[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"        "-oTKIRP-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/KIRP-TP/11541540/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/11588924/KIRP-TP.mergedcluster.txt"

nPatients in clinical file=223, in cluster file=291, common to both=223
[1]  10 223
[1] "CN_CNMF"
[1] 3
 1  2  3  4 
87 52 37 45 
 1  2  3  4 
87 52 37 45 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
54 55 97 
 1  2  3 
54 55 97 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
67 62 39 
 1  2  3 
67 62 39 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7  8 
14 17 21 19 23 32 19 23 
 1  2  3  4  5  6  7  8 
14 17 21 19 23 32 19 23 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3 
55 90 77 
 1  2  3 
55 90 77 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
94 59 33 36 
 1  2  3  4 
94 59 33 36 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
66 81 76 
 1  2  3 
66 81 76 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
41 46 66 70 
 1  2  3  4 
41 46 66 70 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
51 62 58 
 1  2  3 
51 62 58 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
71 62 13 25 
 1  2  3  4 
71 62 13 25 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDISEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 223 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 
         207          554           21          493            3           NA 
TCGA-A4-7585 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 
          NA          582           27           NA            7           49 
TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 
           2          140          780          729           NA          709 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT 
          23          597          600          436          379          516 
TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP 
          NA           NA            2          118           87            4 
TCGA-A4-A772 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
          NA           NA         1778         1636          412          923 
TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 
         763         1357           26           67          595          223 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 
         659          747          513          108          510           14 
TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-3926 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
         200         1029          307          930         1049          379 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 
         309         1536          857          803          627           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 
          35          460         1338          671           64          585 
TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
         207            5          452          167           52         2639 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 
         586          270         1938           NA           NA         1454 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
          NA         1242          792          921          792          771 
TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 
         403           NA          233           29          364           NA 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 
          84         3760           NA         2948         2839           NA 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 
        1864         1533         1516          799          612           NA 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 
         232          214          218          116          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 
        3950         1093         1142          744          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 
         445           92         1240         2429         2460           NA 
TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ 
        1856         1670         1040          578          757           97 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 
          10            7           36           13          208         1575 
TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 
        1479           NA         1194         1059          765          446 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE 
         786          194          197          262           NA         2091 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          378 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-7128 TCGA-HE-7129 
         546           27          341          140           NA           NA 
TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NK 
          NA         2072          408          360         1726         2228 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IA-A83S TCGA-IA-A83T 
         167          511          608           62           NA           NA 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 
          NA          677          649          146          376           NA 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
           4          364          885          161         1043          845 
TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 
         924          841          616           11          369          541 
TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
         493          148         3035         2653           NA           NA 
TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-Q2-A5QZ 
        2584         2816          391          540           84          428 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A71W TCGA-SX-A7SL 
        1457         1443         1005          876          818          823 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR 
          NA          578         1175           NA         1266          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A895 
        1469         1331          579          882          224            2 
TCGA-Y8-A896 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         186          219          181          399          205          106 
TCGA-Y8-A8S1 
         104 
Variable 1:'AGE':	nDistinctValues=52,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=26,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=178,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'KARNOFSKY.PERFORMANCE.SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL.TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'NUMBERPACKYEARSSMOKED':	nDistinctValues=20,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH.NUMBER':	nDistinctValues=25,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                         "NEOPLASM.DISEASESTAGE"      
 [3] "PATHOLOGY.T.STAGE"           "PATHOLOGY.N.STAGE"          
 [5] "PATHOLOGY.M.STAGE"           "GENDER"                     
 [7] "KARNOFSKY.PERFORMANCE.SCORE" "NUMBERPACKYEARSSMOKED"      
 [9] "RACE"                        "ETHNICITY"                  
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 223 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=52, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
148  22  49   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  148    22    51 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
148  22  49   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  148    22    51 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
39 20  4 
[1] "table(vv)"
vv
N0 N1 N2 
39 20  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
39 20  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
39 20  4 
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY.PERFORMANCE.SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBERPACKYEARSSMOKED, nv=20, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 71  1
  subtype2 49  1
  subtype3 33  0
  subtype4 34  5
subtype1 subtype2 subtype3 subtype4 
      72       50       33       39 
subtype1 subtype2 subtype3 subtype4 
       1        1        0        5 
$subtype1
TCGA-2K-A9WE TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
         207           21            3            7           49            2 
TCGA-A4-8516 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A47O 
          23          379         1778          763          595          513 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         510           14          379          207            5          452 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 
          52         2639          586         1938         1242          792 
TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 
         792          771         3760         2839         1864         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7838 
         799          612          232          218         3950          744 
TCGA-DW-7839 TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5902 
         419          445         2460         1856         1670          578 
TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-7773 TCGA-GL-8500 
          13         1479         1059          765          393          841 
TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-IA-A40X TCGA-IZ-8195 TCGA-MH-A560 
          32           27          140          608          677          924 
TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 
         841           11          369          541          493         3035 
TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SO TCGA-WN-A9G9 
        2816          391          823         1973         1175          579 
TCGA-WN-AB4C TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         882          224          219          181          205          104 

$subtype2
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8517 
         493          582           27          780          709          597 
TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3472 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
           4         1636          923          659          747          108 
TCGA-B3-3925 TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-A5W7 
        1029         1049         1536          803           35          585 
TCGA-B9-A8YH TCGA-BQ-5891 TCGA-BQ-7051 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 
         167           29         1533          353          414         1142 
TCGA-DW-7840 TCGA-DW-7842 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6795 TCGA-G7-A4TM 
         114           92         1040          757         1194          194 
TCGA-G7-A8LE TCGA-GL-A59R TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-IZ-A6M8 
        1965          378          408         1726          649          146 
TCGA-IZ-A6M9 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 
         376         1043          845          616          148         2653 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SU 
        1457         1443         1005          578          805         1331 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
         399          106 

$subtype3
TCGA-A4-7286 TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-AL-3471 
         554          729          600          436          516          412 
TCGA-AT-A5NU TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4114 TCGA-B9-5155 
          67          200          930          309          857          460 
TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 
        1338          671         1454         2948          214          116 
TCGA-DW-7836 TCGA-DW-7963 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LB TCGA-GL-6846 
        1093         1240            7         1575          197         5925 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GE TCGA-KV-A74V 
         546          341          360          167          885          161 
TCGA-PJ-A5Z9 TCGA-SX-A7SS TCGA-Y8-A895 
         540         1469            2 

$subtype4
TCGA-A4-8098 TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-7173 
         140         1968            2          118           87         1357 
TCGA-AL-A5DJ TCGA-B1-7332 TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-A44B 
          26          223          307          627           14           64 
TCGA-BQ-5877 TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5894 
         270          921          403          233          364           84 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-7501 
        2429           97           10           36          208          446 
TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-A5NF TCGA-HE-A5NK 
         786          262         1967          112         2072         2228 
TCGA-IA-A40U TCGA-IA-A40Y TCGA-J7-8537 TCGA-KV-A6GD TCGA-P4-A5EB TCGA-Q2-A5QZ 
         511           62            4          364         2584          428 
TCGA-SX-A71V TCGA-SX-A7SQ TCGA-Y8-A896 
         876         1266          186 

subtype1 subtype2 subtype3 subtype4 
       2        4        2        2 
subtype1 subtype2 subtype3 subtype4 
    3950     2653     5925     2584 
subtype1 subtype2 subtype3 subtype4 
   578.5    654.0    540.0    270.0 
[1] "2.0 - 3950.0 (578.5)" "4.0 - 2653.0 (654.0)" "2.0 - 5925.0 (540.0)"
[4] "2.0 - 2584.0 (270.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      55        9        20        2
  subtype2      38        4         5        0
  subtype3      30        1         1        2
  subtype4      14        2        17        9
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         55       38       30       14
  STAGE II         9        4        1        2
  STAGE III       20        5        1       17
  STAGE IV         2        0        2        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"
          vv
clus       T1 T2 T3+T4
  subtype1 59  7    19
  subtype2 40  7     5
  subtype3 31  3     3
  subtype4 16  5    24
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          59       40       31       16
  T2           7        7        3        5
  T3+T4       19        5        3       24
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 17  8  1
  subtype2  7  0  0
  subtype3  7  1  0
  subtype4  8 11  3
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       17        7        7        8
  N1        8        0        1       11
  N2        1        0        0        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 39  2 45
  subtype2 21  0 27
  subtype3 14  0 19
  subtype4 14  6 21
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       39       21       14       14
  M1        2        0        0        6
  MX       45       27       19       21
[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"
D1V7, binary
          cls
clus        0  1
  subtype1 28 59
  subtype2  8 44
  subtype3  6 31
  subtype4 21 24
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28   59
  subtype2    8   44
  subtype3    6   31
  subtype4   21   24
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       28        8        6       21
  MALE         59       44       31       24
[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
D1V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        21
  subtype2                                1     1                        17
  subtype3                                1     0                         5
  subtype4                                0     3                         9
          vv
clus       WHITE
  subtype1    61
  subtype2    29
  subtype3    29
  subtype4    28
D1V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   1        1        0        3
  BLACK OR AFRICAN AMERICAN              21       17        5        9
  WHITE                                  61       29       29       28
[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"
D1V11, binary
          cls
clus        0  1
  subtype1  5 64
  subtype2  1 45
  subtype3  2 30
  subtype4  1 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   64
  subtype2    1   45
  subtype3    2   30
  subtype4    1   36
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        1        2        1
  NOT HISPANIC OR LATINO       64       45       30       36
[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 = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 44  0
  subtype2 40  6
  subtype3 90  0
subtype1 subtype2 subtype3 
      44       46       90 
subtype1 subtype2 subtype3 
       0        6        0 
$subtype1
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-7173 TCGA-B1-5398 
         207          554          600          379         1357          595 
TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A5W8 TCGA-B9-A69E 
         513          510           14          379          207          452 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5888 TCGA-BQ-7055 TCGA-BQ-7059 
        1454         1242          792          403          799          232 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7838 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 
         214          116          744          445         1240         2460 
TCGA-DZ-6134 TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6796 TCGA-GL-A4EM 
        1856          757           10           13         1059           32 
TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NK TCGA-IZ-A6M8 TCGA-J7-8537 TCGA-KV-A6GD 
         341         2072         2228          146            4          364 
TCGA-MH-A560 TCGA-MH-A855 TCGA-MH-A857 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-WN-A9G9 
         924          369          493         2816          391          579 
TCGA-Y8-A896 TCGA-Y8-A8S1 
         186          104 

$subtype2
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 
          21            7          140         1968          118           87 
TCGA-AL-A5DJ TCGA-B9-A44B TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
          26           64            5           52         2639          586 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 
         270         1938          792          771          233           29 
TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 
         364           84         3760         2839         1864         1533 
TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A8NY 
        1516          612          218         2429           97           36 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A9DE 
         208          446         1967         5925          112          140 
TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-8195 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-PJ-A8JU 
         608           62          677         3035         2584           84 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-Y8-A8RZ 
         428         1973         1175          205 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 
         493            3          582           27           49            2 
TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
         780          729          709           23          597          436 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
         516            2            4           67          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-5156 
         747          108          200          309          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5885 TCGA-BQ-7046 TCGA-DW-5560 
         671          585          167          921         2948          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
         414         3950         1093         1142          419          114 
TCGA-DW-7842 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6790 
          92         1670         1040          578            7         1575 
TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1479         1194          765          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LE TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
         262         1965          393          841          378          546 
TCGA-GL-A9DC TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
          27          408          360         1726          167          511 
TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z 
         649          376          885          161         1043          845 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 
         841          616           11          541          148         2653 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A71W 
         540         1457         1443         1005          876          818 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
         823          578         1266          805         1469         1331 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
         224            2          219          181          399          106 

subtype1 subtype2 subtype3 
       4        5        2 
subtype1 subtype2 subtype3 
    2816     5925     3950 
subtype1 subtype2 subtype3 
   472.5    396.0    543.5 
[1] "4.0 - 2816.0 (472.5)" "5.0 - 5925.0 (396.0)" "2.0 - 3950.0 (543.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      38        6         6        2
  subtype2      15        3        28        9
  subtype3      80        4         8        1
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         38       15       80
  STAGE II         6        3        4
  STAGE III        6       28        8
  STAGE IV         2        9        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       T1 T2 T3+T4
  subtype1 40  3     9
  subtype2 17  5    33
  subtype3 83  7     7
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          40       17       83
  T2           3        5        7
  T3+T4        9       33        7
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 10  2  1
  subtype2 13 17  3
  subtype3 14  0  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       10       13       14
  N1        2       17        0
  N2        1        3        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 27  1 23
  subtype2 22  6 26
  subtype3 30  0 63
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       27       22       30
  M1        1        6        0
  MX       23       26       63
[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"
D2V7, binary
          cls
clus        0  1
  subtype1 14 40
  subtype2 24 31
  subtype3 21 76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   40
  subtype2   24   31
  subtype3   21   76
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       14       24       21
  MALE         40       31       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"
D2V8, continuous
D2V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                        14
  subtype2                                0     1                        13
  subtype3                                1     1                        18
          vv
clus       WHITE
  subtype1    32
  subtype2    38
  subtype3    69
D2V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   3        1        1
  BLACK OR AFRICAN AMERICAN              14       13       18
  WHITE                                  32       38       69
[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"
D2V11, binary
          cls
clus        0  1
  subtype1  1 42
  subtype2  3 38
  subtype3  5 80
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   42
  subtype2    3   38
  subtype3    5   80
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        5
  NOT HISPANIC OR LATINO       42       38       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(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 56  3
  subtype2 55  2
  subtype3 33  0
subtype1 subtype2 subtype3 
      59       57       33 
subtype1 subtype2 subtype3 
       3        2        0 
$subtype1
TCGA-2K-A9WE TCGA-A4-7583 TCGA-A4-8517 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ 
         207            3          597          763         1357           26 
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-5156 
         659          513          200          379          309         1338 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A8YH TCGA-BQ-5877 TCGA-BQ-5887 
          64          585          207          167          270          771 
TCGA-BQ-5888 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 
         403         1142          744          114          445         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5903 TCGA-F9-A4JJ 
        2429         2460         1856         1670          757           97 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-7773 
          10           13          208         1194         1059          393 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
         378           27          341          408          360         1726 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-8537 
        2228          167          511           62          677            4 
TCGA-P4-A5E6 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71U TCGA-SX-A7SN 
        3035         2816          391          540         1005          578 
TCGA-SX-A7SR TCGA-WN-A9G9 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
         805          579            2          186          219 

$subtype2
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8516 
          27            7           49            2          729           23 
TCGA-A4-8630 TCGA-A4-A57E TCGA-AL-3472 TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 
         436         1968          923          223          747          108 
TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-5891 
         460          671            5         1938          921           29 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
        1864         1533          116          353          414         3950 
TCGA-DW-7839 TCGA-DW-7842 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY 
         419           92         1040          578            7           36 
TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        1479          765          446          786          194          197 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
         262         1967         1965         5925          112          841 
TCGA-IZ-8196 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A562 
         649          364          885          161          845          616 
TCGA-P4-A5E7 TCGA-SX-A71R TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SS TCGA-Y8-A894 
        2653         1457         1973         1266         1469          224 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
         399          205          106 

$subtype3
TCGA-A4-7288 TCGA-A4-8098 TCGA-B1-5398 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 
         493          140          595          452           52         2639 
TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
        1454         1242          233          364           84         3760 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 
        2948         2839         1516          799          612          232 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-G7-6790 TCGA-GL-A4EM TCGA-GL-A9DE TCGA-HE-A5NF 
         214          218         1575           32          140         2072 
TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-MH-A560 TCGA-MH-A855 TCGA-P4-A5EB TCGA-PJ-A8JU 
         608          146          924          369         2584           84 
TCGA-Q2-A5QZ TCGA-SX-A7SO TCGA-Y8-A8S1 
         428         1175          104 

subtype1 subtype2 subtype3 
       2        2       32 
subtype1 subtype2 subtype3 
    3035     5925     3760 
subtype1 subtype2 subtype3 
     445      460      493 
[1] "2.0 - 3035.0 (445.0)"  "2.0 - 5925.0 (460.0)"  "32.0 - 3760.0 (493.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      39        5        16        4
  subtype2      41        4        11        5
  subtype3      22        1        12        3
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         39       41       22
  STAGE II         5        4        1
  STAGE III       16       11       12
  STAGE IV         4        5        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 43  5    19
  subtype2 41  9    12
  subtype3 23  1    15
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          43       41       23
  T2           5        9        1
  T3+T4       19       12       15
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 17  7  2
  subtype2 13  8  0
  subtype3  6  3  2
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17       13        6
  N1        7        8        3
  N2        2        0        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 24  2 37
  subtype2 24  3 34
  subtype3 19  2 16
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       24       24       19
  M1        2        3        2
  MX       37       34       16
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1 18 49
  subtype2 20 42
  subtype3 11 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   49
  subtype2   20   42
  subtype3   11   28
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       20       11
  MALE         49       42       28
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        16
  subtype2                                0     2                        12
  subtype3                                1     0                         9
          vv
clus       WHITE
  subtype1    40
  subtype2    46
  subtype3    26
D3V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   3        2        0
  BLACK OR AFRICAN AMERICAN              16       12        9
  WHITE                                  40       46       26
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
          cls
clus        0  1
  subtype1  1 50
  subtype2  1 54
  subtype3  2 28
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   50
  subtype2    1   54
  subtype3    2   28
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        2
  NOT HISPANIC OR LATINO       50       54       28
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 13  0
  subtype2 16  0
  subtype3 19  0
  subtype4 17  0
  subtype5 13  5
  subtype6 28  0
  subtype7 19  0
  subtype8 19  0
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
      13       16       19       17       18       28       19       19 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       0        0        0        0        5        0        0        0 
$subtype1
TCGA-2K-A9WE TCGA-A4-7583 TCGA-B3-A6W5 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7838 
         207            3          309          232          116          744 
TCGA-DZ-6132 TCGA-G7-7502 TCGA-GL-A9DC TCGA-HE-A5NH TCGA-KV-A6GD TCGA-P4-A5E7 
        2460          786           27          408          364         2653 
TCGA-PJ-A5Z9 
         540 

$subtype2
TCGA-B1-A47M TCGA-B1-A47O TCGA-B1-A657 TCGA-B9-5156 TCGA-B9-A5W7 TCGA-B9-A8YH 
         659          513          200         1338          585          167 
TCGA-BQ-5888 TCGA-DW-7837 TCGA-DW-7841 TCGA-DZ-6134 TCGA-EV-5903 TCGA-GL-7773 
         403         1142          445         1856          757          393 
TCGA-HE-A5NL TCGA-IA-A40Y TCGA-SX-A71U TCGA-WN-A9G9 
         167           62         1005          579 

$subtype3
TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-8311 TCGA-AL-3472 TCGA-B1-A47N TCGA-B1-A654 
          27           49          729          923          747          108 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7842 TCGA-EV-5901 TCGA-EV-5902 TCGA-G7-6797 
         414         3950           92         1040          578          765 
TCGA-G7-A4TM TCGA-G7-A8LE TCGA-IZ-8196 TCGA-KV-A74V TCGA-SX-A71R TCGA-SX-A7SQ 
         194         1965          649          161         1457         1266 
TCGA-Y8-A8S0 
         106 

$subtype4
TCGA-A4-7997 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A57E TCGA-BQ-5878 TCGA-BQ-5885 
           2           23          436         1968         1938          921 
TCGA-BQ-5891 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-G7-6792 
          29         2948         1864         1516          612         1479 
TCGA-G7-7501 TCGA-IA-A40U TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Y8-A8RZ 
         446          511         3035         2584          205 

$subtype5
TCGA-A4-7915 TCGA-AL-7173 TCGA-B3-8121 TCGA-BQ-5877 TCGA-BQ-5892 TCGA-BQ-5894 
           7         1357          379          270          364           84 
TCGA-DZ-6135 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-A8LD TCGA-GL-7966 
        1670           97           36          208         1967          112 
TCGA-J7-8537 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SS TCGA-Y8-A897 
           4          391          428         1973         1469          219 

$subtype6
TCGA-A4-7288 TCGA-A4-8098 TCGA-A4-8517 TCGA-B1-5398 TCGA-B9-A69E TCGA-B9-A8YI 
         493          140          597          595          452           52 
TCGA-BQ-5875 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5890 TCGA-BQ-7044 TCGA-BQ-7048 
        2639         1454         1242          233         3760         2839 
TCGA-BQ-7055 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7963 TCGA-G7-6790 TCGA-GL-A4EM 
         799          214          218         1240         1575           32 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-MH-A560 
         341          140         2072          677          146          924 
TCGA-MH-A855 TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-Y8-A8S1 
         369           84         1175          104 

$subtype7
TCGA-B1-7332 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-7051 TCGA-DW-5560 
         223          460          671            5         1533          353 
TCGA-DW-7839 TCGA-F9-A7VF TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-6846 TCGA-GL-8500 
         419            7          197          262         5925          841 
TCGA-HE-A5NI TCGA-IA-A40X TCGA-KV-A6GE TCGA-MH-A55Z TCGA-MH-A562 TCGA-Y8-A894 
         360          608          885          845          616          224 
TCGA-Y8-A8RY 
         399 

$subtype8
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5887 TCGA-DW-7840 
         763           26           64          207          771          114 
TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-A59R 
        2429           10           13         1194         1059          378 
TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-P4-A5ED TCGA-SX-A7SN TCGA-SX-A7SR TCGA-Y8-A895 
        1726         2228         2816          578          805            2 
TCGA-Y8-A896 
         186 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       3       62       27        2        4       32        5        2 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
    2653     1856     3950     3035     1973     3760     5925     2816 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
     364      546      649      921      317      544      419      578 
[1] "3.0 - 2653.0 (364.0)"  "62.0 - 1856.0 (546.0)" "27.0 - 3950.0 (649.0)"
[4] "2.0 - 3035.0 (921.0)"  "4.0 - 1973.0 (317.0)"  "32.0 - 3760.0 (544.0)"
[7] "5.0 - 5925.0 (419.0)"  "2.0 - 2816.0 (578.0)" 
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      13        1         0        0
  subtype2      14        0         2        0
  subtype3      19        0         1        0
  subtype4       8        0        10        1
  subtype5       7        1         7        8
  subtype6      20        2         9        0
  subtype7      13        3         1        2
  subtype8       8        3         9        1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I         13       14       19        8        7       20       13
  STAGE II         1        0        0        0        1        2        3
  STAGE III        0        2        1       10        7        9        1
  STAGE IV         0        0        0        1        8        0        2
           clus
vv          subtype8
  STAGE I          8
  STAGE II         3
  STAGE III        9
  STAGE IV         1
[1] 4 8
[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  1     0
  subtype2 15  0     2
  subtype3 19  2     0
  subtype4  9  1     9
  subtype5  7  2    14
  subtype6 21  2     9
  subtype7 13  4     2
  subtype8 10  3    10
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  T1          13       15       19        9        7       21       13       10
  T2           1        0        2        1        2        2        4        3
  T3+T4        0        2        0        9       14        9        2       10
[1] 3 8
[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  2  0  0
  subtype2  4  1  0
  subtype3  3  0  0
  subtype4  8  3  0
  subtype5  4 10  3
  subtype6  5  1  1
  subtype7  2  1  0
  subtype8  8  2  0
D4V5, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       2        5        3       11       17        7        3       10 
 [1] "subtype6" "subtype5" "subtype4" "subtype3" "subtype8" "subtype5"
 [7] "subtype6" "subtype2" "subtype2" "subtype7" "subtype5" "subtype4"
[13] "subtype5" "subtype6" "subtype8" "subtype4" "subtype8" "subtype2"
[19] "subtype8" "subtype6" "subtype4" "subtype5" "subtype5" "subtype5"
[25] "subtype6" "subtype4" "subtype7" "subtype4" "subtype6" "subtype6"
[31] "subtype8" "subtype5" "subtype8" "subtype5" "subtype5" "subtype8"
[37] "subtype4" "subtype5" "subtype7" "subtype5" "subtype8" "subtype4"
[43] "subtype2" "subtype8" "subtype4" "subtype5" "subtype3" "subtype4"
[49] "subtype5" "subtype8" "subtype3" "subtype5" "subtype2" "subtype5"
[55] "subtype5" "subtype4"
    clus
vv   subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  N0        4        3        8        4        5        2        8
  N1        1        0        3       10        1        1        2
  N2        0        0        0        3        1        0        0
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1  5  0  8
  subtype2  5  0 10
  subtype3  9  0 12
  subtype4 10  1  8
  subtype5  8  5 10
  subtype6 14  0 16
  subtype7  5  0 13
  subtype8 11  1 10
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8
  M0        5        5        9       10        8       14        5       11
  M1        0        0        0        1        5        0        0        1
  MX        8       10       12        8       10       16       13       10
[1] 3 8
[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  3 11
  subtype2  4 13
  subtype3  5 16
  subtype4  8 11
  subtype5 14  9
  subtype6  6 26
  subtype7  6 13
  subtype8  3 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   11
  subtype2    4   13
  subtype3    5   16
  subtype4    8   11
  subtype5   14    9
  subtype6    6   26
  subtype7    6   13
  subtype8    3   20
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        3        4        5        8       14        6        6
  MALE         11       13       16       11        9       26       13
        clus
vv       subtype8
  FEMALE        3
  MALE         20
[1] 2 8
[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
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       2        6       11        4        6        3        5        4 
 [1] "subtype3" "subtype4" "subtype4" "subtype7" "subtype3" "subtype3"
 [7] "subtype2" "subtype7" "subtype8" "subtype2" "subtype3" "subtype6"
[13] "subtype3" "subtype3" "subtype2" "subtype6" "subtype5" "subtype8"
[19] "subtype3" "subtype4" "subtype3" "subtype7" "subtype7" "subtype5"
[25] "subtype3" "subtype4" "subtype7" "subtype2" "subtype5" "subtype5"
[31] "subtype3" "subtype2" "subtype5" "subtype8" "subtype6" "subtype2"
[37] "subtype3" "subtype8" "subtype5"
D4V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 subtype8 
       2        3        2        4        4        4        3        6 
 [1] "subtype4" "subtype8" "subtype6" "subtype8" "subtype7" "subtype5"
 [7] "subtype2" "subtype6" "subtype7" "subtype8" "subtype8" "subtype4"
[13] "subtype6" "subtype4" "subtype6" "subtype5" "subtype2" "subtype5"
[19] "subtype8" "subtype5" "subtype2" "subtype7" "subtype8" "subtype4"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         3
  subtype2                                0     0                         5
  subtype3                                0     0                         4
  subtype4                                0     1                         4
  subtype5                                0     2                         6
  subtype6                                1     0                         8
  subtype7                                0     0                         4
  subtype8                                0     2                         3
          vv
clus       WHITE
  subtype1     8
  subtype2    11
  subtype3    16
  subtype4    13
  subtype5    13
  subtype6    22
  subtype7    14
  subtype8    15
D4V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   0        0        0        1        2
  BLACK OR AFRICAN AMERICAN               3        5        4        4        6
  WHITE                                   8       11       16       13       13
                                  clus
vv                                 subtype6 subtype7 subtype8
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   0        0        2
  BLACK OR AFRICAN AMERICAN               8        4        3
  WHITE                                  22       14       15
[1] 4 8
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, binary
          cls
clus        0  1
  subtype1  0 11
  subtype2  0 14
  subtype3  0 17
  subtype4  2 14
  subtype5  1 17
  subtype6  0 25
  subtype7  0 17
  subtype8  1 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   11
  subtype2    0   14
  subtype3    0   17
  subtype4    2   14
  subtype5    1   17
  subtype6    0   25
  subtype7    0   17
  subtype8    1   17
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        0        0        2        1        0
  NOT HISPANIC OR LATINO       11       14       17       14       17       25
                        clus
vv                       subtype7 subtype8
  HISPANIC OR LATINO            0        1
  NOT HISPANIC OR LATINO       17       17
[1] 2 8
[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 = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 49  0
  subtype2 82  1
  subtype3 57  6
subtype1 subtype2 subtype3 
      49       83       63 
subtype1 subtype2 subtype3 
       0        1        6 
$subtype1
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         207          554          493           49            2          780 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5XZ TCGA-AL-3473 
         597          600          379         1968            2          763 
TCGA-B1-A655 TCGA-B1-A657 TCGA-B3-4103 TCGA-B9-5156 TCGA-B9-A5W8 TCGA-B9-A8YI 
         510          200          930         1338          207           52 
TCGA-BQ-5881 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 TCGA-BQ-7050 
        1454          921          792          233         2948         1864 
TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6134 
        1533          232          214          744         1240         1856 
TCGA-G7-6790 TCGA-G7-6796 TCGA-GL-A59T TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF 
        1575         1059          546          341          140         2072 
TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-KV-A6GD TCGA-KV-A6GE 
         167          511          608          146          364          885 
TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-SX-A71V TCGA-SX-A7SO TCGA-WN-A9G9 
         161         3035         2584          876         1175          579 
TCGA-Y8-A8RZ 
         205 

$subtype2
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 
           3          582           27          729          709           23 
TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 
         436          516            4         1636          412          923 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 
          67          223          659          747          108         1029 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
         309         1536          857          803           14           35 
TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-7062 TCGA-DW-5560 
         460          671          585          167          116          353 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
         414         3950         1093         1142          419          114 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-EV-5903 
         445           92         1670         1040          578          757 
TCGA-F9-A7VF TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM 
           7         1479         1194          765          786          194 
TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-HE-A5NH 
         197         1965          841          378           27          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-MH-A55W TCGA-MH-A55Z 
         360         1726          649          376         1043          845 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 
         841          616           11          541          148         2653 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL 
         540         1457         1443         1005          818          823 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
         578         1266          805         1469         1331          224 
TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
           2          219          181          399          106 

$subtype3
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3467 
          21            7          140          118           87         1778 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A656 TCGA-B3-3926 
        1357           26          595          513           14          307 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W9 TCGA-B9-A69E 
        1049          379          627           64            5          452 
TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 
        2639          586          270         1938         1242          792 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 
         771          403           29          364           84         3760 
TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 
        2839         1516          799          612          218         2429 
TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
        2460           97           10           36           13          208 
TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
         446          262         1967         5925          393          112 
TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 
          32         2228           62          677            4          924 
TCGA-MH-A855 TCGA-MH-A857 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM 
         369          493         2816          391          428         1973 
TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8S1 
         882          186          104 

subtype1 subtype2 subtype3 
       2        2        4 
subtype1 subtype2 subtype3 
    3035     3950     5925 
subtype1 subtype2 subtype3 
     597      578      403 
[1] "2.0 - 3035.0 (597.0)" "2.0 - 3950.0 (578.0)" "4.0 - 5925.0 (403.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      37        7         7        1
  subtype2      73        4         6        1
  subtype3      28        5        30       11
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         37       73       28
  STAGE II         7        4        5
  STAGE III        7        6       30
  STAGE IV         1        1       11
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 40  6     7
  subtype2 75 10     5
  subtype3 32  6    39
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          40       75       32
  T2           6       10        6
  T3+T4        7        5       39
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 13  1  1
  subtype2 12  0  0
  subtype3 14 19  3
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       13       12       14
  N1        1        0       19
  N2        1        0        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 22  1 29
  subtype2 32  0 51
  subtype3 35  7 32
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       22       32       35
  M1        1        0        7
  MX       29       51       32
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  7 48
  subtype2 19 71
  subtype3 37 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   48
  subtype2   19   71
  subtype3   37   40
        clus
vv       subtype1 subtype2 subtype3
  FEMALE        7       19       37
  MALE         48       71       40
[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
D5V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     0                         9
  subtype2                                1     1                        26
  subtype3                                0     4                        17
          vv
clus       WHITE
  subtype1    42
  subtype2    55
  subtype3    51
D5V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   0        1        4
  BLACK OR AFRICAN AMERICAN               9       26       17
  WHITE                                  42       55       51
[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"
D5V11, binary
          cls
clus        0  1
  subtype1  1 46
  subtype2  5 75
  subtype3  3 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   46
  subtype2    5   75
  subtype3    3   55
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        3
  NOT HISPANIC OR LATINO       46       75       55
[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 = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 80  3
  subtype2 53  1
  subtype3 32  0
  subtype4 23  3
subtype1 subtype2 subtype3 subtype4 
      83       54       32       26 
subtype1 subtype2 subtype3 subtype4 
       3        1        0        3 
$subtype1
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-8098 TCGA-A4-8310 
         207          554          493           49          140          780 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         597          600          379         1968          118           87 
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 
         763           26          595          513          510           14 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A5W8 
         930          379          857           14           64          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 
           5          452           52         2639          586         1938 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 
        1454          792          921          792          771          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7050 
          29          364         3760         2948         2839         1864 
TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-BQ-7062 
        1516          612          232          214          218          116 
TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 TCGA-F9-A97G TCGA-G7-6796 
         744         1240         2429         1856           13         1059 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A4EM TCGA-GL-A59T 
         446          786         1967         5925           32          546 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         341          140         2072          511          608           62 
TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A560 TCGA-MH-A855 
         677          146            4          364          924          369 
TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SO 
        3035         2584          428          876         1973         1175 
TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         579          882          219          205          104 

$subtype2
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 
           3          582          729          709           23          436 
TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU 
         516            2            4         1636          412           67 
TCGA-B1-A47N TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4617 
         747          200          309         1536          803           35 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-7051 
         460         1338          671          585          167         1533 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-EV-5902 
         414         3950         1142          114          445          578 
TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A8LB TCGA-GL-8500 
           7         1575         1194          765          197          841 
TCGA-GL-A59R TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         378          360          167          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A7SL 
         845          616          540         1457         1005          823 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
         805         1469            2          181          399          106 

$subtype3
TCGA-A4-7734 TCGA-A4-7997 TCGA-AL-3467 TCGA-AL-3472 TCGA-B1-7332 TCGA-B1-A47M 
          27            2         1778          923          223          659 
TCGA-B1-A654 TCGA-B3-3925 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7839 TCGA-DW-7842 
         108         1029          353         1093          419           92 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6792 TCGA-G7-A4TM TCGA-G7-A8LE 
        1670         1040          757         1479          194         1965 
TCGA-GL-A9DC TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-MH-A561 
          27          408         1726          649          376          841 
TCGA-MH-A854 TCGA-O9-A75Z TCGA-SX-A71S TCGA-SX-A71W TCGA-SX-A7SN TCGA-SX-A7SQ 
          11          148         1443          818          578         1266 
TCGA-SX-A7SU TCGA-Y8-A894 
        1331          224 

$subtype4
TCGA-A4-7287 TCGA-A4-7915 TCGA-AL-7173 TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 
          21            7         1357          307         1049          627 
TCGA-BQ-5877 TCGA-BQ-5883 TCGA-BQ-5888 TCGA-BQ-5894 TCGA-BQ-7055 TCGA-DZ-6132 
         270         1242          403           84          799         2460 
TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-A8LC TCGA-GL-7773 
          97           10           36          208          262          393 
TCGA-GL-7966 TCGA-HE-A5NK TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E7 TCGA-P4-A5ED 
         112         2228          541          493         2653         2816 
TCGA-PJ-A5Z8 TCGA-Y8-A896 
         391          186 

subtype1 subtype2 subtype3 subtype4 
       4        2        2        7 
subtype1 subtype2 subtype3 subtype4 
    5925     3950     1965     2816 
subtype1 subtype2 subtype3 subtype4 
     554      559      654      392 
[1] "4.0 - 5925.0 (554.0)" "2.0 - 3950.0 (559.0)" "2.0 - 1965.0 (654.0)"
[4] "7.0 - 2816.0 (392.0)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      49        7        30        4
  subtype2      46        5         4        1
  subtype3      27        1         2        0
  subtype4      16        3         7        8
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         49       46       27       16
  STAGE II         7        5        1        3
  STAGE III       30        4        2        7
  STAGE IV         4        1        0        8
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 52  8    32
  subtype2 48  8     3
  subtype3 29  2     2
  subtype4 18  4    14
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          52       48       29       18
  T2           8        8        2        4
  T3+T4       32        3        2       14
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 24 11  1
  subtype2 10  0  0
  subtype3  3  0  0
  subtype4  2  9  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       24       10        3        2
  N1       11        0        0        9
  N2        1        0        0        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 39  3 46
  subtype2 19  0 35
  subtype3 15  0 17
  subtype4 16  5 14
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       39       19       15       16
  M1        3        0        0        5
  MX       46       35       17       14
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 25 69
  subtype2  7 52
  subtype3 11 22
  subtype4 20 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   69
  subtype2    7   52
  subtype3   11   22
  subtype4   20   16
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       25        7       11       20
  MALE         69       52       22       16
[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
D6V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                        22
  subtype2                                1     1                        15
  subtype3                                0     0                         7
  subtype4                                0     2                         8
          vv
clus       WHITE
  subtype1    66
  subtype2    38
  subtype3    22
  subtype4    22
D6V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0        0
  ASIAN                                   2        1        0        2
  BLACK OR AFRICAN AMERICAN              22       15        7        8
  WHITE                                  66       38       22       22
[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"
D6V11, binary
          cls
clus        0  1
  subtype1  2 76
  subtype2  2 50
  subtype3  2 27
  subtype4  3 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   76
  subtype2    2   50
  subtype3    2   27
  subtype4    3   23
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        2        2        3
  NOT HISPANIC OR LATINO       76       50       27       23
[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 = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 58  0
  subtype2 74  1
  subtype3 57  6
subtype1 subtype2 subtype3 
      58       75       63 
subtype1 subtype2 subtype3 
       0        1        6 
$subtype1
TCGA-2K-A9WE TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8518 
         207            2          140          780           23          600 
TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3473 TCGA-B1-5398 
         379         1968            2          118          763          595 
TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3925 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 
         223          510         1029          857          803           14 
TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
        1338           64          207          167           52         2639 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 
        1938         1454          792          792          233           29 
TCGA-BQ-5892 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7837 
         364         1864         1533          232          116         1142 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6135 TCGA-F9-A97G TCGA-G7-6790 
         114          445         1240         1670           13         1575 
TCGA-G7-6792 TCGA-G7-7501 TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NL TCGA-IZ-A6M8 
        1479          446          341          140          167          146 
TCGA-KV-A74V TCGA-MH-A560 TCGA-MH-A855 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-PJ-A8JU 
         161          924          369         3035         2584           84 
TCGA-SX-A7SO TCGA-WN-A9G9 TCGA-Y8-A897 TCGA-Y8-A8RZ 
        1175          579          219          205 

$subtype2
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 
         554          493            3          582           49          729 
TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A6HP TCGA-AL-3467 
         709          597          436          516            4         1778 
TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47O TCGA-B3-3926 
        1636          412           26           67          513          307 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 
         309         1536          627           35          460          671 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-7044 
         585            5          452          921          403         3760 
TCGA-BQ-7046 TCGA-BQ-7055 TCGA-DW-7839 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF 
        2948          799          419          578           10            7 
TCGA-F9-A8NY TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7773 
          36         1194          765          197          262          393 
TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-HE-A5NF TCGA-HE-A5NH 
         841          378          546           27         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-A6M9 
         360         2228          511          608           62          376 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
         885         1043          845          841          616           11 
TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
        2816          540         1457         1005          876          823 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-WN-AB4C TCGA-Y8-A894 
         578         1266          805         1469          882          224 
TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S0 
         186          399          106 

$subtype3
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-A5Y1 TCGA-AL-3472 TCGA-AL-7173 
          21           27            7           87          923         1357 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-4103 
         659          747          108           14          200          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5883 TCGA-BQ-5887 
        1049          379          586          270         1242          771 
TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7060 TCGA-BQ-7061 
          84         2839         1516          612          214          218 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7842 
         353          414         3950         1093          744           92 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ 
        2429         2460         1856         1040          757           97 
TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE 
         208         1059          786          194         1967         1965 
TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-A5NJ TCGA-IZ-8195 TCGA-IZ-8196 
        5925          112           32         1726          677          649 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 
           4          364          541          493          148         2653 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A71W TCGA-SX-A7SM TCGA-SX-A7SU 
         391          428         1443          818         1973         1331 
TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8S1 
           2          181          104 

subtype1 subtype2 subtype3 
       2        3        2 
subtype1 subtype2 subtype3 
    3035     3760     5925 
subtype1 subtype2 subtype3 
     412      546      612 
[1] "2.0 - 3035.0 (412.0)" "3.0 - 3760.0 (546.0)" "2.0 - 5925.0 (612.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      37        8        17        1
  subtype2      57        3        11        3
  subtype3      45        5        15        9
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         37       57       45
  STAGE II         8        3        5
  STAGE III       17       11       15
  STAGE IV         1        3        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 39 10    16
  subtype2 61  7    13
  subtype3 48  5    22
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          39       61       48
  T2          10        7        5
  T3+T4       16       13       22
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 18  4  1
  subtype2 11  3  0
  subtype3 10 13  3
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       18       11       10
  N1        4        3       13
  N2        1        0        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 28  1 32
  subtype2 27  2 44
  subtype3 34  5 37
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       28       27       34
  M1        1        2        5
  MX       32       44       37
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 15 51
  subtype2 24 57
  subtype3 25 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   51
  subtype2   24   57
  subtype3   25   51
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       24       25
  MALE         51       57       51
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        22
  subtype2                                1     2                        13
  subtype3                                1     2                        17
          vv
clus       WHITE
  subtype1    40
  subtype2    58
  subtype3    51
D7V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1
  ASIAN                                   1        2        2
  BLACK OR AFRICAN AMERICAN              22       13       17
  WHITE                                  40       58       51
[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"
D7V11, binary
          cls
clus        0  1
  subtype1  2 55
  subtype2  3 64
  subtype3  4 58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   55
  subtype2    3   64
  subtype3    4   58
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        3        4
  NOT HISPANIC OR LATINO       55       64       58
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 32  2
  subtype2 41  0
  subtype3 62  1
  subtype4 54  4
subtype1 subtype2 subtype3 subtype4 
      34       41       63       58 
subtype1 subtype2 subtype3 subtype4 
       2        0        1        4 
$subtype1
TCGA-2K-A9WE TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8518 TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         207            2          140          600          118           87 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 TCGA-B9-5156 TCGA-B9-A5W8 TCGA-BQ-5878 
         763          595         1029         1338          207         1938 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7051 
         921          792          233           29          364         1533 
TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DZ-6135 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 
         232          218         1670           13         1575         1479 
TCGA-G7-7501 TCGA-GL-A9DD TCGA-MH-A55Z TCGA-MH-A562 TCGA-MH-A855 TCGA-P4-A5EB 
         446          341          845          616          369         2584 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-WN-A9G9 TCGA-Y8-A8RZ 
        1973         1175          579          205 

$subtype2
TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A57E 
         554          780           23          436          379         1968 
TCGA-AL-3467 TCGA-B1-7332 TCGA-B1-A655 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
        1778          223          510          857          803          627 
TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 
          14           64          167           52         2639          586 
TCGA-BQ-5881 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7060 TCGA-BQ-7062 
        1454         3760         2948         1864          214          116 
TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 
         414         1142          419          114          445         1240 
TCGA-EV-5902 TCGA-G7-A4TM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-HE-A5NK TCGA-IA-A40X 
         578          194           27          140         2228          608 
TCGA-IZ-A6M8 TCGA-MH-A560 TCGA-O9-A75Z TCGA-PJ-A8JU TCGA-SX-A7SL 
         146          924          148           84          823 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 
         493            3          582           49          729          709 
TCGA-A4-8517 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 
         597          516            2            4         1636          412 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-3926 
          26           67          747          513          200          307 
TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 
         930          309         1536           35          460          671 
TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-BQ-7055 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6796 
         585          403          799           10            7         1059 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-8500 TCGA-GL-A59R 
         765          786          197          262          841          378 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NL TCGA-IA-A40U 
         546         2072          408          360          167          511 
TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A854 TCGA-P4-A5E6 
         376          885          161         1043           11         3035 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN TCGA-SX-A7SQ 
         540         1457         1005          876          578         1266 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 
         805         1469         1331          224            2          186 
TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
         219          399          106 

$subtype4
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-A47M 
          21           27            7          923         1357          659 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-A5W9 TCGA-B9-A69E 
         108           14         1049          379            5          452 
TCGA-BQ-5877 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7048 
         270         1242          792          771           84         2839 
TCGA-BQ-7053 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
        1516          612          353         3950         1093          744 
TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 
          92         2429         2460         1856         1040          757 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-A8LD TCGA-G7-A8LE 
          97           36          208         1194         1967         1965 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-A5NJ TCGA-IA-A40Y 
        5925          393          112           32         1726           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A561 TCGA-MH-A856 
         677          649            4          364          841          541 
TCGA-MH-A857 TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S 
         493         2653         2816          391          428         1443 
TCGA-SX-A71W TCGA-WN-AB4C TCGA-Y8-A898 TCGA-Y8-A8S1 
         818          882          181          104 

subtype1 subtype2 subtype3 subtype4 
       2       14        2        4 
subtype1 subtype2 subtype3 subtype4 
    2584     3760     3035     5925 
subtype1 subtype2 subtype3 subtype4 
     587      510      511      654 
[1] "2.0 - 2584.0 (587.0)"  "14.0 - 3760.0 (510.0)" "2.0 - 3035.0 (511.0)" 
[4] "4.0 - 5925.0 (654.0)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      18        7        13        2
  subtype2      32        1         6        1
  subtype3      51        4         7        1
  subtype4      38        4        17        9
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         18       32       51       38
  STAGE II         7        1        4        4
  STAGE III       13        6        7       17
  STAGE IV         2        1        1        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"
          vv
clus       T1 T2 T3+T4
  subtype1 20  5    14
  subtype2 34  5     7
  subtype3 54  7     5
  subtype4 40  5    25
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          20       34       54       40
  T2           5        5        7        5
  T3+T4       14        7        5       25
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 11  6  1
  subtype2  7  0  0
  subtype3 11  1  0
  subtype4 10 13  3
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       11        7       11       10
  N1        6        0        1       13
  N2        1        0        0        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 21  2 17
  subtype2 16  1 23
  subtype3 23  0 38
  subtype4 29  5 35
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       21       16       23       29
  M1        2        1        0        5
  MX       17       23       38       35
[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"
D8V7, binary
          cls
clus        0  1
  subtype1  6 35
  subtype2 13 33
  subtype3 16 50
  subtype4 29 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   35
  subtype2   13   33
  subtype3   16   50
  subtype4   29   41
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6       13       16       29
  MALE         35       33       50       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"
D8V8, continuous
D8V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         8
  subtype2                                1     0                        20
  subtype3                                1     1                         9
  subtype4                                0     3                        15
          vv
clus       WHITE
  subtype1    31
  subtype2    21
  subtype3    49
  subtype4    48
D8V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   1        0        1        3
  BLACK OR AFRICAN AMERICAN               8       20        9       15
  WHITE                                  31       21       49       48
[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"
D8V11, binary
          cls
clus        0  1
  subtype1  0 36
  subtype2  2 35
  subtype3  2 55
  subtype4  5 51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   36
  subtype2    2   35
  subtype3    2   55
  subtype4    5   51
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        2        2        5
  NOT HISPANIC OR LATINO       36       35       55       51
[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(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 45  0
  subtype2 58  0
  subtype3 38  6
subtype1 subtype2 subtype3 
      45       58       44 
subtype1 subtype2 subtype3 
       0        0        6 
$subtype1
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
         207          554          493           49            2          140 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3473 
         597          600         1968            2          118          763 
TCGA-B1-5398 TCGA-B1-A47O TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A69E TCGA-B9-A8YI 
         595          513           14         1338          452           52 
TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
        1454          792          792          233           29          364 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
        2948         1864          799          232          214          116 
TCGA-DZ-6131 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-A9DD 
        2429           13         1575         1059          446          341 
TCGA-GL-A9DE TCGA-IA-A40X TCGA-MH-A855 TCGA-SX-A7SO TCGA-WN-A9G9 TCGA-WN-AB4C 
         140          608          369         1175          579          882 
TCGA-Y8-A897 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
         219          205          104 

$subtype2
TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-AL-3472 TCGA-AT-A5NU 
         780          709           23          436          923           67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-5155 
         747          108          200         1029          803          460 
TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5878 TCGA-BQ-7044 TCGA-BQ-7051 TCGA-DW-5560 
           5          167         1938         3760         1533          353 
TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
         414         1093         1142          419          114           92 
TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-A4TM 
        1670          578           10         1479         1194          194 
TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59T TCGA-GL-A9DC 
         197          262          393          841          546           27 
TCGA-HE-A5NJ TCGA-IA-A40U TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-KV-A6GE 
        1726          511           62          649          376          885 
TCGA-KV-A74V TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-PJ-A5Z9 
         161           11          541          148         3035          540 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SR 
        1457         1443         1005          823          578          805 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A8RY TCGA-Y8-A8S0 
        1469         1331          399          106 

$subtype3
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-A5Y1 TCGA-AL-7173 TCGA-B1-A656 
          21           27            7           87         1357           14 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5883 
        1049          379           64          586          270         1242 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7056 
         771          403           84         2839         1516          612 
TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 
         218         3950          744         2460         1856         1040 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-7502 TCGA-G7-A8LD 
         757           97           36          208          786         1967 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-J7-8537 
        1965         5925          112           32          677            4 
TCGA-KV-A6GD TCGA-MH-A857 TCGA-P4-A5E7 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71W 
         364          493         2653          391          428          818 
TCGA-SX-A7SM TCGA-Y8-A898 
        1973          181 

subtype1 subtype2 subtype3 
       2        5        4 
subtype1 subtype2 subtype3 
    2948     3760     5925 
subtype1 subtype2 subtype3 
   452.0    543.5    539.5 
[1] "2.0 - 2948.0 (452.0)" "5.0 - 3760.0 (543.5)" "4.0 - 5925.0 (539.5)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      30        4        12        1
  subtype2      48        2         9        1
  subtype3      26        6        15       11
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         30       48       26
  STAGE II         4        2        6
  STAGE III       12        9       15
  STAGE IV         1        1       11
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 32  6    13
  subtype2 50  4     8
  subtype3 28  4    24
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          32       50       28
  T2           6        4        4
  T3+T4       13        8       24
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 15  2  1
  subtype2 10  3  0
  subtype3  8 15  3
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       15       10        8
  N1        2        3       15
  N2        1        0        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 23  1 23
  subtype2 23  0 37
  subtype3 25  7 25
D9V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       23       23       25
  M1        1        0        7
  MX       23       37       25
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 15 36
  subtype2 12 50
  subtype3 25 33
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   36
  subtype2   12   50
  subtype3   25   33
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       15       12       25
  MALE         36       50       33
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                         9
  subtype2                                1     2                        12
  subtype3                                0     2                        12
          vv
clus       WHITE
  subtype1    38
  subtype2    43
  subtype3    41
D9V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   1        2        2
  BLACK OR AFRICAN AMERICAN               9       12       12
  WHITE                                  38       43       41
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, binary
          cls
clus        0  1
  subtype1  1 41
  subtype2  4 50
  subtype3  2 43
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   41
  subtype2    4   50
  subtype3    2   43
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        4        2
  NOT HISPANIC OR LATINO       41       50       43
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 67  0
  subtype2 43  5
  subtype3  6  1
  subtype4 25  0
subtype1 subtype2 subtype3 subtype4 
      67       48        7       25 
subtype1 subtype2 subtype3 subtype4 
       0        5        1        0 
$subtype1
TCGA-2K-A9WE TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 
         207          554          493           49            2          140 
TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A5XZ 
         780          709           23          597          436            2 
TCGA-A4-A5Y0 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-4117 
         118          763          595         1029          803           14 
TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5878 TCGA-BQ-5886 
         460         1338          167           52         1938          792 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7055 
         233           29         3760         2948         1533          799 
TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
         232          214          116         1142          419          114 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-G7-6790 TCGA-G7-6792 
        1670         1040          578           10         1575         1479 
TCGA-G7-6795 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-8500 TCGA-GL-A59T TCGA-GL-A9DC 
        1194          197          262          841          546           27 
TCGA-GL-A9DE TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-A6M9 TCGA-KV-A6GE 
         140          511          608           62          376          885 
TCGA-KV-A74V TCGA-MH-A855 TCGA-P4-A5E6 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71W 
         161          369         3035         1457         1005          818 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SS TCGA-WN-A9G9 TCGA-Y8-A897 
         823          578          805         1469          579          219 
TCGA-Y8-A8RZ 
         205 

$subtype2
TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-7173 TCGA-B1-A47O TCGA-B1-A656 
         600         1968           87         1357          513           14 
TCGA-B3-8121 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5881 
         379           64          452          586          270         1454 
TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5892 TCGA-BQ-7048 
        1242          792          771          403          364         2839 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7838 
        1864         1516          612          218         3950          744 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 TCGA-F9-A97G TCGA-G7-6789 
        2429         2460         1856          757           13          208 
TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A4EM 
        1059          446          786         1967         5925           32 
TCGA-GL-A9DD TCGA-IZ-8195 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A857 TCGA-PJ-A5Z8 
         341          677            4          364          493          391 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-WN-AB4C TCGA-Y8-A898 TCGA-Y8-A8S1 
         428         1973         1175          882          181          104 

$subtype3
TCGA-A4-7287 TCGA-A4-7915 TCGA-B3-4104 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A8NY 
          21            7         1049           84           97           36 
TCGA-GL-7966 
         112 

$subtype4
TCGA-A4-7734 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 
          27          923           67          747          108          200 
TCGA-B9-A5W9 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7842 TCGA-G7-A4TM 
           5          353          414         1093           92          194 
TCGA-G7-A8LE TCGA-GL-7773 TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-MH-A854 TCGA-MH-A856 
        1965          393         1726          649           11          541 
TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-SX-A71S TCGA-SX-A7SU TCGA-Y8-A8RY 
         148         2653          540         1443         1331          399 
TCGA-Y8-A8S0 
         106 

subtype1 subtype2 subtype3 subtype4 
       2        4        7        5 
subtype1 subtype2 subtype3 subtype4 
    3760     5925     1049     2653 
subtype1 subtype2 subtype3 subtype4 
     554      606       84      399 
[1] "2.0 - 3760.0 (554.0)" "4.0 - 5925.0 (606.0)" "7.0 - 1049.0 (84.0)" 
[4] "5.0 - 2653.0 (399.0)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      47        6        13        1
  subtype2      33        3        17        9
  subtype3       1        3         6        3
  subtype4      23        0         0        0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         47       33        1       23
  STAGE II         6        3        3        0
  STAGE III       13       17        6        0
  STAGE IV         1        9        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       T1 T2 T3+T4
  subtype1 50  8    13
  subtype2 34  2    24
  subtype3  2  3     8
  subtype4 24  1     0
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          50       34        2       24
  T2           8        2        3        1
  T3+T4       13       24        8        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 14  3  0
  subtype2 16 10  4
  subtype3  1  7  0
  subtype4  2  0  0
D10V5, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
      17       30        8        2 
 [1] "subtype2" "subtype3" "subtype2" "subtype2" "subtype2" "subtype1"
 [7] "subtype2" "subtype1" "subtype2" "subtype2" "subtype2" "subtype1"
[13] "subtype3" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
[19] "subtype1" "subtype1" "subtype2" "subtype3" "subtype3" "subtype2"
[25] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[31] "subtype3" "subtype2" "subtype2" "subtype2" "subtype1" "subtype2"
[37] "subtype2" "subtype2" "subtype3" "subtype1" "subtype1" "subtype1"
[43] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype3"
[49] "subtype3" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[55] "subtype1"
    clus
vv   subtype1 subtype2 subtype3
  N0       14       16        1
  N1        3       10        7
  N2        0        4        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 28  0 38
  subtype2 29  5 26
  subtype3  5  3  5
  subtype4  9  0 16
D10V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       28       29        5        9
  M1        0        5        3        0
  MX       38       26        5       16
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 17 54
  subtype2 19 43
  subtype3  9  4
  subtype4  7 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   54
  subtype2   19   43
  subtype3    9    4
  subtype4    7   18
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       19        9        7
  MALE         54       43        4       18
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
      22       17        1        8 
 [1] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [7] "subtype1" "subtype2" "subtype4" "subtype4" "subtype2" "subtype4"
[13] "subtype1" "subtype2" "subtype1" "subtype1" "subtype4" "subtype1"
[19] "subtype1" "subtype2" "subtype1" "subtype2" "subtype2" "subtype2"
[25] "subtype2" "subtype4" "subtype1" "subtype1" "subtype2" "subtype4"
[31] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype1"
[37] "subtype4" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[43] "subtype2" "subtype2" "subtype1" "subtype1" "subtype4"
D10V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     1                        13
  subtype2                                0     3                        12
  subtype3                                0     1                         3
  subtype4                                0     0                         5
          vv
clus       WHITE
  subtype1    52
  subtype2    45
  subtype3     7
  subtype4    18
D10V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0        0
  ASIAN                                   1        3        1        0
  BLACK OR AFRICAN AMERICAN              13       12        3        5
  WHITE                                  52       45        7       18
[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"
D10V11, binary
          cls
clus        0  1
  subtype1  1 57
  subtype2  2 47
  subtype3  1  9
  subtype4  3 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   57
  subtype2    2   47
  subtype3    1    9
  subtype4    3   21
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        2        1        3
  NOT HISPANIC OR LATINO       57       47        9       21
[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"
