9        4
  STAGE IV          3        0        1
[1] 7 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  6 32  7  2
  subtype2  4 44  1  7
  subtype3 20 24  4  3
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        6        4       20
  T2       32       44       24
  T3        7        1        4
  T4        2        7        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 28 14  4  1
  subtype2 30 18  5  3
  subtype3 38  8  4  1
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       28       30       38
  N1       14       18        8
  N2        4        5        4
  N3        1        3        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1
  subtype1 42  3
  subtype2 54  0
  subtype3 50  1
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       42       54       50
  M1        3        0        1
[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 10 37
  subtype2 13 43
  subtype3 21 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   37
  subtype2   13   43
  subtype3   21   30
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       10       13       21
  MALE         37       43       30
[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
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     3
  subtype3                                     2
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      0
  subtype3                                      0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          46
  subtype2                                                          53
  subtype3                                                          49
D2V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       46       53
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       49
[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 46
  subtype2  0 56
  subtype3  1 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   46
  subtype2    0   56
  subtype3    1   50
     clus
vv    subtype1 subtype2 subtype3
  NO         1        0        1
  YES       46       56       50
[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 R1 R2 RX
  subtype1 42  0  1  2
  subtype2 51  1  1  1
  subtype3 46  2  0  2
D2V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       42       51       46
  R1        0        1        2
  R2        1        1        0
  RX        2        1        2
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         2    27
  subtype2     1                         3    30
  subtype3     1                         2    34
D2V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        1
  BLACK OR AFRICAN AMERICAN        2        3        2
  WHITE                           27       30       34
[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  3 25
  subtype2  1 29
  subtype3  0 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   25
  subtype2    1   29
  subtype3    0   34
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        0
  NOT HISPANIC OR LATINO       25       29       34
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = CN_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 91 55
  subtype2 92 37
  subtype3 82 31
subtype1 subtype2 subtype3 
     146      129      113 
subtype1 subtype2 subtype3 
      55       37       31 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3409 TCGA-18-4086 TCGA-18-4721 TCGA-18-5595 
         370          136         2417           85         2754          827 
TCGA-21-1076 TCGA-21-1078 TCGA-21-5784 TCGA-22-0940 TCGA-22-1000 TCGA-22-1002 
        1852          474         1268          608         1945          131 
TCGA-22-1005 TCGA-22-1011 TCGA-22-1016 TCGA-22-1017 TCGA-22-4594 TCGA-22-4596 
        1952           53          822         1485         1470           17 
TCGA-22-4605 TCGA-22-4607 TCGA-22-5472 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 
        1946          587         1964         1651         1952         1952 
TCGA-33-4566 TCGA-33-4583 TCGA-33-4587 TCGA-33-4589 TCGA-34-2604 TCGA-34-2608 
        5287         1941         1970         1948          958         1000 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5241 TCGA-34-8454 TCGA-37-3783 
        2062         1715          707          428          166          120 
TCGA-37-3792 TCGA-37-4129 TCGA-37-4132 TCGA-39-5011 TCGA-39-5021 TCGA-39-5022 
          12          200          227         1454         1947         1996 
TCGA-39-5024 TCGA-39-5028 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5039 
        1964           52           59         1107          474          544 
TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-5668 TCGA-43-6647 TCGA-43-6771 
        1964         1223         1176          349          757         1936 
TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 TCGA-43-A56U TCGA-52-7622 TCGA-52-7811 
         407         1971          296          432          541         1958 
TCGA-52-7812 TCGA-56-5897 TCGA-56-6546 TCGA-56-7221 TCGA-56-7731 TCGA-56-8503 
        1967            3           26           30         1961           41 
TCGA-56-8504 TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-A4ZJ TCGA-56-A5DS 
         178           36           63           17           25            8 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2696 TCGA-60-2704 TCGA-60-2707 TCGA-60-2709 
        1058         2589          109         1943          661         1505 
TCGA-60-2712 TCGA-60-2714 TCGA-60-2715 TCGA-60-2716 TCGA-60-2720 TCGA-60-2725 
         274         1531         1075         1475           97          816 
TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-66-2734 TCGA-66-2737 TCGA-66-2755 
        1973         1955         1947         1311           61           28 
TCGA-66-2765 TCGA-66-2771 TCGA-66-2773 TCGA-66-2778 TCGA-66-2782 TCGA-66-2783 
          61          578         1946          578         1954          759 
TCGA-66-2788 TCGA-68-7756 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-7138 
         699          202          211           96          121         1959 
TCGA-77-7335 TCGA-77-8007 TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 
        1954         1960         1945         1941         1947         1946 
TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G7 
        1951          833         1943         1953         1942         1963 
TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6561 TCGA-85-7697 TCGA-85-7844 TCGA-85-7950 
        1939          713          395           10          911           60 
TCGA-85-8048 TCGA-85-8049 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8580 
          26           60           54           61           21          445 
TCGA-85-8582 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A50Z TCGA-85-A511 
         424          475         1972           19         1973         1972 
TCGA-85-A513 TCGA-90-6837 TCGA-90-A4ED TCGA-90-A59Q TCGA-92-7340 TCGA-92-8064 
          24          758          244          269           82          160 
TCGA-92-8065 TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8023 
          70          189          211          183          256          308 
TCGA-L3-A4E7 TCGA-NC-A5HE 
          35         1722 

$subtype2
TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
        2464         1415          345         1810          862          758 
TCGA-18-4083 TCGA-18-5592 TCGA-21-1070 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
         187           92         3636         1426         3016         2134 
TCGA-21-1077 TCGA-21-1083 TCGA-22-0944 TCGA-22-1012 TCGA-22-4595 TCGA-22-4599 
        1058          267          223          429          734         1161 
TCGA-22-4604 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 
         399          358          965         1933          445         1346 
TCGA-22-5483 TCGA-22-5485 TCGA-22-5489 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 
         573          916         1912         2524         1940         2979 
TCGA-33-4582 TCGA-33-4586 TCGA-34-2596 TCGA-34-2600 TCGA-34-2605 TCGA-34-5231 
        1966          428           80         1874          881         1528 
TCGA-34-5240 TCGA-34-5927 TCGA-37-4133 TCGA-37-5819 TCGA-39-5016 TCGA-39-5019 
         365          941          238          103         2253         1361 
TCGA-39-5027 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6143 TCGA-43-6770 
        1849         1084         1086          822          376          310 
TCGA-43-7657 TCGA-43-7658 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         236         1970          324          423           12           12 
TCGA-51-4081 TCGA-52-7809 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 TCGA-56-A4BX 
         911         1948           30           26            6           46 
TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8391 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N 
          30            4         2167         1723         1072          910 
TCGA-60-2698 TCGA-60-2710 TCGA-60-2711 TCGA-60-2713 TCGA-60-2722 TCGA-63-7023 
         311         1963         1260         1731          908         1952 
TCGA-66-2742 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 
         641          639           31           61          700           61 
TCGA-66-2781 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 
         121         1217         1977          913         1645          122 
TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 
        1492           83          104         1941         1952         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7465 TCGA-77-8009 TCGA-77-8128 
          15         1286         1952          479         1641         1953 
TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 
        1941          293         1961         1684           10         1959 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 
        1290         1280          839           34           18           49 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 TCGA-85-8664 
          16          960          513           11           61            3 
TCGA-85-A4CL TCGA-85-A512 TCGA-85-A53L TCGA-85-A5B5 TCGA-90-7769 TCGA-90-A4EE 
          15         1987           13          111          358          331 
TCGA-92-7341 TCGA-92-8063 TCGA-94-7943 TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH 
         106          122          356         1344          273          222 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         449           36           83 

$subtype3
TCGA-18-3410 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1079 TCGA-21-1080 
         146          396           50         1331          965         3724 
TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-21-A5DI 
         284         3644          962         1032          329          979 
TCGA-22-4591 TCGA-22-4593 TCGA-22-4601 TCGA-22-5478 TCGA-22-5482 TCGA-22-5491 
         623         1067         1057           24          357         1713 
TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4547 TCGA-33-6738 TCGA-34-2609 TCGA-34-5928 
         506           29         1311          822          951          552 
TCGA-37-3789 TCGA-37-4130 TCGA-37-4135 TCGA-37-4141 TCGA-39-5029 TCGA-39-5031 
          13          247          207           12          740          833 
TCGA-43-2578 TCGA-43-3920 TCGA-43-5670 TCGA-43-7656 TCGA-43-8116 TCGA-43-A474 
         684         1007          849          212          358          353 
TCGA-43-A56V TCGA-52-7810 TCGA-56-1622 TCGA-56-5898 TCGA-56-6545 TCGA-56-7222 
         366          923          881          555           62           13 
TCGA-56-7579 TCGA-56-7580 TCGA-56-7822 TCGA-56-8622 TCGA-56-8628 TCGA-56-8629 
          44           40            1           55           16           34 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A5DR TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 
          38            2            4          378          911          642 
TCGA-60-2703 TCGA-60-2706 TCGA-60-2708 TCGA-60-2719 TCGA-60-2721 TCGA-60-2723 
        1950         1958         1963         1297          983         1092 
TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-66-2727 TCGA-66-2744 TCGA-66-2753 
         717          358         1957         1967           30           31 
TCGA-66-2754 TCGA-66-2756 TCGA-66-2757 TCGA-66-2759 TCGA-66-2763 TCGA-66-2768 
          61           30           30          762           30           61 
TCGA-66-2769 TCGA-66-2780 TCGA-66-2785 TCGA-66-2786 TCGA-66-2789 TCGA-66-2790 
        1947         1956           60          790         1955          699 
TCGA-66-2793 TCGA-68-8250 TCGA-77-6842 TCGA-77-6844 TCGA-77-7337 TCGA-77-7463 
        1952          244         1950         1942         1942         1954 
TCGA-77-8130 TCGA-77-8140 TCGA-77-8154 TCGA-77-A5G6 TCGA-85-6560 TCGA-85-7699 
        1945         1962         1092         1955          364            1 
TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 
        1965           35          428           13           13           54 
TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 TCGA-85-A4QQ TCGA-85-A4QR 
          60           55           67           22         1960           25 
TCGA-85-A510 TCGA-90-7766 TCGA-90-7767 TCGA-90-7964 TCGA-94-7033 TCGA-94-A4VJ 
        1967          289           89          428           87          430 
TCGA-96-7544 TCGA-98-8021 TCGA-98-8022 TCGA-NC-A5HG TCGA-NC-A5HI 
        1213          413          224         1548         1135 

subtype1 subtype2 subtype3 
       3        3        1 
subtype1 subtype2 subtype3 
    5287     3636     3724 
subtype1 subtype2 subtype3 
     710      734      430 
[1] "3.0 - 5287.0 (710.0)" "3.0 - 3636.0 (734.0)" "1.0 - 3724.0 (430.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       29       57        0        20        26         17
  subtype2       0       18       46        1        19        24         19
  subtype3       1       25       34        0        13        21         21
          vv
clus       STAGE IIIB STAGE IV
  subtype1          6        1
  subtype2          9        2
  subtype3          5        3
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        1
  STAGE IA         29       18       25
  STAGE IB         57       46       34
  STAGE II          0        1        0
  STAGE IIA        20       19       13
  STAGE IIB        26       24       21
  STAGE IIIA       17       19       21
  STAGE IIIB        6        9        5
  STAGE IV          1        2        3
[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"
          vv
clus       T1 T2 T3 T4
  subtype1 36 94 22  6
  subtype2 28 88 16  6
  subtype3 34 72 10  8
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       36       28       34
  T2       94       88       72
  T3       22       16       10
  T4        6        6        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        N0  N1  N2  N3
  subtype1 107  35  10   2
  subtype2  77  46  12   2
  subtype3  77  32  13   1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      107       77       77
  N1       35       46       32
  N2       10       12       13
  N3        2        2        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1 M1A  MX
  subtype1 133   1   0  23
  subtype2 118   2   0  15
  subtype3 107   2   1  12
D3V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       133      118      107
  M1         1        2        2
  M1A        0        0        1
  MX        23       15       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus         0   1
  subtype1  54 104
  subtype2  26 112
  subtype3  27  97
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   54  104
  subtype2   26  112
  subtype3   27   97
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       54       26       27
  MALE        104      112       97
[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 BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     8
  subtype3                                     3
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      4
  subtype2                                      1
  subtype3                                      1
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       1
  subtype2                                       0
  subtype3                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         152
  subtype2                                                         129
  subtype3                                                         120
D3V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        8
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             4        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      152      129
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      120
[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"
D3V10, binary
          cls
clus         0   1
  subtype1   5 153
  subtype2   6 132
  subtype3   2 122
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  153
  subtype2    6  132
  subtype3    2  122
     clus
vv    subtype1 subtype2 subtype3
  NO         5        6        2
  YES      153      132      122
[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 122   3   2  11
  subtype2 113   3   2   7
  subtype3 107   2   0   0
D3V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      122      113      107
  R1        3        3        2
  R2        2        2        0
  RX       11        7        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     6                         4   114
  subtype2     2                         6    97
  subtype3     1                         7    87
D3V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        2        1
  BLACK OR AFRICAN AMERICAN        4        6        7
  WHITE                          114       97       87
[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"
D3V14, binary
          cls
clus         0   1
  subtype1   6 106
  subtype2   1  81
  subtype3   1  80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6  106
  subtype2    1   81
  subtype3    1   80
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            6        1        1
  NOT HISPANIC OR LATINO      106       81       80
[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 73 31
  subtype2 61 21
  subtype3 55 19
subtype1 subtype2 subtype3 
     104       82       74 
subtype1 subtype2 subtype3 
      31       21       19 
$subtype1
TCGA-18-3417 TCGA-21-5784 TCGA-21-5787 TCGA-21-A5DI TCGA-22-4605 TCGA-22-5481 
         758         1268          329          979         1946         1952 
TCGA-22-5489 TCGA-33-4566 TCGA-33-4589 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 
        1912         5287         1948         2062         1715          428 
TCGA-34-5928 TCGA-34-8454 TCGA-39-5011 TCGA-39-5022 TCGA-39-5024 TCGA-39-5028 
         552          166         1454         1996         1964           52 
TCGA-39-5030 TCGA-39-5034 TCGA-39-5039 TCGA-39-5040 TCGA-43-5668 TCGA-43-6647 
          59         1107          544         1964          349          757 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-43-A56U TCGA-52-7811 TCGA-52-7812 
        1936          212         1970          432         1958         1967 
TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 TCGA-56-7580 TCGA-56-7731 TCGA-56-8503 
           3           62           26           40         1961           41 
TCGA-56-8624 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-A49D TCGA-56-A4ZJ 
          36           63           17           16           38           25 
TCGA-56-A5DR TCGA-56-A5DS TCGA-58-8388 TCGA-58-8393 TCGA-58-A46J TCGA-60-2703 
           4            8          378         1058         2589         1950 
TCGA-60-2704 TCGA-60-2709 TCGA-63-6202 TCGA-63-7021 TCGA-63-7022 TCGA-68-7756 
        1943         1505         1973         1955         1947          202 
TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I TCGA-77-6842 TCGA-77-7138 TCGA-77-8007 
         211           96          121         1950         1959         1960 
TCGA-77-8008 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8145 TCGA-77-8146 
        1945         1941         1947         1946         1943         1954 
TCGA-77-8156 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 
          10         1953         1942         1939          713          364 
TCGA-85-7697 TCGA-85-7950 TCGA-85-8048 TCGA-85-8049 TCGA-85-8287 TCGA-85-8350 
          10           60           26           60           13           60 
TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A50M 
          61           21          424          475         1972           19 
TCGA-85-A50Z TCGA-85-A510 TCGA-85-A511 TCGA-85-A513 TCGA-85-A53L TCGA-90-6837 
        1973         1967         1972           24           13          758 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 
         331          269          122           70           87          356 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 
         189          211          183          256          224          308 
TCGA-L3-A4E7 TCGA-NC-A5HE 
          35         1722 

$subtype2
TCGA-18-4721 TCGA-18-5592 TCGA-21-5786 TCGA-22-4599 TCGA-22-4601 TCGA-22-4613 
        2754           92         1032         1161         1057          358 
TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5482 TCGA-22-5483 
         965         1933          445         1346          357          573 
TCGA-22-5485 TCGA-33-4582 TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-34-5240 
         916         1966         1941          428          822          365 
TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5027 TCGA-39-5031 TCGA-39-5036 
        2253         1361         1947         1849          833         1084 
TCGA-39-5037 TCGA-43-6770 TCGA-43-7657 TCGA-43-8115 TCGA-43-8118 TCGA-43-A475 
        1086          310          236          407         1971          296 
TCGA-46-6025 TCGA-52-7622 TCGA-56-5898 TCGA-56-7223 TCGA-56-7582 TCGA-56-7730 
         324          541          555           30           26            6 
TCGA-56-8629 TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8391 TCGA-58-A46L TCGA-58-A46M 
          34           30            4         2167         1723         1072 
TCGA-58-A46N TCGA-68-7755 TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7141 
         910           83          104         1941         1952           15 
TCGA-77-7142 TCGA-77-7335 TCGA-77-7338 TCGA-77-8009 TCGA-77-8133 TCGA-77-8150 
        1286         1954         1952         1641         1941         1961 
TCGA-77-8153 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 
        1684         1959         1290         1280          839          395 
TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7844 TCGA-85-8052 TCGA-85-8072 
          34           18           49          911           16          513 
TCGA-85-8276 TCGA-85-8277 TCGA-85-8353 TCGA-85-8354 TCGA-85-8580 TCGA-85-A4CL 
          13           11           54           61          445           15 
TCGA-85-A512 TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 TCGA-96-7545 TCGA-96-A4JK 
        1987          358          106          160         1344          273 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         222          449           36           83 

$subtype3
TCGA-18-5595 TCGA-21-5782 TCGA-22-4593 TCGA-22-5472 TCGA-22-5478 TCGA-22-5479 
         827          962         1067         1964           24         1651 
TCGA-22-5480 TCGA-22-5491 TCGA-22-5492 TCGA-22-A5C4 TCGA-33-4587 TCGA-34-5231 
        1952         1713          506           29         1970         1528 
TCGA-34-5239 TCGA-34-5927 TCGA-37-5819 TCGA-39-5029 TCGA-39-5035 TCGA-43-5670 
         707          941          103          740          474          849 
TCGA-43-6143 TCGA-43-8116 TCGA-43-A474 TCGA-43-A56V TCGA-46-6026 TCGA-52-7809 
         376          358          353          366          423         1948 
TCGA-52-7810 TCGA-56-7221 TCGA-56-7222 TCGA-56-7579 TCGA-56-7822 TCGA-56-8504 
         923           30           13           44            1          178 
TCGA-56-8622 TCGA-56-A4BW TCGA-56-A4BX TCGA-58-8390 TCGA-63-7020 TCGA-63-7023 
          55            2           46          911         1957         1952 
TCGA-68-8250 TCGA-77-6844 TCGA-77-7139 TCGA-77-7337 TCGA-77-7463 TCGA-77-7465 
         244         1942         1968         1942         1954          479 
TCGA-77-8128 TCGA-77-8130 TCGA-77-8139 TCGA-77-8140 TCGA-77-8144 TCGA-77-8148 
        1953         1945         1951         1962          833          293 
TCGA-77-8154 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-85-7699 TCGA-85-7710 TCGA-85-7843 
        1092         1955         1963            1         1965           35 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8288 TCGA-85-8351 TCGA-85-8352 TCGA-85-8479 
         960          428           54           55           67           22 
TCGA-85-8664 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A5B5 TCGA-90-7766 TCGA-90-7767 
           3         1960           25          111          289           89 
TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 TCGA-94-A4VJ TCGA-96-7544 TCGA-98-8021 
         428          244           82          430         1213          413 
TCGA-NC-A5HG TCGA-NC-A5HI 
        1548         1135 

subtype1 subtype2 subtype3 
       3        4        1 
subtype1 subtype2 subtype3 
    5287     2754     1970 
subtype1 subtype2 subtype3 
   430.0    548.0    492.5 
[1] "3.0 - 5287.0 (430.0)" "4.0 - 2754.0 (548.0)" "1.0 - 1970.0 (492.5)"
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       25       30        0        19        23         15
  subtype2       1       15       33        1        15        12         12
  subtype3       0       17       19        0        13        13         14
          vv
clus       STAGE IIIB STAGE IV
  subtype1          2        3
  subtype2          2        0
  subtype3          1        0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        0
  STAGE IA         25       15       17
  STAGE IB         30       33       19
  STAGE II          0        1        0
  STAGE IIA        19       15       13
  STAGE IIB        23       12       13
  STAGE IIIA       15       12       14
  STAGE IIIB        2        2        1
  STAGE IV          3        0        0
[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"
          vv
clus       T1 T2 T3 T4
  subtype1 30 66 17  5
  subtype2 26 49 14  2
  subtype3 20 51  6  2
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       30       26       20
  T2       66       49       51
  T3       17       14        6
  T4        5        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
  subtype1 72 32  9
  subtype2 60 24  6
  subtype3 47 23  9
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       72       60       47
  N1       32       24       23
  N2        9        6        9
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A MX
  subtype1 90  2   1 25
  subtype2 76  0   0 15
  subtype3 67  0   0 10
D4V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        90       76       67
  M1         2        0        0
  M1A        1        0        0
  MX        25       15       10
[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"
D4V7, binary
          cls
clus        0  1
  subtype1 33 85
  subtype2 23 68
  subtype3 17 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   85
  subtype2   23   68
  subtype3   17   62
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       33       23       17
  MALE         85       68       62
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     5
  subtype3                                     3
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      3
  subtype2                                      1
  subtype3                                      1
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         114
  subtype2                                                          85
  subtype3                                                          74
D4V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      114       85
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       74
[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"
D4V10, binary
          cls
clus         0   1
  subtype1   5 113
  subtype2   2  89
  subtype3   4  75
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5  113
  subtype2    2   89
  subtype3    4   75
     clus
vv    subtype1 subtype2 subtype3
  NO         5        2        4
  YES      113       89       75
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 88  1  0  8
  subtype2 73  3  1  4
  subtype3 61  1  1  1
D4V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       88       73       61
  R1        1        3        1
  R2        0        1        1
  RX        8        4        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     6                         5    88
  subtype2     1                         1    77
  subtype3     0                         4    59
D4V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            6        1        0
  BLACK OR AFRICAN AMERICAN        5        1        4
  WHITE                           88       77       59
[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"
D4V14, binary
          cls
clus        0  1
  subtype1  4 81
  subtype2  1 59
  subtype3  1 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   81
  subtype2    1   59
  subtype3    1   49
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        1        1
  NOT HISPANIC OR LATINO       81       59       49
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = RPPA_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 40 17
  subtype2 39 30
  subtype3 32 23
subtype1 subtype2 subtype3 
      57       69       55 
subtype1 subtype2 subtype3 
      17       30       23 
$subtype1
TCGA-18-4721 TCGA-21-1072 TCGA-21-1076 TCGA-21-1080 TCGA-21-1083 TCGA-22-5483 
        2754         3016         1852         3724          267          573 
TCGA-22-5489 TCGA-33-4532 TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-6738 
        1912         2524         5287         1966          428          822 
TCGA-34-2605 TCGA-34-5231 TCGA-34-5239 TCGA-34-5927 TCGA-37-4133 TCGA-37-4135 
         881         1528          707          941          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5022 TCGA-39-5034 TCGA-39-5040 
          12          103         2253         1996         1107         1964 
TCGA-43-2578 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 TCGA-43-7658 TCGA-46-6026 
         684          376         1936          212         1970          423 
TCGA-52-7810 TCGA-52-7812 TCGA-60-2708 TCGA-60-2709 TCGA-60-2711 TCGA-60-2714 
         923         1967         1963         1505         1260         1531 
TCGA-60-2716 TCGA-63-7023 TCGA-66-2727 TCGA-66-2758 TCGA-66-2766 TCGA-66-2767 
        1475         1952         1967          639           31           61 
TCGA-66-2783 TCGA-66-2785 TCGA-66-2790 TCGA-66-2794 TCGA-66-2795 TCGA-77-6842 
         759           60          699         1645          122         1950 
TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7465 TCGA-85-7698 TCGA-85-7699 
        1941         1968           15          479           49            1 
TCGA-85-7950 TCGA-90-7767 TCGA-96-7544 
          60           89         1213 

$subtype2
TCGA-18-5592 TCGA-18-5595 TCGA-21-1070 TCGA-21-1071 TCGA-21-1075 TCGA-21-1081 
          92          827         3636         1426         2134          284 
TCGA-21-5784 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-4607 TCGA-22-5471 
        1268         1032          329          608          587          965 
TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5479 TCGA-22-5480 TCGA-22-5492 
        1964         1933         1346         1651         1952          506 
TCGA-33-4547 TCGA-33-4589 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 
        1311         1948          951         2062         1715          428 
TCGA-34-5928 TCGA-37-3789 TCGA-37-3792 TCGA-39-5011 TCGA-39-5019 TCGA-39-5021 
         552           13           12         1454         1361         1947 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5028 TCGA-39-5029 TCGA-39-5035 TCGA-39-5037 
        1964         1849           52          740          474         1086 
TCGA-43-5670 TCGA-43-6770 TCGA-46-6025 TCGA-52-7811 TCGA-56-6545 TCGA-56-6546 
         849          310          324         1958           62           26 
TCGA-56-7222 TCGA-60-2696 TCGA-60-2698 TCGA-60-2703 TCGA-60-2720 TCGA-60-2721 
          13          109          311         1950           97          983 
TCGA-60-2724 TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-66-2768 TCGA-66-2769 
         717          358         1957         1955           61         1947 
TCGA-66-2778 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2791 TCGA-77-6845 
         578          121         1954          699         1977         1952 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-85-6561 TCGA-85-6798 TCGA-85-7843 
        1942         1952         1954          395           34           35 
TCGA-85-7844 TCGA-92-7340 TCGA-94-7033 
         911           82           87 

$subtype3
TCGA-21-1078 TCGA-21-1079 TCGA-21-1082 TCGA-21-5782 TCGA-22-1000 TCGA-22-1011 
         474          965         3644          962         1945           53 
TCGA-22-4591 TCGA-22-4596 TCGA-22-4605 TCGA-22-5474 TCGA-22-5478 TCGA-22-5482 
         623           17         1946          445           24          357 
TCGA-22-5485 TCGA-22-5491 TCGA-34-2596 TCGA-34-2604 TCGA-34-2608 TCGA-37-4129 
         916         1713           80          958         1000          200 
TCGA-39-5030 TCGA-39-5031 TCGA-43-2581 TCGA-43-3394 TCGA-43-5668 TCGA-56-5897 
          59          833         1176          822          349            3 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7730 TCGA-60-2695 TCGA-60-2704 TCGA-60-2706 
         555           30            6          642         1943         1958 
TCGA-60-2710 TCGA-60-2712 TCGA-60-2713 TCGA-60-2719 TCGA-60-2725 TCGA-63-6202 
        1963          274         1731         1297          816         1973 
TCGA-63-7022 TCGA-66-2737 TCGA-66-2770 TCGA-66-2773 TCGA-66-2777 TCGA-66-2800 
        1947           61          700         1946           61         1492 
TCGA-68-7756 TCGA-77-6844 TCGA-77-7142 TCGA-77-7335 TCGA-85-6560 TCGA-85-7696 
         202         1942         1286         1954          364           18 
TCGA-85-7697 TCGA-85-7710 TCGA-90-6837 TCGA-90-7766 TCGA-90-7769 TCGA-94-7943 
          10         1965          758          289          358          356 
TCGA-98-7454 
         256 

subtype1 subtype2 subtype3 
       1       12        3 
subtype1 subtype2 subtype3 
    5287     3636     3644 
subtype1 subtype2 subtype3 
     941      911      700 
[1] "1.0 - 5287.0 (941.0)"  "12.0 - 3636.0 (911.0)" "3.0 - 3644.0 (700.0)" 
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       10       17        0         7        11          7
  subtype2       0        7       28        0        10        15          8
  subtype3       1       11       26        1         6         7          7
          vv
clus       STAGE IIIB
  subtype1          8
  subtype2          4
  subtype3          2
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           0        0        1
  STAGE IA         10        7       11
  STAGE IB         17       28       26
  STAGE II          0        0        1
  STAGE IIA         7       10        6
  STAGE IIB        11       15        7
  STAGE IIIA        7        8        7
  STAGE IIIB        8        4        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 15 35  4  6
  subtype2 11 51  9  2
  subtype3 19 33  7  3
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       15       11       19
  T2       35       51       33
  T3        4        9        7
  T4        6        2        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 34 17  7  2
  subtype2 44 21  5  2
  subtype3 46 11  4  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       34       44       46
  N1       17       21       11
  N2        7        5        4
  N3        2        2        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       M0 MX
  subtype1 54  6
  subtype2 67  4
  subtype3 55  6
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       54       67       55
  MX        6        4        6
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 12 48
  subtype2 17 56
  subtype3 20 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   48
  subtype2   17   56
  subtype3   20   42
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       17       20
  MALE         48       56       42
[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 BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     2
  subtype2                                     0
  subtype3                                     1
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      2
  subtype2                                      0
  subtype3                                      0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          56
  subtype2                                                          73
  subtype3                                                          61
D5V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       56       73
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       61
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
          cls
clus        0  1
  subtype1  4 56
  subtype2  3 70
  subtype3  3 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   56
  subtype2    3   70
  subtype3    3   59
     clus
vv    subtype1 subtype2 subtype3
  NO         4        3        3
  YES       56       70       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"
D5V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 43  0  2  5
  subtype2 55  4  2  4
  subtype3 51  0  0  0
D5V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       43       55       51
  R1        0        4        0
  R2        2        2        0
  RX        5        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     2                         1    46
  subtype2     0                         6    53
  subtype3     1                         2    48
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        0        1
  BLACK OR AFRICAN AMERICAN        1        6        2
  WHITE                           46       53       48
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
          cls
clus        0  1
  subtype1  1 37
  subtype2  3 45
  subtype3  0 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   37
  subtype2    3   45
  subtype3    0   38
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        0
  NOT HISPANIC OR LATINO       37       45       38
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = RPPA_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 34 19
  subtype2 17 19
  subtype3 30 20
  subtype4 30 12
subtype1 subtype2 subtype3 subtype4 
      53       36       50       42 
subtype1 subtype2 subtype3 subtype4 
      19       19       20       12 
$subtype1
TCGA-18-4721 TCGA-18-5592 TCGA-21-1076 TCGA-21-1080 TCGA-21-1082 TCGA-21-1083 
        2754           92         1852         3724         3644          267 
TCGA-21-5787 TCGA-22-1000 TCGA-22-5480 TCGA-22-5483 TCGA-22-5489 TCGA-33-4566 
         329         1945         1952          573         1912         5287 
TCGA-33-4582 TCGA-34-2608 TCGA-34-5239 TCGA-37-3792 TCGA-37-4133 TCGA-37-4135 
        1966         1000          707           12          238          207 
TCGA-37-4141 TCGA-37-5819 TCGA-39-5016 TCGA-39-5024 TCGA-39-5029 TCGA-39-5030 
          12          103         2253         1964          740           59 
TCGA-39-5034 TCGA-39-5035 TCGA-43-2581 TCGA-43-6143 TCGA-43-6771 TCGA-43-7656 
        1107          474         1176          376         1936          212 
TCGA-43-7658 TCGA-52-7812 TCGA-60-2695 TCGA-60-2709 TCGA-60-2711 TCGA-60-2712 
        1970         1967          642         1505         1260          274 
TCGA-60-2714 TCGA-60-2716 TCGA-63-6202 TCGA-63-7023 TCGA-66-2773 TCGA-66-2785 
        1531         1475         1973         1952         1946           60 
TCGA-66-2794 TCGA-77-6842 TCGA-77-6843 TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 
        1645         1950         1941         1968           15         1954 
TCGA-77-7465 TCGA-85-7699 TCGA-85-7950 TCGA-90-7767 TCGA-96-7544 
         479            1           60           89         1213 

$subtype2
TCGA-18-5595 TCGA-21-5784 TCGA-22-1011 TCGA-22-4596 TCGA-22-5472 TCGA-22-5473 
         827         1268           53           17         1964         1933 
TCGA-22-5477 TCGA-22-5478 TCGA-22-5482 TCGA-22-5485 TCGA-34-2596 TCGA-34-2604 
        1346           24          357          916           80          958 
TCGA-34-2609 TCGA-34-5231 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-39-5027 
         951         1528         1715          428          941         1849 
TCGA-39-5037 TCGA-39-5040 TCGA-52-7811 TCGA-56-6546 TCGA-56-7221 TCGA-60-2696 
        1086         1964         1958           26           30          109 
TCGA-60-2706 TCGA-60-2725 TCGA-66-2727 TCGA-66-2737 TCGA-66-2795 TCGA-85-7697 
        1958          816         1967           61          122           10 
TCGA-85-7710 TCGA-85-7844 TCGA-90-6837 TCGA-90-7769 TCGA-94-7033 TCGA-98-7454 
        1965          911          758          358           87          256 

$subtype3
TCGA-21-1070 TCGA-21-1071 TCGA-21-1081 TCGA-21-5782 TCGA-21-5786 TCGA-22-0940 
        3636         1426          284          962         1032          608 
TCGA-22-4607 TCGA-22-5471 TCGA-22-5474 TCGA-22-5479 TCGA-22-5492 TCGA-33-4547 
         587          965          445         1651          506         1311 
TCGA-33-4589 TCGA-34-5232 TCGA-34-5928 TCGA-37-3789 TCGA-39-5011 TCGA-39-5019 
        1948         2062          552           13         1454         1361 
TCGA-39-5021 TCGA-39-5028 TCGA-43-5670 TCGA-46-6025 TCGA-56-5897 TCGA-56-6545 
        1947           52          849          324            3           62 
TCGA-56-7222 TCGA-60-2698 TCGA-60-2703 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
          13          311         1950           97          983          717 
TCGA-60-2726 TCGA-63-7020 TCGA-63-7021 TCGA-66-2768 TCGA-66-2769 TCGA-66-2778 
         358         1957         1955           61         1947          578 
TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-66-2791 TCGA-68-7756 TCGA-77-6845 
         121         1954          699         1977          202         1952 
TCGA-77-7337 TCGA-77-7338 TCGA-77-7463 TCGA-85-6560 TCGA-85-6561 TCGA-85-6798 
        1942         1952         1954          364          395           34 
TCGA-85-7843 TCGA-92-7340 
          35           82 

$subtype4
TCGA-21-1072 TCGA-21-1075 TCGA-21-1078 TCGA-21-1079 TCGA-22-4591 TCGA-22-4605 
        3016         2134          474          965          623         1946 
TCGA-22-5491 TCGA-33-4532 TCGA-33-4586 TCGA-33-6738 TCGA-34-2605 TCGA-37-4129 
        1713         2524          428          822          881          200 
TCGA-39-5022 TCGA-39-5031 TCGA-43-2578 TCGA-43-3394 TCGA-43-5668 TCGA-43-6770 
        1996          833          684          822          349          310 
TCGA-46-6026 TCGA-52-7810 TCGA-56-5898 TCGA-56-7730 TCGA-60-2704 TCGA-60-2708 
         423          923          555            6         1943         1963 
TCGA-60-2710 TCGA-60-2713 TCGA-60-2719 TCGA-63-7022 TCGA-66-2758 TCGA-66-2766 
        1963         1731         1297         1947          639           31 
TCGA-66-2767 TCGA-66-2770 TCGA-66-2777 TCGA-66-2783 TCGA-66-2790 TCGA-66-2800 
          61          700           61          759          699         1492 
TCGA-77-6844 TCGA-77-7142 TCGA-85-7696 TCGA-85-7698 TCGA-90-7766 TCGA-94-7943 
        1942         1286           18           49          289          356 

subtype1 subtype2 subtype3 subtype4 
       1       10        3        6 
subtype1 subtype2 subtype3 subtype4 
    5287     1967     3636     3016 
subtype1 subtype2 subtype3 subtype4 
  1213.0    869.0    708.0    790.5 
[1] "1.0 - 5287.0 (1213.0)" "10.0 - 1967.0 (869.0)" "3.0 - 3636.0 (708.0)" 
[4] "6.0 - 3016.0 (790.5)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0        9       16        0         7         9          8
  subtype2       0        7       17        1         6         5          3
  subtype3       0        4       19        0         7        12          5
  subtype4       1        8       19        0         3         7          6
          vv
clus       STAGE IIIB
  subtype1          5
  subtype2          1
  subtype3          4
  subtype4          4
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        0        0        1
  STAGE IA          9        7        4        8
  STAGE IB         16       17       19       19
  STAGE II          0        1        0        0
  STAGE IIA         7        6        7        3
  STAGE IIB         9        5       12        7
  STAGE IIIA        8        3        5        6
  STAGE IIIB        5        1        4        4
[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 13 32  4  5
  subtype2  9 26  5  1
  subtype3  7 36  6  3
  subtype4 16 25  5  2
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       13        9        7       16
  T2       32       26       36       25
  T3        4        5        6        5
  T4        5        1        3        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 32 14  8  0
  subtype2 31  7  3  0
  subtype3 29 19  1  2
  subtype4 32  9  4  2
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       32       31       29       32
  N1       14        7       19        9
  N2        8        3        1        4
  N3        0        0        2        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       M0 MX
  subtype1 49  5
  subtype2 36  4
  subtype3 47  3
  subtype4 44  4
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       49       36       47       44
  MX        5        4        3        4
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 14 40
  subtype2  9 32
  subtype3 11 41
  subtype4 15 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   40
  subtype2    9   32
  subtype3   11   41
  subtype4   15   33
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       14        9       11       15
  MALE         40       32       41       33
[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"
D6V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     3
  subtype2                                     0
  subtype3                                     0
  subtype4                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      1
  subtype3                                      0
  subtype4                                      0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          50
  subtype2                                                          40
  subtype3                                                          52
  subtype4                                                          48
D6V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              3        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       50       40
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       52       48
[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"
D6V10, binary
          cls
clus        0  1
  subtype1  3 51
  subtype2  1 40
  subtype3  3 49
  subtype4  3 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   51
  subtype2    1   40
  subtype3    3   49
  subtype4    3   45
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3        1        3        3
  YES       51       40       49       45
[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"
D6V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 46  0  0  4
  subtype2 29  0  0  3
  subtype3 37  4  2  1
  subtype4 37  0  2  1
D6V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       46       29       37       37
  R1        0        0        4        0
  R2        0        0        2        2
  RX        4        3        1        1
[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     2                         2    43
  subtype2     1                         2    32
  subtype3     0                         2    39
  subtype4     0                         3    33
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        0        0
  BLACK OR AFRICAN AMERICAN        2        2        2        3
  WHITE                           43       32       39       33
[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"
D6V14, binary
          cls
clus        0  1
  subtype1  2 34
  subtype2  1 26
  subtype3  1 30
  subtype4  0 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   34
  subtype2    1   26
  subtype3    1   30
  subtype4    0   30
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        1        1        0
  NOT HISPANIC OR LATINO       34       26       30       30
[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(7) Variable = MRNASEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 62 29
  subtype2 85 32
  subtype3 81 36
  subtype4 38 23
subtype1 subtype2 subtype3 subtype4 
      91      117      117       61 
subtype1 subtype2 subtype3 subtype4 
      29       32       36       23 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3412 TCGA-18-3414 TCGA-18-3419 TCGA-21-1070 
         370          136          345          396           50         3636 
TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-A5DI TCGA-22-0944 TCGA-22-1011 
        3724          284         3644          979          223           53 
TCGA-22-1012 TCGA-22-4607 TCGA-22-5471 TCGA-22-5491 TCGA-33-4547 TCGA-33-4589 
         429          587          965         1713         1311         1948 
TCGA-34-5232 TCGA-34-5241 TCGA-37-3783 TCGA-37-3789 TCGA-39-5024 TCGA-39-5028 
        2062          428          120           13         1964           52 
TCGA-39-5029 TCGA-39-5031 TCGA-43-6771 TCGA-43-8118 TCGA-43-A56U TCGA-43-A56V 
         740          833         1936         1971          432          366 
TCGA-52-7810 TCGA-52-7811 TCGA-56-5897 TCGA-56-7221 TCGA-56-7579 TCGA-56-7822 
         923         1958            3           30           44            1 
TCGA-56-8504 TCGA-56-8622 TCGA-56-A4BW TCGA-56-A5DR TCGA-56-A5DS TCGA-58-A46L 
         178           55            2            4            8         1723 
TCGA-60-2707 TCGA-60-2708 TCGA-60-2716 TCGA-60-2721 TCGA-60-2724 TCGA-63-7021 
         661         1963         1475          983          717         1955 
TCGA-66-2734 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2771 TCGA-66-2778 
        1311          762           30           61          578          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2788 TCGA-68-7757 TCGA-77-6844 
        1956          121         1954          699          211         1942 
TCGA-77-7138 TCGA-77-7337 TCGA-77-7463 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 
        1959         1942         1954         1945         1945         1941 
TCGA-77-8140 TCGA-77-8144 TCGA-77-8145 TCGA-77-8154 TCGA-77-A5G7 TCGA-77-A5GB 
        1962          833         1943         1092         1963         1939 
TCGA-85-7697 TCGA-85-7710 TCGA-85-7843 TCGA-85-8071 TCGA-85-8479 TCGA-85-8582 
          10         1965           35          428           22          424 
TCGA-85-8666 TCGA-85-A4QQ TCGA-85-A50Z TCGA-90-6837 TCGA-90-7766 TCGA-92-7340 
         475         1960         1973          758          289           82 
TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-8170 TCGA-NC-A5HG 
          70           87          430         1213          211         1548 
TCGA-NC-A5HI 
        1135 

$subtype2
TCGA-18-3408 TCGA-18-3411 TCGA-18-3415 TCGA-18-3416 TCGA-18-4083 TCGA-18-4086 
        2464         1415         1810          862          187           85 
TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 TCGA-21-1072 TCGA-21-1075 
        2754           92          827         1426         3016         2134 
TCGA-21-1076 TCGA-21-1077 TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-4613 
        1852         1058         1161         1057          399          358 
TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 
        1933          445         1346         1651          357          916 
TCGA-33-4532 TCGA-33-4538 TCGA-33-4583 TCGA-33-4586 TCGA-34-2596 TCGA-34-5240 
        2524         2979         1941          428           80          365 
TCGA-37-4133 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
         238         2253         1361         1947         1996         1849 
TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 TCGA-43-A474 TCGA-43-A475 
        1084         1086          822          310          353          296 
TCGA-46-6025 TCGA-51-4079 TCGA-51-4080 TCGA-51-4081 TCGA-56-5898 TCGA-56-7582 
         324           12           12          911          555           26 
TCGA-56-7730 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-58-8391 TCGA-58-A46M 
           6           46           30            4         2167         1072 
TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 TCGA-60-2711 TCGA-60-2722 TCGA-60-2723 
         910         1505         1963         1260          908         1092 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2766 TCGA-66-2770 TCGA-66-2787 
        1967           61          639           31          700         1217 
TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        1977          913         1645          122         1492           83 
TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 TCGA-77-7139 TCGA-77-7141 TCGA-77-7142 
         104         1941         1952         1968           15         1286 
TCGA-77-7335 TCGA-77-7338 TCGA-77-8009 TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 
        1954         1952         1641         1953         1941          293 
TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G8 TCGA-77-A5GA 
        1961         1684           10         1959         1290         1280 
TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 TCGA-85-7698 TCGA-85-7844 
         839          395           34           18           49          911 
TCGA-85-8052 TCGA-85-8070 TCGA-85-8072 TCGA-85-8276 TCGA-85-8277 TCGA-85-8354 
          16          960          513           13           11           61 
TCGA-85-8355 TCGA-85-8580 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A512 TCGA-85-A5B5 
          61          445           15           25         1987          111 
TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 TCGA-96-7545 TCGA-96-A4JK TCGA-J1-A4AH 
         358          106          160         1344          273          222 
TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         449           36           83 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-18-3417 TCGA-21-1078 TCGA-21-1079 TCGA-21-1083 
        2417          146          758          474          965          267 
TCGA-21-5782 TCGA-21-5786 TCGA-22-0940 TCGA-22-1016 TCGA-22-4593 TCGA-22-4595 
         962         1032          608          822         1067          734 
TCGA-22-5478 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 TCGA-22-A5C4 
          24         1952         1952          573         1912           29 
TCGA-33-4533 TCGA-33-4566 TCGA-33-4582 TCGA-33-4587 TCGA-34-2600 TCGA-34-5231 
        1940         5287         1966         1970         1874         1528 
TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-37-3792 TCGA-37-4129 TCGA-37-4130 
         707          941          552           12          200          247 
TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 TCGA-39-5030 TCGA-39-5034 
         227          207           12          103           59         1107 
TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 TCGA-43-2581 TCGA-43-3920 TCGA-43-5668 
         474         1964         1223         1176         1007          349 
TCGA-43-5670 TCGA-43-6143 TCGA-43-6647 TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 
         849          376          757          212          236         1970 
TCGA-43-8115 TCGA-43-8116 TCGA-46-6026 TCGA-52-7809 TCGA-56-6545 TCGA-56-6546 
         407          358          423         1948           62           26 
TCGA-56-7223 TCGA-56-7580 TCGA-56-8503 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 
          30           40           41           63           17           16 
TCGA-56-8629 TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 TCGA-60-2703 TCGA-60-2712 
          34          378          911          642         1950          274 
TCGA-60-2713 TCGA-60-2720 TCGA-60-2726 TCGA-63-6202 TCGA-63-7022 TCGA-63-7023 
        1731           97          358         1973         1947         1952 
TCGA-66-2744 TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2768 
          30           61           28           30           30           61 
TCGA-66-2769 TCGA-66-2785 TCGA-66-2789 TCGA-66-2790 TCGA-66-2793 TCGA-68-8251 
        1947           60         1955          699         1952           96 
TCGA-68-A59I TCGA-77-6842 TCGA-77-7465 TCGA-77-8007 TCGA-77-8136 TCGA-77-8139 
         121         1950          479         1960         1947         1951 
TCGA-77-A5G1 TCGA-77-A5G6 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7950 
        1942         1955          713          364            1           60 
TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8481 
          26           13           54           60           67           21 
TCGA-85-8664 TCGA-85-A4PA TCGA-85-A510 TCGA-85-A511 TCGA-85-A53L TCGA-90-7767 
           3         1972         1967         1972           13           89 
TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-96-A4JL TCGA-98-8021 
         244          331          269          122          183          413 
TCGA-98-8022 TCGA-98-8023 TCGA-NC-A5HE 
         224          308         1722 

$subtype4
TCGA-18-3421 TCGA-21-5784 TCGA-21-5787 TCGA-22-1000 TCGA-22-1002 TCGA-22-1005 
        1331         1268          329         1945          131         1952 
TCGA-22-1017 TCGA-22-4591 TCGA-22-4594 TCGA-22-4596 TCGA-22-4605 TCGA-22-5472 
        1485          623         1470           17         1946         1964 
TCGA-22-5492 TCGA-33-6738 TCGA-34-2608 TCGA-34-5234 TCGA-34-8454 TCGA-39-5011 
         506          822         1000         1715          166         1454 
TCGA-39-5039 TCGA-43-2578 TCGA-52-7622 TCGA-52-7812 TCGA-56-1622 TCGA-56-7222 
         544          684          541         1967          881           13 
TCGA-56-7731 TCGA-56-8624 TCGA-56-A49D TCGA-56-A4ZJ TCGA-58-8393 TCGA-58-A46J 
        1961           36           38           25         1058         2589 
TCGA-60-2696 TCGA-60-2698 TCGA-60-2704 TCGA-60-2706 TCGA-60-2714 TCGA-60-2715 
         109          311         1943         1958         1531         1075 
TCGA-60-2719 TCGA-60-2725 TCGA-63-7020 TCGA-66-2742 TCGA-66-2753 TCGA-66-2767 
        1297          816         1957          641           31           61 
TCGA-66-2773 TCGA-66-2777 TCGA-66-2783 TCGA-66-2786 TCGA-68-7756 TCGA-68-8250 
        1946           61          759          790          202          244 
TCGA-77-8138 TCGA-77-8146 TCGA-77-A5FZ TCGA-85-8049 TCGA-85-8351 TCGA-85-8353 
        1946         1954         1953           60           55           54 
TCGA-85-A50M TCGA-85-A513 TCGA-90-7964 TCGA-94-7943 TCGA-96-8169 TCGA-98-7454 
          19           24          428          356          189          256 
TCGA-L3-A4E7 
          35 

subtype1 subtype2 subtype3 subtype4 
       1        4        1       13 
subtype1 subtype2 subtype3 subtype4 
    3724     3016     5287     2589 
subtype1 subtype2 subtype3 subtype4 
     717      862      407      684 
[1] "1.0 - 3724.0 (717.0)"  "4.0 - 3016.0 (862.0)"  "1.0 - 5287.0 (407.0)" 
[4] "13.0 - 2589.0 (684.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       17       35        0         8        17         14
  subtype2       1       14       51        1        16        23         14
  subtype3       0       23       30        0        21        23         18
  subtype4       0       19       20        0         7         7         11
          vv
clus       STAGE IIIB STAGE IV
  subtype1          2        1
  subtype2          8        0
  subtype3          6        2
  subtype4          3        3
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        1        0        0
  STAGE IA         17       14       23       19
  STAGE IB         35       51       30       20
  STAGE II          0        1        0        0
  STAGE IIA         8       16       21        7
  STAGE IIB        17       23       23        7
  STAGE IIIA       14       14       18       11
  STAGE IIIB        2        8        6        3
  STAGE IV          1        0        2        3
[1] 9 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 21 61 11  3
  subtype2 24 83 14  7
  subtype3 33 70 15  6
  subtype4 22 38  8  3
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       21       24       33       22
  T2       61       83       70       38
  T3       11       14       15        8
  T4        3        7        6        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 60 24  9  1
  subtype2 80 37  9  1
  subtype3 77 38  8  1
  subtype4 45 12  9  2
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       60       80       77       45
  N1       24       37       38       12
  N2        9        9        8        9
  N3        1        1        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1 M1A  MX
  subtype1  80   1   0  13
  subtype2 114   0   0  12
  subtype3 105   2   0  16
  subtype4  58   2   1   9
D7V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        80      114      105       58
  M1         1        0        2        2
  M1A        0        0        0        1
  MX        13       12       16        9
[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"
D7V7, binary
          cls
clus         0   1
  subtype1  23  73
  subtype2  28 100
  subtype3  35  89
  subtype4  21  50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   73
  subtype2   28  100
  subtype3   35   89
  subtype4   21   50
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       23       28       35       21
  MALE         73      100       89       50
[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"
D7V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     2
  subtype2                                     5
  subtype3                                     5
  subtype4                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      2
  subtype2                                      1
  subtype3                                      1
  subtype4                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  subtype4                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          92
  subtype2                                                         122
  subtype3                                                         117
  subtype4                                                          69
D7V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              2        5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       92      122
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              5        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      117       69
[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"
D7V10, binary
          cls
clus         0   1
  subtype1   2  94
  subtype2   2 126
  subtype3   6 118
  subtype4   3  68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   94
  subtype2    2  126
  subtype3    6  118
  subtype4    3   68
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         2        2        6        3
  YES       94      126      118       68
[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"
D7V11, continuous
          vv
clus        R0  R1  R2  RX
  subtype1  75   2   2   3
  subtype2 111   4   0   5
  subtype3  99   2   1   5
  subtype4  56   0   1   5
D7V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       75      111       99       56
  R1        2        4        2        0
  R2        2        0        1        1
  RX        3        5        5        5
[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     2                         5    62
  subtype2     1                         5    91
  subtype3     3                         3    94
  subtype4     3                         3    50
D7V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        1        3        3
  BLACK OR AFRICAN AMERICAN        5        5        3        3
  WHITE                           62       91       94       50
[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"
D7V14, binary
          cls
clus        0  1
  subtype1  4 57
  subtype2  1 77
  subtype3  1 87
  subtype4  2 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   57
  subtype2    1   77
  subtype3    1   87
  subtype4    2   44
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            4        1        1        2
  NOT HISPANIC OR LATINO       57       77       87       44
[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(8) Variable = MRNASEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  97  48
  subtype2 105  38
  subtype3  64  34
subtype1 subtype2 subtype3 
     145      143       98 
subtype1 subtype2 subtype3 
      48       38       34 
$subtype1
TCGA-18-3406 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1070 TCGA-21-1078 
         370          396           50         1331         3636          474 
TCGA-21-1079 TCGA-21-1080 TCGA-21-1081 TCGA-21-1082 TCGA-21-5782 TCGA-21-5784 
         965         3724          284         3644          962         1268 
TCGA-21-A5DI TCGA-22-1000 TCGA-22-1011 TCGA-22-4591 TCGA-22-4595 TCGA-22-4605 
         979         1945           53          623          734         1946 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5472 TCGA-22-5478 TCGA-22-5492 TCGA-22-A5C4 
         587          358         1964           24          506           29 
TCGA-33-4532 TCGA-33-4547 TCGA-33-4582 TCGA-33-4589 TCGA-34-2600 TCGA-34-2608 
        2524         1311         1966         1948         1874         1000 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5241 TCGA-34-5927 TCGA-34-8454 TCGA-37-3783 
        2062         1715          428          941          166          120 
TCGA-37-3789 TCGA-39-5024 TCGA-39-5028 TCGA-39-5029 TCGA-39-5039 TCGA-43-3920 
          13         1964           52          740          544         1007 
TCGA-43-5670 TCGA-43-6647 TCGA-43-6771 TCGA-43-8115 TCGA-43-A56U TCGA-43-A56V 
         849          757         1936          407          432          366 
TCGA-52-7810 TCGA-52-7811 TCGA-56-1622 TCGA-56-5897 TCGA-56-6545 TCGA-56-7222 
         923         1958          881            3           62           13 
TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 
          40         1961            1           41           55           36 
TCGA-56-8625 TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4ZJ TCGA-56-A5DR TCGA-56-A5DS 
          63           38            2           25            4            8 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2696 TCGA-60-2698 TCGA-60-2707 TCGA-60-2708 
        1058         2589          109          311          661         1963 
TCGA-60-2715 TCGA-60-2716 TCGA-60-2719 TCGA-60-2720 TCGA-60-2721 TCGA-60-2724 
        1075         1475         1297           97          983          717 
TCGA-60-2725 TCGA-60-2726 TCGA-63-7020 TCGA-63-7022 TCGA-66-2734 TCGA-66-2742 
         816          358         1957         1947         1311          641 
TCGA-66-2753 TCGA-66-2763 TCGA-66-2765 TCGA-66-2768 TCGA-66-2771 TCGA-66-2773 
          31           30           61           61          578         1946 
TCGA-66-2777 TCGA-66-2778 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 
          61          578         1956          121         1954          790 
TCGA-66-2788 TCGA-66-2793 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I 
         699         1952          202          211          244          121 
TCGA-77-6844 TCGA-77-7138 TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-8008 
        1942         1959         1286         1942         1954         1945 
TCGA-77-8130 TCGA-77-8131 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1945         1941         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8146 TCGA-77-8154 TCGA-77-A5G1 TCGA-77-A5G6 
         833         1943         1954         1092         1942         1955 
TCGA-77-A5G7 TCGA-77-A5GB TCGA-85-8276 TCGA-85-8351 TCGA-85-8479 TCGA-85-8481 
        1963         1939           13           55           22           21 
TCGA-85-8582 TCGA-85-A4QQ TCGA-85-A4QR TCGA-85-A50Z TCGA-90-6837 TCGA-90-7766 
         424         1960           25         1973          758          289 
TCGA-90-7964 TCGA-92-7340 TCGA-92-8065 TCGA-94-7033 TCGA-94-A4VJ TCGA-96-7544 
         428           82           70           87          430         1213 
TCGA-96-8169 TCGA-96-8170 TCGA-96-A4JL TCGA-98-8021 TCGA-L3-A4E7 TCGA-NC-A5HG 
         189          211          183          413           35         1548 
TCGA-NC-A5HI 
        1135 

$subtype2
TCGA-18-3407 TCGA-18-3408 TCGA-18-3411 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 
         136         2464         1415          345         1810          862 
TCGA-18-4083 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-18-5595 TCGA-21-1071 
         187           85         2754           92          827         1426 
TCGA-21-1072 TCGA-21-1075 TCGA-21-1076 TCGA-21-1077 TCGA-22-0944 TCGA-22-1012 
        3016         2134         1852         1058          223          429 
TCGA-22-4599 TCGA-22-4601 TCGA-22-4604 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 
        1161         1057          399          965         1933          445 
TCGA-22-5477 TCGA-22-5479 TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 TCGA-33-4538 
        1346         1651          357          916         1713         2979 
TCGA-33-4583 TCGA-33-4586 TCGA-33-6738 TCGA-34-2596 TCGA-34-5231 TCGA-34-5240 
        1941          428          822           80         1528          365 
TCGA-37-4133 TCGA-39-5016 TCGA-39-5019 TCGA-39-5021 TCGA-39-5022 TCGA-39-5027 
         238         2253         1361         1947         1996         1849 
TCGA-39-5031 TCGA-39-5036 TCGA-39-5037 TCGA-43-3394 TCGA-43-6770 TCGA-43-8118 
         833         1084         1086          822          310         1971 
TCGA-43-A474 TCGA-43-A475 TCGA-46-6025 TCGA-46-6026 TCGA-51-4079 TCGA-51-4080 
         353          296          324          423           12           12 
TCGA-51-4081 TCGA-52-7622 TCGA-56-5898 TCGA-56-7221 TCGA-56-7579 TCGA-56-7582 
         911          541          555           30           44           26 
TCGA-56-7730 TCGA-56-8504 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK 
           6          178           34           46           30            4 
TCGA-58-8391 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 
        2167         1723         1072          910         1505         1963 
TCGA-60-2711 TCGA-60-2713 TCGA-60-2722 TCGA-60-2723 TCGA-63-7021 TCGA-63-7023 
        1260         1731          908         1092         1955         1952 
TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2759 TCGA-66-2766 TCGA-66-2767 
        1967           61          639          762           31           61 
TCGA-66-2770 TCGA-66-2783 TCGA-66-2787 TCGA-66-2791 TCGA-66-2792 TCGA-66-2794 
         700          759         1217         1977          913         1645 
TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 TCGA-68-A59J TCGA-77-6843 TCGA-77-6845 
         122         1492           83          104         1941         1952 
TCGA-77-7139 TCGA-77-7141 TCGA-77-7335 TCGA-77-7338 TCGA-77-8009 TCGA-77-8128 
        1968           15         1954         1952         1641         1953 
TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 
        1941          293         1961         1684           10         1959 
TCGA-77-A5G8 TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6561 TCGA-85-6798 TCGA-85-7696 
        1290         1280          839          395           34           18 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7843 TCGA-85-7844 TCGA-85-8049 TCGA-85-8052 
          10           49           35          911           60           16 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8277 TCGA-85-8354 TCGA-85-8355 
         960          428          513           11           61           61 
TCGA-85-8580 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 
         445          475           15         1972         1987          111 
TCGA-90-7769 TCGA-92-7341 TCGA-92-8063 TCGA-92-8064 TCGA-96-7545 TCGA-96-A4JK 
         358          106          122          160         1344          273 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE 
         222          449           36           83         1722 

$subtype3
TCGA-18-3409 TCGA-18-3410 TCGA-18-3417 TCGA-21-1083 TCGA-21-5786 TCGA-21-5787 
        2417          146          758          267         1032          329 
TCGA-22-0940 TCGA-22-1002 TCGA-22-1005 TCGA-22-1016 TCGA-22-1017 TCGA-22-4593 
         608          131         1952          822         1485         1067 
TCGA-22-4594 TCGA-22-4596 TCGA-22-5480 TCGA-22-5481 TCGA-22-5483 TCGA-22-5489 
        1470           17         1952         1952          573         1912 
TCGA-33-4533 TCGA-33-4566 TCGA-33-4587 TCGA-34-5239 TCGA-34-5928 TCGA-37-3792 
        1940         5287         1970          707          552           12 
TCGA-37-4129 TCGA-37-4130 TCGA-37-4132 TCGA-37-4135 TCGA-37-4141 TCGA-37-5819 
         200          247          227          207           12          103 
TCGA-39-5011 TCGA-39-5030 TCGA-39-5034 TCGA-39-5035 TCGA-39-5040 TCGA-43-2576 
        1454           59         1107          474         1964         1223 
TCGA-43-2578 TCGA-43-2581 TCGA-43-5668 TCGA-43-6143 TCGA-43-7656 TCGA-43-7657 
         684         1176          349          376          212          236 
TCGA-43-7658 TCGA-43-8116 TCGA-52-7809 TCGA-52-7812 TCGA-56-6546 TCGA-56-7223 
        1970          358         1948         1967           26           30 
TCGA-56-8626 TCGA-56-8628 TCGA-58-8388 TCGA-58-8390 TCGA-60-2695 TCGA-60-2703 
          17           16          378          911          642         1950 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2712 TCGA-60-2714 TCGA-63-6202 TCGA-66-2744 
        1943         1958          274         1531         1973           30 
TCGA-66-2754 TCGA-66-2755 TCGA-66-2756 TCGA-66-2757 TCGA-66-2769 TCGA-66-2785 
          61           28           30           30         1947           60 
TCGA-66-2789 TCGA-66-2790 TCGA-68-8251 TCGA-77-6842 TCGA-77-7465 TCGA-77-8007 
        1955          699           96         1950          479         1960 
TCGA-77-A5FZ TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7710 TCGA-85-7950 
        1953          713          364            1         1965           60 
TCGA-85-8048 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8352 TCGA-85-8353 
          26           13           54           60           67           54 
TCGA-85-8664 TCGA-85-A4PA TCGA-85-A50M TCGA-85-A510 TCGA-85-A513 TCGA-85-A53L 
           3         1972           19         1967           24           13 
TCGA-90-7767 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-94-7943 TCGA-98-7454 
          89          244          331          269          356          256 
TCGA-98-8022 TCGA-98-8023 
         224          308 

subtype1 subtype2 subtype3 
       1        4        1 
subtype1 subtype2 subtype3 
    3724     3016     5287 
subtype1 subtype2 subtype3 
     734      822      361 
[1] "1.0 - 3724.0 (734.0)" "4.0 - 3016.0 (822.0)" "1.0 - 5287.0 (361.0)"
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       26       56        0        16        26         23
  subtype2       1       21       57        1        19        28         19
  subtype3       0       26       23        0        17        16         15
          vv
clus       STAGE IIIB STAGE IV
  subtype1          3        4
  subtype2         10        0
  subtype3          6        2
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        0
  STAGE IA         26       21       26
  STAGE IB         56       57       23
  STAGE II          0        1        0
  STAGE IIA        16       19       17
  STAGE IIB        26       28       16
  STAGE IIIA       23       19       15
  STAGE IIIB        3       10        6
  STAGE IV          4        0        2
[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"
          vv
clus        T1  T2  T3  T4
  subtype1  32  96  22   6
  subtype2  32 101  17   7
  subtype3  36  55   9   6
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       32       32       36
  T2       96      101       55
  T3       22       17        9
  T4        6        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        N0  N1  N2  N3
  subtype1 101  39  12   1
  subtype2  96  44  13   3
  subtype3  65  28  10   1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0      101       96       65
  N1       39       44       28
  N2       12       13       10
  N3        1        3        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1 M1A  MX
  subtype1 128   3   1  21
  subtype2 137   0   0  17
  subtype3  92   2   0  12
D8V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0       128      137       92
  M1         3        0        2
  M1A        1        0        0
  MX        21       17       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  50 106
  subtype2  30 127
  subtype3  27  79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   50  106
  subtype2   30  127
  subtype3   27   79
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       50       30       27
  MALE        106      127       79
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     6
  subtype3                                     5
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      3
  subtype2                                      1
  subtype3                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         152
  subtype2                                                         150
  subtype3                                                          98
D8V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        6
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      152      150
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       98
[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"
D8V10, binary
          cls
clus         0   1
  subtype1   4 152
  subtype2   6 151
  subtype3   3 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  152
  subtype2    6  151
  subtype3    3  103
     clus
vv    subtype1 subtype2 subtype3
  NO         4        6        3
  YES      152      151      103
[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"
D8V11, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 125   2   1   9
  subtype2 130   4   3   6
  subtype3  86   2   0   3
D8V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      125      130       86
  R1        2        4        2
  R2        1        3        0
  RX        9        6        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     3                         8   102
  subtype2     2                         5   113
  subtype3     4                         3    82
D8V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            3        2        4
  BLACK OR AFRICAN AMERICAN        8        5        3
  WHITE                          102      113       82
[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"
D8V14, binary
          cls
clus        0  1
  subtype1  4 95
  subtype2  2 94
  subtype3  2 76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   95
  subtype2    2   94
  subtype3    2   76
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        2        2
  NOT HISPANIC OR LATINO       95       94       76
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 67 48
  subtype2 68 14
  subtype3 65 23
  subtype4 37 14
  subtype5 17 10
subtype1 subtype2 subtype3 subtype4 subtype5 
     115       82       88       51       27 
subtype1 subtype2 subtype3 subtype4 subtype5 
      48       14       23       14       10 
$subtype1
TCGA-18-3406 TCGA-18-3407 TCGA-18-3408 TCGA-18-3410 TCGA-18-3411 TCGA-18-3412 
         370          136         2464          146         1415          345 
TCGA-18-3414 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 TCGA-18-3419 TCGA-18-3421 
         396         1810          862          758           50         1331 
TCGA-18-5592 TCGA-21-1072 TCGA-21-1078 TCGA-21-1079 TCGA-21-1080 TCGA-21-1083 
          92         3016          474          965         3724          267 
TCGA-21-5782 TCGA-21-5786 TCGA-21-5787 TCGA-22-0940 TCGA-22-0944 TCGA-22-1011 
         962         1032          329          608          223           53 
TCGA-22-1012 TCGA-22-4594 TCGA-22-4595 TCGA-22-4596 TCGA-22-4601 TCGA-22-4604 
         429         1470          734           17         1057          399 
TCGA-22-4607 TCGA-22-4613 TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5480 
         587          358          965         1933          445         1952 
TCGA-22-5489 TCGA-22-5492 TCGA-33-4532 TCGA-33-4533 TCGA-33-4538 TCGA-33-4547 
        1912          506         2524         1940         2979         1311 
TCGA-33-4566 TCGA-33-4582 TCGA-33-4586 TCGA-33-4589 TCGA-34-2605 TCGA-34-5241 
        5287         1966          428         1948          881          428 
TCGA-37-3789 TCGA-37-3792 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
          13           12          247          238          207           12 
TCGA-37-5819 TCGA-39-5011 TCGA-39-5021 TCGA-39-5028 TCGA-39-5029 TCGA-39-5030 
         103         1454         1947           52          740           59 
TCGA-39-5034 TCGA-39-5035 TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 
        1107          474         1084          544         1223         1176 
TCGA-43-3394 TCGA-43-3920 TCGA-43-5668 TCGA-51-4081 TCGA-56-1622 TCGA-56-5897 
         822         1007          349          911          881            3 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2706 TCGA-60-2708 TCGA-60-2712 TCGA-60-2713 
         642          109         1958         1963          274         1731 
TCGA-60-2714 TCGA-60-2716 TCGA-60-2721 TCGA-60-2723 TCGA-60-2724 TCGA-66-2734 
        1531         1475          983         1092          717         1311 
TCGA-66-2737 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2754 TCGA-66-2755 
          61          641           30           31           61           28 
TCGA-66-2758 TCGA-66-2759 TCGA-66-2763 TCGA-66-2765 TCGA-66-2767 TCGA-66-2771 
         639          762           30           61           61          578 
TCGA-66-2777 TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2783 TCGA-66-2785 
          61         1956          121         1954          759           60 
TCGA-66-2786 TCGA-66-2787 TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2791 
         790         1217          699         1955          699         1977 
TCGA-66-2792 TCGA-66-2795 TCGA-77-8007 TCGA-77-8144 TCGA-85-7699 TCGA-90-A59Q 
         913          122         1960          833            1          269 
TCGA-94-7033 
          87 

$subtype2
TCGA-18-5595 TCGA-21-1075 TCGA-22-5481 TCGA-22-5491 TCGA-33-4587 TCGA-34-5231 
         827         2134         1952         1713         1970         1528 
TCGA-34-5928 TCGA-37-3783 TCGA-39-5037 TCGA-43-5670 TCGA-43-6143 TCGA-43-7657 
         552          120         1086          849          376          236 
TCGA-43-7658 TCGA-43-8115 TCGA-43-A474 TCGA-46-6025 TCGA-52-7809 TCGA-56-7222 
        1970          407          353          324         1948           13 
TCGA-56-7223 TCGA-56-7579 TCGA-56-7580 TCGA-56-7582 TCGA-56-8504 TCGA-56-8629 
          30           44           40           26          178           34 
TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8391 
           2           46           30            4            4         2167 
TCGA-58-A46N TCGA-60-2703 TCGA-63-7021 TCGA-66-2766 TCGA-66-2768 TCGA-68-7755 
         910         1950         1955           31           61           83 
TCGA-68-8251 TCGA-77-6845 TCGA-77-7138 TCGA-77-7139 TCGA-77-7335 TCGA-77-7465 
          96         1952         1959         1968         1954          479 
TCGA-77-8128 TCGA-77-8133 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
        1953         1941          293         1961         1684         1092 
TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G8 TCGA-85-6561 TCGA-85-7710 
          10         1959         1955         1290          395         1965 
TCGA-85-7843 TCGA-85-8070 TCGA-85-8276 TCGA-85-8288 TCGA-85-8352 TCGA-85-8354 
          35          960           13           54           67           61 
TCGA-85-8479 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A511 
          22          445          475           25         1973         1972 
TCGA-85-A512 TCGA-85-A53L TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 TCGA-92-8063 
        1987           13           89          358          106          122 
TCGA-92-8064 TCGA-92-8065 TCGA-94-7943 TCGA-96-A4JK TCGA-J1-A4AH TCGA-L3-A524 
         160           70          356          273          222          449 
TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
          83         1722         1548         1135 

$subtype3
TCGA-21-5784 TCGA-21-A5DI TCGA-22-4593 TCGA-22-4605 TCGA-22-5472 TCGA-22-5479 
        1268          979         1067         1946         1964         1651 
TCGA-22-5483 TCGA-22-A5C4 TCGA-33-6738 TCGA-34-2609 TCGA-34-5232 TCGA-34-5234 
         573           29          822          951         2062         1715 
TCGA-34-5239 TCGA-34-8454 TCGA-39-5019 TCGA-39-5024 TCGA-39-5027 TCGA-39-5040 
         707          166         1361         1964         1849         1964 
TCGA-43-6647 TCGA-43-6771 TCGA-43-7656 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
         757         1936          212          923         1958         1967 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7731 TCGA-56-7822 TCGA-56-8503 TCGA-56-8624 
          62           26         1961            1           41           36 
TCGA-56-8626 TCGA-56-8628 TCGA-56-A4ZJ TCGA-58-8388 TCGA-58-8393 TCGA-58-A46J 
          17           16           25          378         1058         2589 
TCGA-60-2698 TCGA-60-2704 TCGA-60-2720 TCGA-60-2725 TCGA-63-6202 TCGA-63-7020 
         311         1943           97          816         1973         1957 
TCGA-63-7022 TCGA-68-7756 TCGA-68-7757 TCGA-68-8250 TCGA-68-A59I TCGA-77-6844 
        1947          202          211          244          121         1942 
TCGA-77-7142 TCGA-77-7337 TCGA-77-7463 TCGA-77-8008 TCGA-77-8130 TCGA-77-8131 
        1286         1942         1954         1945         1945         1941 
TCGA-77-8138 TCGA-77-8145 TCGA-77-8146 TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5GB 
        1946         1943         1954         1953         1942         1939 
TCGA-85-6560 TCGA-85-7697 TCGA-85-7698 TCGA-85-8048 TCGA-85-8049 TCGA-85-8350 
         364           10           49           26           60           60 
TCGA-85-8351 TCGA-85-8353 TCGA-85-8355 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4PA 
          55           54           61           21          424         1972 
TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A513 TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 
        1960           19           24          758          289          428 
TCGA-92-7340 TCGA-94-A4VJ TCGA-96-7544 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL 
          82          430         1213         1344          211          183 
TCGA-98-7454 TCGA-98-8022 TCGA-98-8023 TCGA-L3-A4E7 
         256          224          308           35 

$subtype4
TCGA-18-4086 TCGA-18-4721 TCGA-21-1076 TCGA-21-1077 TCGA-22-5477 TCGA-22-5482 
          85         2754         1852         1058         1346          357 
TCGA-22-5485 TCGA-33-4583 TCGA-34-2596 TCGA-34-2608 TCGA-34-5240 TCGA-39-5022 
         916         1941           80         1000          365         1996 
TCGA-43-6770 TCGA-43-8118 TCGA-43-A475 TCGA-51-4079 TCGA-51-4080 TCGA-52-7622 
         310         1971          296           12           12          541 
TCGA-56-5898 TCGA-56-7221 TCGA-56-7730 TCGA-56-8622 TCGA-58-A46L TCGA-58-A46M 
         555           30            6           55         1723         1072 
TCGA-60-2709 TCGA-60-2710 TCGA-60-2722 TCGA-66-2727 TCGA-66-2770 TCGA-66-2794 
        1505         1963          908         1967          700         1645 
TCGA-66-2800 TCGA-68-A59J TCGA-77-6843 TCGA-77-7141 TCGA-77-7338 TCGA-77-8009 
        1492          104         1941           15         1952         1641 
TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-7696 TCGA-85-7844 
        1280          839          713           34           18          911 
TCGA-85-7950 TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-A4CL TCGA-90-A4ED 
          60           16          428          513           15          244 
TCGA-90-A4EE TCGA-98-8021 TCGA-LA-A446 
         331          413           36 

$subtype5
TCGA-22-4591 TCGA-22-5478 TCGA-34-2600 TCGA-34-2604 TCGA-34-5927 TCGA-39-5031 
         623           24         1874          958          941          833 
TCGA-43-2578 TCGA-43-8116 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-56-8625 
         684          358          432          366          423           63 
TCGA-56-A49D TCGA-58-8390 TCGA-60-2711 TCGA-60-2719 TCGA-66-2793 TCGA-77-6842 
          38          911         1260         1297         1952         1950 
TCGA-77-8136 TCGA-77-8139 TCGA-77-8140 TCGA-77-A5G7 TCGA-85-8287 TCGA-85-8664 
        1947         1951         1962         1963           13            3 
TCGA-85-A510 TCGA-85-A5B5 TCGA-96-8169 
        1967          111          189 

subtype1 subtype2 subtype3 subtype4 subtype5 
       1        2        1        6        3 
subtype1 subtype2 subtype3 subtype4 subtype5 
    5287     2167     2589     2754     1967 
subtype1 subtype2 subtype3 subtype4 subtype5 
   699.0    385.5    757.5    555.0    833.0 
[1] "1.0 - 5287.0 (699.0)" "2.0 - 2167.0 (385.5)" "1.0 - 2589.0 (757.5)"
[4] "6.0 - 2754.0 (555.0)" "3.0 - 1967.0 (833.0)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       16       48        0         6        19         21
  subtype2       1       10       27        1        20        18         15
  subtype3       1       20       27        0        17        17         12
  subtype4       0       12       21        0         5         7          3
  subtype5       0       10        5        0         1         8          4
          vv
clus       STAGE IIIB STAGE IV
  subtype1          8        3
  subtype2          1        0
  subtype3          3        2
  subtype4          4        0
  subtype5          1        0
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        1        1        0        0
  STAGE IA         16       10       20       12       10
  STAGE IB         48       27       27       21        5
  STAGE II          0        1        0        0        0
  STAGE IIA         6       20       17        5        1
  STAGE IIB        19       18       17        7        8
  STAGE IIIA       21       15       12        3        4
  STAGE IIIB        8        1        3        4        1
  STAGE IV          3        0        2        0        0
[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"
          vv
clus       T1 T2 T3 T4
  subtype1 22 80 11  8
  subtype2 17 64 12  1
  subtype3 27 51 16  5
  subtype4 15 32  3  3
  subtype5 11 13  4  1
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1       22       17       27       15       11
  T2       80       64       51       32       13
  T3       11       12       16        3        4
  T4        8        1        5        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 76 28 13  4
  subtype2 51 31 10  0
  subtype3 62 27  6  0
  subtype4 37 13  3  0
  subtype5 18  8  3  0
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       76       51       62       37       18
  N1       28       31       27       13        8
  N2       13       10        6        3        3
  N3        4        0        0        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        M0  M1 M1A  MX
  subtype1 113   3   0   3
  subtype2  75   0   0  18
  subtype3  78   1   1  19
  subtype4  44   0   0   6
  subtype5  26   0   0   3
D9V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0       113       75       78       44       26
  M1         3        0        1        0        0
  M1A        0        0        1        0        0
  MX         3       18       19        6        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"
D9V7, binary
          cls
clus        0  1
  subtype1 31 90
  subtype2 20 74
  subtype3 25 74
  subtype4 12 41
  subtype5 13 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   90
  subtype2   20   74
  subtype3   25   74
  subtype4   12   41
  subtype5   13   16
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       31       20       25       12       13
  MALE         90       74       74       41       16
[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"
D9V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     1
  subtype2                                     4
  subtype3                                     1
  subtype4                                     4
  subtype5                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      2
  subtype3                                      3
  subtype4                                      0
  subtype5                                      0
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       1
  subtype3                                       0
  subtype4                                       0
  subtype5                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                         119
  subtype2                                                          87
  subtype3                                                          95
  subtype4                                                          49
  subtype5                                                          29
D9V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      119       87
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             3        0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       95       49
                                                             clus
vv                                                            subtype5
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       29
[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"
D9V10, binary
          cls
clus         0   1
  subtype1   4 117
  subtype2   3  91
  subtype3   4  95
  subtype4   0  53
  subtype5   1  28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4  117
  subtype2    3   91
  subtype3    4   95
  subtype4    0   53
  subtype5    1   28
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         4        3        4        0        1
  YES      117       91       95       53       28
[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"
D9V11, continuous
          vv
clus        R0  R1  R2  RX
  subtype1 109   2   2   2
  subtype2  74   1   0   6
  subtype3  75   2   0   5
  subtype4  42   2   0   2
  subtype5  22   0   1   1
D9V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0      109       74       75       42       22
  R1        2        1        2        2        0
  R2        2        0        0        0        1
  RX        2        6        5        2        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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         4    73
  subtype2     2                         0    75
  subtype3     4                         6    75
  subtype4     0                         4    39
  subtype5     0                         2    20
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        2        4        0        0
  BLACK OR AFRICAN AMERICAN        4        0        6        4        2
  WHITE                           73       75       75       39       20
[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"
D9V14, binary
          cls
clus        0  1
  subtype1  3 67
  subtype2  1 63
  subtype3  2 69
  subtype4  1 35
  subtype5  0 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   67
  subtype2    1   63
  subtype3    2   69
  subtype4    1   35
  subtype5    0   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        1        2        1        0
  NOT HISPANIC OR LATINO       67       63       69       35       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"

Clustering(10) Variable = MIRSEQ_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  52  19
  subtype2  63  34
  subtype3 102  43
  subtype4  37  13
subtype1 subtype2 subtype3 subtype4 
      71       97      145       50 
subtype1 subtype2 subtype3 subtype4 
      19       34       43       13 
$subtype1
TCGA-18-3406 TCGA-18-3408 TCGA-18-4086 TCGA-18-4721 TCGA-18-5592 TCGA-21-1072 
         370         2464           85         2754           92         3016 
TCGA-21-1076 TCGA-21-1077 TCGA-22-1012 TCGA-22-5471 TCGA-22-5473 TCGA-22-5477 
        1852         1058          429          965         1933         1346 
TCGA-22-5482 TCGA-33-4583 TCGA-33-4586 TCGA-33-4589 TCGA-34-2596 TCGA-34-2605 
         357         1941          428         1948           80          881 
TCGA-34-5240 TCGA-39-5022 TCGA-43-6770 TCGA-43-A474 TCGA-43-A475 TCGA-51-4079 
         365         1996          310          353          296           12 
TCGA-51-4080 TCGA-51-4081 TCGA-56-7582 TCGA-56-7730 TCGA-56-8622 TCGA-58-8391 
          12          911           26            6           55         2167 
TCGA-58-A46M TCGA-58-A46N TCGA-60-2709 TCGA-60-2710 TCGA-60-2713 TCGA-60-2722 
        1072          910         1505         1963         1731          908 
TCGA-60-2723 TCGA-63-7022 TCGA-66-2727 TCGA-66-2737 TCGA-66-2758 TCGA-66-2770 
        1092         1947         1967           61          639          700 
TCGA-66-2787 TCGA-66-2791 TCGA-66-2794 TCGA-66-2795 TCGA-66-2800 TCGA-68-7755 
        1217         1977         1645          122         1492           83 
TCGA-68-A59J TCGA-77-6843 TCGA-77-7141 TCGA-77-7338 TCGA-77-8009 TCGA-77-A5G3 
         104         1941           15         1952         1641         1959 
TCGA-77-A5G6 TCGA-77-A5GF TCGA-85-6798 TCGA-85-7696 TCGA-85-7844 TCGA-85-7950 
        1955          839           34           18          911           60 
TCGA-85-8052 TCGA-85-8071 TCGA-85-8072 TCGA-85-8352 TCGA-85-A4CL TCGA-85-A512 
          16          428          513           67           15         1987 
TCGA-90-7769 TCGA-90-A4EE TCGA-98-8023 TCGA-J1-A4AH TCGA-LA-A446 
         358          331          308          222           36 

$subtype2
TCGA-18-3407 TCGA-18-3410 TCGA-18-3412 TCGA-18-3415 TCGA-18-3416 TCGA-18-3417 
         136          146          345         1810          862          758 
TCGA-18-5595 TCGA-21-1078 TCGA-21-1080 TCGA-21-1083 TCGA-21-5786 TCGA-22-0940 
         827          474         3724          267         1032          608 
TCGA-22-0944 TCGA-22-1011 TCGA-22-4594 TCGA-22-4601 TCGA-22-4604 TCGA-22-4607 
         223           53         1470         1057          399          587 
TCGA-22-5474 TCGA-22-5479 TCGA-22-5480 TCGA-22-5481 TCGA-22-5489 TCGA-22-5491 
         445         1651         1952         1952         1912         1713 
TCGA-33-4547 TCGA-33-4566 TCGA-37-3783 TCGA-37-3792 TCGA-39-5011 TCGA-39-5021 
        1311         5287          120           12         1454         1947 
TCGA-39-5036 TCGA-39-5039 TCGA-43-2576 TCGA-43-2581 TCGA-43-6771 TCGA-43-7657 
        1084          544         1223         1176         1936          236 
TCGA-43-7658 TCGA-52-7809 TCGA-52-7810 TCGA-56-5897 TCGA-56-6545 TCGA-56-7579 
        1970         1948          923            3           62           44 
TCGA-56-7580 TCGA-56-8504 TCGA-56-A4BW TCGA-56-A4ZK TCGA-58-8388 TCGA-58-A46L 
          40          178            2            4          378         1723 
TCGA-60-2695 TCGA-60-2696 TCGA-60-2712 TCGA-60-2716 TCGA-60-2721 TCGA-63-7021 
         642          109          274         1475          983         1955 
TCGA-66-2734 TCGA-66-2742 TCGA-66-2744 TCGA-66-2753 TCGA-66-2755 TCGA-66-2759 
        1311          641           30           31           28          762 
TCGA-66-2763 TCGA-66-2765 TCGA-66-2766 TCGA-66-2767 TCGA-66-2768 TCGA-66-2771 
          30           61           31           61           61          578 
TCGA-66-2780 TCGA-66-2781 TCGA-66-2782 TCGA-66-2786 TCGA-68-8251 TCGA-77-6845 
        1956          121         1954          790           96         1952 
TCGA-77-7138 TCGA-77-7335 TCGA-77-7337 TCGA-77-7465 TCGA-77-8128 TCGA-77-8133 
        1959         1954         1942          479         1953         1941 
TCGA-77-A5G8 TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-8048 TCGA-85-8276 
        1290           10           49         1965           26           13 
TCGA-85-8288 TCGA-85-8355 TCGA-85-8479 TCGA-85-A53L TCGA-90-7767 TCGA-90-A59Q 
          54           61           22           13           89          269 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-96-7544 TCGA-L3-A524 TCGA-NC-A5HE 
         106          160           87         1213          449         1722 
TCGA-NC-A5HG 
        1548 

$subtype3
TCGA-18-3411 TCGA-18-3414 TCGA-18-3419 TCGA-18-3421 TCGA-21-1075 TCGA-21-1079 
        1415          396           50         1331         2134          965 
TCGA-21-5782 TCGA-21-5787 TCGA-21-A5DI TCGA-22-4591 TCGA-22-4593 TCGA-22-4595 
         962          329          979          623         1067          734 
TCGA-22-4605 TCGA-22-4613 TCGA-22-5478 TCGA-22-5483 TCGA-22-5485 TCGA-22-5492 
        1946          358           24          573          916          506 
TCGA-22-A5C4 TCGA-33-4532 TCGA-33-4533 TCGA-33-4582 TCGA-33-4587 TCGA-34-2600 
          29         2524         1940         1966         1970         1874 
TCGA-34-2604 TCGA-34-2609 TCGA-34-5231 TCGA-34-5241 TCGA-34-5927 TCGA-34-5928 
         958          951         1528          428          941          552 
TCGA-34-8454 TCGA-37-3789 TCGA-37-4130 TCGA-37-4133 TCGA-37-4135 TCGA-37-4141 
         166           13          247          238          207           12 
TCGA-37-5819 TCGA-39-5024 TCGA-39-5027 TCGA-39-5029 TCGA-39-5030 TCGA-39-5031 
         103         1964         1849          740           59          833 
TCGA-39-5034 TCGA-39-5037 TCGA-39-5040 TCGA-43-2578 TCGA-43-3394 TCGA-43-3920 
        1107         1086         1964          684          822         1007 
TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 TCGA-43-7656 TCGA-43-8115 TCGA-43-8116 
         349          849          376          212          407          358 
TCGA-43-8118 TCGA-43-A56U TCGA-43-A56V TCGA-46-6026 TCGA-52-7622 TCGA-52-7811 
        1971          432          366          423          541         1958 
TCGA-56-1622 TCGA-56-5898 TCGA-56-7221 TCGA-56-7222 TCGA-56-7223 TCGA-56-7731 
         881          555           30           13           30         1961 
TCGA-56-7822 TCGA-56-8503 TCGA-56-8625 TCGA-56-8626 TCGA-56-8628 TCGA-56-8629 
           1           41           63           17           16           34 
TCGA-56-A49D TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A5DR TCGA-58-8390 TCGA-60-2703 
          38           46           30            4          911         1950 
TCGA-60-2704 TCGA-60-2706 TCGA-60-2708 TCGA-60-2711 TCGA-60-2714 TCGA-60-2719 
        1943         1958         1963         1260         1531         1297 
TCGA-60-2724 TCGA-60-2725 TCGA-63-7020 TCGA-66-2754 TCGA-66-2777 TCGA-66-2785 
         717          816         1957           61           61           60 
TCGA-66-2788 TCGA-66-2789 TCGA-66-2790 TCGA-66-2792 TCGA-66-2793 TCGA-68-7757 
         699         1955          699          913         1952          211 
TCGA-68-8250 TCGA-68-A59I TCGA-77-6842 TCGA-77-6844 TCGA-77-7139 TCGA-77-7142 
         244          121         1950         1942         1968         1286 
TCGA-77-7463 TCGA-77-8008 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8140 
        1954         1945         1947         1946         1951         1962 
TCGA-77-8144 TCGA-77-8145 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 
         833         1943          293         1961         1684           10 
TCGA-77-A5G1 TCGA-77-A5G7 TCGA-77-A5GH TCGA-85-6560 TCGA-85-7699 TCGA-85-7843 
        1942         1963          713          364            1           35 
TCGA-85-8049 TCGA-85-8070 TCGA-85-8287 TCGA-85-8351 TCGA-85-8354 TCGA-85-8481 
          60          960           13           55           61           21 
TCGA-85-8580 TCGA-85-8582 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4QR TCGA-85-A510 
         445          424            3          475           25         1967 
TCGA-85-A511 TCGA-85-A5B5 TCGA-90-7766 TCGA-90-A4ED TCGA-92-8063 TCGA-92-8065 
        1972          111          289          244          122           70 
TCGA-94-A4VJ TCGA-96-8169 TCGA-96-A4JK TCGA-98-8021 TCGA-98-8022 TCGA-MF-A522 
         430          189          273          413          224           83 
TCGA-NC-A5HI 
        1135 

$subtype4
TCGA-21-5784 TCGA-22-4596 TCGA-22-5472 TCGA-33-4538 TCGA-33-6738 TCGA-34-2608 
        1268           17         1964         2979          822         1000 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-39-5019 TCGA-39-5028 TCGA-39-5035 
        2062         1715          707         1361           52          474 
TCGA-43-6647 TCGA-46-6025 TCGA-52-7812 TCGA-56-6546 TCGA-56-8624 TCGA-56-A4ZJ 
         757          324         1967           26           36           25 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2698 TCGA-60-2720 TCGA-63-6202 TCGA-66-2783 
        1058         2589          311           97         1973          759 
TCGA-68-7756 TCGA-77-8007 TCGA-77-8130 TCGA-77-8131 TCGA-77-8146 TCGA-77-8154 
         202         1960         1945         1941         1954         1092 
TCGA-77-A5FZ TCGA-77-A5GA TCGA-77-A5GB TCGA-85-6561 TCGA-85-8350 TCGA-85-8353 
        1953         1280         1939          395           60           54 
TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A50Z TCGA-85-A513 TCGA-90-6837 
        1972         1960           19         1973           24          758 
TCGA-90-7964 TCGA-92-7340 TCGA-94-7943 TCGA-96-7545 TCGA-96-8170 TCGA-96-A4JL 
         428           82          356         1344          211          183 
TCGA-98-7454 TCGA-L3-A4E7 
         256           35 

subtype1 subtype2 subtype3 subtype4 
       6        2        1       17 
subtype1 subtype2 subtype3 subtype4 
    3016     5287     2524     2979 
subtype1 subtype2 subtype3 subtype4 
   700.0    578.0    573.0    758.5 
[1] "6.0 - 3016.0 (700.0)"  "2.0 - 5287.0 (578.0)"  "1.0 - 2524.0 (573.0)" 
[4] "17.0 - 2979.0 (758.5)"
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       0       11       27        0         9        14          7
  subtype2       0       16       40        1        13        18         13
  subtype3       2       32       45        0        15        26         28
  subtype4       0        9       16        0        12        11          7
          vv
clus       STAGE IIIB STAGE IV
  subtype1          7        0
  subtype2          2        2
  subtype3          5        1
  subtype4          3        2
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           0        0        2        0
  STAGE IA         11       16       32        9
  STAGE IB         27       40       45       16
  STAGE II          0        1        0        0
  STAGE IIA         9       13       15       12
  STAGE IIB        14       18       26       11
  STAGE IIIA        7       13       28        7
  STAGE IIIB        7        2        5        3
  STAGE IV          0        2        1        2
[1] 9 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 16 47  7  5
  subtype2 21 68 13  3
  subtype3 42 90 19  5
  subtype4 13 35  7  5
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       16       21       42       13
  T2       47       68       90       35
  T3        7       13       19        7
  T4        5        3        5        5
[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 44 25  5  1
  subtype2 70 25  9  1
  subtype3 98 41 16  1
  subtype4 32 16  5  1
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       44       70       98       32
  N1       25       25       41       16
  N2        5        9       16        5
  N3        1        1        1        1
[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        M0  M1 M1A  MX
  subtype1  66   0   0   7
  subtype2  93   2   0  10
  subtype3 130   1   0  21
  subtype4  47   1   1  11
D10V6, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        66       93      130       47
  M1         0        2        1        1
  M1A        0        0        0        1
  MX         7       10       21       11
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  16  59
  subtype2  25  80
  subtype3  46 110
  subtype4  14  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   59
  subtype2   25   80
  subtype3   46  110
  subtype4   14   46
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       16       25       46       14
  MALE         59       80      110       46
[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 BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     4
  subtype2                                     5
  subtype3                                     1
  subtype4                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      0
  subtype2                                      3
  subtype3                                      1
  subtype4                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       0
  subtype3                                       1
  subtype4                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          71
  subtype2                                                          97
  subtype3                                                         153
  subtype4                                                          58
D10V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              4        5
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             0        3
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       71       97
                                                             clus
vv                                                            subtype3 subtype4
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              1        0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            1        0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      153       58
[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"
D10V10, binary
          cls
clus         0   1
  subtype1   1  74
  subtype2   1 104
  subtype3   8 148
  subtype4   2  58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   74
  subtype2    1  104
  subtype3    8  148
  subtype4    2   58
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         1        1        8        2
  YES       74      104      148       58
[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  62   3   1   2
  subtype2  90   2   0   4
  subtype3 127   1   1   5
  subtype4  43   1   1   5
D10V12, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       62       90      127       43
  R1        3        2        1        1
  R2        1        0        1        1
  RX        2        4        5        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         4    54
  subtype2     3                         1    72
  subtype3     2                        10   113
  subtype4     4                         1    43
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            0        3        2        4
  BLACK OR AFRICAN AMERICAN        4        1       10        1
  WHITE                           54       72      113       43
[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   1  50
  subtype2   1  57
  subtype3   3 104
  subtype4   2  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   50
  subtype2    1   57
  subtype3    3  104
  subtype4    2   41
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        1        3        2
  NOT HISPANIC OR LATINO       50       57      104       41
[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 44 12
  subtype2 80 25
  subtype3 53 16
subtype1 subtype2 subtype3 
      56      105       69 
subtype1 subtype2 subtype3 
      12       25       16 
$subtype1
TCGA-21-5782 TCGA-21-5784 TCGA-21-5786 TCGA-21-A5DI TCGA-22-5478 TCGA-22-A5C4 
         962         1268         1032          979           24           29 
TCGA-34-5234 TCGA-34-5239 TCGA-34-5927 TCGA-34-5928 TCGA-39-5019 TCGA-43-6647 
        1715          707          941          552         1361          757 
TCGA-43-6771 TCGA-43-8115 TCGA-43-A56V TCGA-56-5897 TCGA-56-7580 TCGA-56-7731 
        1936          407          366            3           40         1961 
TCGA-56-8503 TCGA-56-8622 TCGA-56-8624 TCGA-56-8625 TCGA-56-8628 TCGA-56-A4ZJ 
          41           55           36           63           16           25 
TCGA-60-2709 TCGA-63-7021 TCGA-63-7022 TCGA-68-7757 TCGA-68-8251 TCGA-68-A59I 
        1505         1955         1947          211           96          121 
TCGA-77-7335 TCGA-77-7337 TCGA-77-8008 TCGA-77-8128 TCGA-77-8130 TCGA-77-8131 
        1954         1942         1945         1953         1945         1941 
TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 TCGA-77-8144 TCGA-77-8145 TCGA-77-A5GB 
        1947         1946         1951          833         1943         1939 
TCGA-85-7950 TCGA-85-8049 TCGA-85-8276 TCGA-85-8481 TCGA-85-8582 TCGA-85-A4QQ 
          60           60           13           21          424         1960 
TCGA-85-A50M TCGA-85-A511 TCGA-90-7964 TCGA-92-7340 TCGA-94-A4VJ TCGA-96-8170 
          19         1972          428           82          430          211 
TCGA-98-7454 TCGA-98-8023 
         256          308 

$subtype2
TCGA-22-4605 TCGA-22-5474 TCGA-22-5479 TCGA-22-5483 TCGA-22-5489 TCGA-33-4587 
        1946          445         1651          573         1912         1970 
TCGA-33-6738 TCGA-34-5231 TCGA-34-5232 TCGA-34-8454 TCGA-37-3783 TCGA-39-5022 
         822         1528         2062          166          120         1996 
TCGA-39-5024 TCGA-39-5027 TCGA-39-5040 TCGA-43-5670 TCGA-43-6143 TCGA-43-6770 
        1964         1849         1964          849          376          310 
TCGA-43-7656 TCGA-43-7657 TCGA-43-7658 TCGA-43-8116 TCGA-43-8118 TCGA-46-6025 
         212          236         1970          358         1971          324 
TCGA-46-6026 TCGA-52-7622 TCGA-52-7809 TCGA-52-7810 TCGA-52-7811 TCGA-52-7812 
         423          541         1948          923         1958         1967 
TCGA-56-6545 TCGA-56-6546 TCGA-56-7221 TCGA-56-7222 TCGA-56-7582 TCGA-56-7730 
          62           26           30           13           26            6 
TCGA-56-7822 TCGA-56-8504 TCGA-56-8626 TCGA-56-8629 TCGA-58-8388 TCGA-58-8390 
           1          178           17           34          378          911 
TCGA-58-8391 TCGA-58-8393 TCGA-60-2703 TCGA-60-2704 TCGA-63-6202 TCGA-63-7020 
        2167         1058         1950         1943         1973         1957 
TCGA-68-7755 TCGA-68-7756 TCGA-68-8250 TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 
          83          202          244         1950         1941         1942 
TCGA-77-7138 TCGA-77-7141 TCGA-77-7142 TCGA-77-7338 TCGA-77-7463 TCGA-77-7465 
        1959           15         1286         1952         1954          479 
TCGA-77-8007 TCGA-77-8009 TCGA-77-8133 TCGA-77-8146 TCGA-77-8156 TCGA-85-6560 
        1960         1641         1941         1954           10          364 
TCGA-85-6561 TCGA-85-7696 TCGA-85-7697 TCGA-85-7698 TCGA-85-7699 TCGA-85-7710 
         395           18           10           49            1         1965 
TCGA-85-7843 TCGA-85-7844 TCGA-85-8048 TCGA-85-8052 TCGA-85-8072 TCGA-85-8287 
          35          911           26           16          513           13 
TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 TCGA-85-8352 TCGA-85-8353 TCGA-85-8354 
          54           60           55           67           54           61 
TCGA-85-8355 TCGA-85-8479 TCGA-85-8580 TCGA-85-8666 TCGA-85-A4PA TCGA-85-A513 
          61           22          445          475         1972           24 
TCGA-90-6837 TCGA-90-7766 TCGA-90-7767 TCGA-90-7769 TCGA-92-7341 TCGA-92-8064 
         758          289           89          358          106          160 
TCGA-92-8065 TCGA-94-7033 TCGA-94-7943 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
          70           87          356         1213         1344          189 
TCGA-96-A4JL TCGA-98-8021 TCGA-98-8022 
         183          413          224 

$subtype3
TCGA-22-5471 TCGA-22-5472 TCGA-22-5473 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
         965         1964         1933         1346         1952         1952 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5491 TCGA-22-5492 TCGA-37-5819 TCGA-43-5668 
         357          916         1713          506          103          349 
TCGA-43-A474 TCGA-43-A475 TCGA-43-A56U TCGA-56-5898 TCGA-56-7223 TCGA-56-7579 
         353          296          432          555           30           44 
TCGA-56-A49D TCGA-56-A4BW TCGA-56-A4BX TCGA-56-A4BY TCGA-56-A4ZK TCGA-56-A5DR 
          38            2           46           30            4            4 
TCGA-58-A46J TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-68-A59J TCGA-77-6845 
        2589         1723         1072          910          104         1952 
TCGA-77-7139 TCGA-77-8140 TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8154 
        1968         1962          293         1961         1684         1092 
TCGA-77-A5FZ TCGA-77-A5G1 TCGA-77-A5G3 TCGA-77-A5G6 TCGA-77-A5G7 TCGA-77-A5G8 
        1953         1942         1959         1955         1963         1290 
TCGA-77-A5GA TCGA-77-A5GF TCGA-77-A5GH TCGA-85-6798 TCGA-85-8070 TCGA-85-8071 
        1280          839          713           34          960          428 
TCGA-85-8664 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50Z TCGA-85-A510 TCGA-85-A512 
           3           15           25         1973         1967         1987 
TCGA-85-A53L TCGA-85-A5B5 TCGA-90-A4ED TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 
          13          111          244          331          269          122 
TCGA-96-A4JK TCGA-J1-A4AH TCGA-L3-A4E7 TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 
         273          222           35          449           36           83 
TCGA-NC-A5HE TCGA-NC-A5HG TCGA-NC-A5HI 
        1722         1548         1135 

subtype1 subtype2 subtype3 
       3        1        2 
subtype1 subtype2 subtype3 
    1972     2167     2589 
subtype1 subtype2 subtype3 
   629.5    378.0    555.0 
[1] "3.0 - 1972.0 (629.5)" "1.0 - 2167.0 (378.0)" "2.0 - 2589.0 (555.0)"
D11V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1       10       21        0         9        14          7
  subtype2       1       27       36        1        20        15         14
  subtype3       0       13       17        0        13        14         13
          vv
clus       STAGE IIIB STAGE IV
  subtype1          3        0
  subtype2          0        2
  subtype3          2        0
D11V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        0
  STAGE IA         10       27       13
  STAGE IB         21       36       17
  STAGE II          0        1        0
  STAGE IIA         9       20       13
  STAGE IIB        14       15       14
  STAGE IIIA        7       14       13
  STAGE IIIB        3        0        2
  STAGE IV          0        2        0
[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"
          vv
clus       T1 T2 T3 T4
  subtype1 13 38 11  3
  subtype2 38 66 11  3
  subtype3 15 44 12  1
D11V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       13       38       15
  T2       38       66       44
  T3       11       11       12
  T4        3        3        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 41 17  5
  subtype2 78 28  8
  subtype3 40 24  8
D11V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       41       78       40
  N1       17       28       24
  N2        5        8        8
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A MX
  subtype1 52  0   0 13
  subtype2 92  1   1 22
  subtype3 58  0   0 14
D11V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        52       92       58
  M1         0        1        0
  M1A        0        1        0
  MX        13       22       14
[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"
D11V7, binary
          cls
clus        0  1
  subtype1 20 45
  subtype2 27 91
  subtype3 15 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   45
  subtype2   27   91
  subtype3   15   57
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       27       15
  MALE         45       91       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"
D11V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     3
  subtype3                                     4
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      2
  subtype2                                      1
  subtype3                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       1
  subtype3                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          63
  subtype2                                                         113
  subtype3                                                          66
D11V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        3
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2        1
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       63      113
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              4
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       66
[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"
D11V10, binary
          cls
clus         0   1
  subtype1   0  65
  subtype2   6 112
  subtype3   3  69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   65
  subtype2    6  112
  subtype3    3   69
     clus
vv    subtype1 subtype2 subtype3
  NO         0        6        3
  YES       65      112       69
[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 44  2  0  6
  subtype2 87  1  1  4
  subtype3 62  2  1  3
D11V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       44       87       62
  R1        2        1        2
  R2        0        1        1
  RX        6        4        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         4    46
  subtype2     2                         5   100
  subtype3     2                         0    55
D11V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        2        2
  BLACK OR AFRICAN AMERICAN        4        5        0
  WHITE                           46      100       55
[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  1 45
  subtype2  3 85
  subtype3  0 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   45
  subtype2    3   85
  subtype3    0   44
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        0
  NOT HISPANIC OR LATINO       45       85       44
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(12) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D12V1, survival
          sevent
clus2       0  1
  subtype1 17  7
  subtype2 73 24
  subtype3 87 22
subtype1 subtype2 subtype3 
      24       97      109 
subtype1 subtype2 subtype3 
       7       24       22 
$subtype1
TCGA-21-5782 TCGA-21-5786 TCGA-21-A5DI TCGA-22-5478 TCGA-22-A5C4 TCGA-34-5927 
         962         1032          979           24           29          941 
TCGA-43-A56V TCGA-56-7223 TCGA-56-8503 TCGA-56-8625 TCGA-56-8628 TCGA-56-A49D 
         366           30           41           63           16           38 
TCGA-68-7757 TCGA-68-A59I TCGA-77-8008 TCGA-77-8136 TCGA-77-8138 TCGA-77-8139 
         211          121         1945         1947         1946         1951 
TCGA-77-8144 TCGA-77-8145 TCGA-77-A5G6 TCGA-85-8481 TCGA-85-8582 TCGA-94-A4VJ 
         833         1943         1955           21          424          430 

$subtype2
TCGA-22-5471 TCGA-22-5473 TCGA-22-5474 TCGA-22-5477 TCGA-22-5480 TCGA-22-5481 
         965         1933          445         1346         1952         1952 
TCGA-22-5482 TCGA-22-5485 TCGA-22-5489 TCGA-22-5491 TCGA-22-5492 TCGA-33-4587 
         357          916         1912         1713          506         1970 
TCGA-34-5231 TCGA-37-5819 TCGA-39-5027 TCGA-43-5668 TCGA-43-5670 TCGA-43-6143 
        1528          103         1849          349          849          376 
TCGA-43-7658 TCGA-43-8115 TCGA-43-8116 TCGA-43-A474 TCGA-43-A475 TCGA-46-6026 
        1970          407          358          353          296          423 
TCGA-52-7809 TCGA-52-7810 TCGA-56-5898 TCGA-56-7222 TCGA-56-7579 TCGA-56-7582 
        1948          923          555           13           44           26 
TCGA-56-7730 TCGA-56-8629 TCGA-56-A4BX TCGA-56-A4ZK TCGA-56-A5DR TCGA-58-8388 
           6           34           46            4            4          378 
TCGA-58-8391 TCGA-58-A46L TCGA-58-A46M TCGA-58-A46N TCGA-60-2703 TCGA-68-7755 
        2167         1723         1072          910         1950           83 
TCGA-68-A59J TCGA-77-6842 TCGA-77-6843 TCGA-77-6844 TCGA-77-6845 TCGA-77-7139 
         104         1950         1941         1942         1952         1968 
TCGA-77-7141 TCGA-77-7142 TCGA-77-7463 TCGA-77-7465 TCGA-77-8009 TCGA-77-8140 
          15         1286         1954          479         1641         1962 
TCGA-77-8148 TCGA-77-8150 TCGA-77-8153 TCGA-77-8156 TCGA-77-A5G3 TCGA-77-A5G7 
         293         1961         1684           10         1959         1963 
TCGA-77-A5GA TCGA-77-A5GF TCGA-85-6798 TCGA-85-7699 TCGA-85-7843 TCGA-85-8052 
        1280          839           34            1           35           16 
TCGA-85-8070 TCGA-85-8071 TCGA-85-8072 TCGA-85-8352 TCGA-85-8354 TCGA-85-8479 
         960          428          513           67           61           22 
TCGA-85-8580 TCGA-85-8664 TCGA-85-8666 TCGA-85-A4CL TCGA-85-A4QR TCGA-85-A50Z 
         445            3          475           15           25         1973 
TCGA-85-A510 TCGA-85-A511 TCGA-85-A512 TCGA-85-A5B5 TCGA-90-7767 TCGA-90-7769 
        1967         1972         1987          111           89          358 
TCGA-90-A4EE TCGA-90-A59Q TCGA-92-8063 TCGA-92-8065 TCGA-94-7943 TCGA-96-A4JK 
         331          269          122           70          356          273 
TCGA-J1-A4AH TCGA-L3-A524 TCGA-LA-A446 TCGA-MF-A522 TCGA-NC-A5HE TCGA-NC-A5HG 
         222          449           36           83         1722         1548 
TCGA-NC-A5HI 
        1135 

$subtype3
TCGA-21-5784 TCGA-22-4605 TCGA-22-5472 TCGA-22-5479 TCGA-22-5483 TCGA-33-6738 
        1268         1946         1964         1651          573          822 
TCGA-34-5232 TCGA-34-5234 TCGA-34-5239 TCGA-34-5928 TCGA-34-8454 TCGA-37-3783 
        2062         1715          707          552          166          120 
TCGA-39-5019 TCGA-39-5022 TCGA-39-5024 TCGA-39-5040 TCGA-43-6647 TCGA-43-6770 
        1361         1996         1964         1964          757          310 
TCGA-43-6771 TCGA-43-7656 TCGA-43-7657 TCGA-43-8118 TCGA-43-A56U TCGA-46-6025 
        1936          212          236         1971          432          324 
TCGA-52-7622 TCGA-52-7811 TCGA-52-7812 TCGA-56-5897 TCGA-56-6545 TCGA-56-6546 
         541         1958         1967            3           62           26 
TCGA-56-7221 TCGA-56-7580 TCGA-56-7731 TCGA-56-7822 TCGA-56-8504 TCGA-56-8622 
          30           40         1961            1          178           55 
TCGA-56-8624 TCGA-56-8626 TCGA-56-A4BW TCGA-56-A4BY TCGA-56-A4ZJ TCGA-58-8390 
          36           17            2           30           25          911 
TCGA-58-8393 TCGA-58-A46J TCGA-60-2704 TCGA-60-2709 TCGA-63-6202 TCGA-63-7020 
        1058         2589         1943         1505         1973         1957 
TCGA-63-7021 TCGA-63-7022 TCGA-68-7756 TCGA-68-8250 TCGA-68-8251 TCGA-77-7138 
        1955         1947          202          244           96         1959 
TCGA-77-7335 TCGA-77-7337 TCGA-77-7338 TCGA-77-8007 TCGA-77-8128 TCGA-77-8130 
        1954         1942         1952         1960         1953         1945 
TCGA-77-8131 TCGA-77-8133 TCGA-77-8146 TCGA-77-8154 TCGA-77-A5FZ TCGA-77-A5G1 
        1941         1941         1954         1092         1953         1942 
TCGA-77-A5G8 TCGA-77-A5GB TCGA-77-A5GH TCGA-85-6560 TCGA-85-6561 TCGA-85-7696 
        1290         1939          713          364          395           18 
TCGA-85-7697 TCGA-85-7698 TCGA-85-7710 TCGA-85-7844 TCGA-85-7950 TCGA-85-8048 
          10           49         1965          911           60           26 
TCGA-85-8049 TCGA-85-8276 TCGA-85-8287 TCGA-85-8288 TCGA-85-8350 TCGA-85-8351 
          60           13           13           54           60           55 
TCGA-85-8353 TCGA-85-8355 TCGA-85-A4PA TCGA-85-A4QQ TCGA-85-A50M TCGA-85-A513 
          54           61         1972         1960           19           24 
TCGA-85-A53L TCGA-90-6837 TCGA-90-7766 TCGA-90-7964 TCGA-90-A4ED TCGA-92-7340 
          13          758          289          428          244           82 
TCGA-92-7341 TCGA-92-8064 TCGA-94-7033 TCGA-96-7544 TCGA-96-7545 TCGA-96-8169 
         106          160           87         1213         1344          189 
TCGA-96-8170 TCGA-96-A4JL TCGA-98-7454 TCGA-98-8021 TCGA-98-8022 TCGA-98-8023 
         211          183          256          413          224          308 
TCGA-L3-A4E7 
          35 

subtype1 subtype2 subtype3 
      16        1        1 
subtype1 subtype2 subtype3 
    1955     2167     2589 
subtype1 subtype2 subtype3 
     427      449      428 
[1] "16.0 - 1955.0 (427.0)" "1.0 - 2167.0 (449.0)"  "1.0 - 2589.0 (428.0)" 
D12V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE IIIA
  subtype1       1        5        6        0         1         5          7
  subtype2       1       18       28        0        20        22         16
  subtype3       0       27       40        1        21        16         11
          vv
clus       STAGE IIIB STAGE IV
  subtype1          1        0
  subtype2          1        0
  subtype3          3        2
D12V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        1        0
  STAGE IA          5       18       27
  STAGE IB          6       28       40
  STAGE II          0        0        1
  STAGE IIA         1       20       21
  STAGE IIB         5       22       16
  STAGE IIIA        7       16       11
  STAGE IIIB        1        1        3
  STAGE IV          0        0        2
[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"
          vv
clus       T1 T2 T3 T4
  subtype1  6 12  7  1
  subtype2 23 69 14  1
  subtype3 37 67 13  5
D12V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1        6       23       37
  T2       12       69       67
  T3        7       14       13
  T4        1        1        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
  subtype1 17  5  4
  subtype2 62 35  9
  subtype3 80 29  8
D12V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17       62       80
  N1        5       35       29
  N2        4        9        8
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A MX
  subtype1 21  0   0  5
  subtype2 90  0   0 16
  subtype3 91  1   1 28
D12V6, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        21       90       91
  M1         0        0        1
  M1A        0        0        1
  MX         5       16       28
[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"
D12V7, binary
          cls
clus        0  1
  subtype1  8 18
  subtype2 25 82
  subtype3 29 93
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   18
  subtype2   25   82
  subtype3   29   93
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        8       25       29
  MALE         18       82       93
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V8, continuous
          vv
clus       LUNG BASALOID SQUAMOUS CELL CARCINOMA
  subtype1                                     0
  subtype2                                     7
  subtype3                                     0
          vv
clus       LUNG PAPILLARY SQUAMOUS CELL CARICNOMA
  subtype1                                      1
  subtype2                                      2
  subtype3                                      2
          vv
clus       LUNG SMALL CELL SQUAMOUS CELL CARCINOMA
  subtype1                                       0
  subtype2                                       1
  subtype3                                       0
          vv
clus       LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                          25
  subtype2                                                          97
  subtype3                                                         120
D12V9, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0        7
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             1        2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0        1
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)       25       97
                                                             clus
vv                                                            subtype3
  LUNG BASALOID SQUAMOUS CELL CARCINOMA                              0
  LUNG PAPILLARY SQUAMOUS CELL CARICNOMA                             2
  LUNG SMALL CELL SQUAMOUS CELL CARCINOMA                            0
  LUNG SQUAMOUS CELL CARCINOMA- NOT OTHERWISE SPECIFIED (NOS)      120
[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"
D12V10, binary
          cls
clus         0   1
  subtype1   0  26
  subtype2   5 102
  subtype3   4 118
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   26
  subtype2    5  102
  subtype3    4  118
     clus
vv    subtype1 subtype2 subtype3
  NO         0        5        4
  YES       26      102      118
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D12V11, continuous
          vv
clus       R0 R1 R2 RX
  subtype1 19  1  0  1
  subtype2 87  2  2  4
  subtype3 87  2  0  8
D12V12, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       19       87       87
  R1        1        2        2
  R2        0        2        0
  RX        1        4        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     0                         3    15
  subtype2     1                         0    94
  subtype3     5                         6    92
D12V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            0        1        5
  BLACK OR AFRICAN AMERICAN        3        0        6
  WHITE                           15       94       92
[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 16
  subtype2  0 71
  subtype3  4 87
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   16
  subtype2    0   71
  subtype3    4   87
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        0        4
  NOT HISPANIC OR LATINO       16       71       87
[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"
