[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/10005964/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/10668117/KIRP-TP.mergedcluster.txt"

nPatients in clinical file=202, in cluster file=242, common to both=202
[1]   8 202
[1] "CN_CNMF"
[1] 3
 1  2  3 
76 93 29 
 1  2  3 
76 93 29 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3 
44 54 88 
 1  2  3 
44 54 88 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
42 65 62 28 
 1  2  3  4 
42 65 62 28 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
67 64 66 
 1  2  3 
67 64 66 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3 
67 65 70 
 1  2  3 
67 65 70 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3 
95 43 64 
 1  2  3 
95 43 64 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
68 62 72 
 1  2  3 
68 62 72 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
23 31 33 27 33 37 18 
 1  2  3  4  5  6  7 
23 31 33 27 33 37 18 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "PRIMARYSITEOFDESEASE"                  
 [6] "NEOPLASM.DISEASESTAGE"                 
 [7] "PATHOLOGY.T.STAGE"                     
 [8] "PATHOLOGY.N.STAGE"                     
 [9] "PATHOLOGY.M.STAGE"                     
[10] "DCCUPLOADDATE"                         
[11] "GENDER"                                
[12] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[13] "DAYSTOLASTKNOWNALIVE"                  
[14] "RADIATIONTHERAPY"                      
[15] "KARNOFSKYPERFORMANCESCORE"             
[16] "HISTOLOGICALTYPE"                      
[17] "RADIATIONS.RADIATION.REGIMENINDICATION"
[18] "NUMBERPACKYEARSSMOKED"                 
[19] "YEAROFTOBACCOSMOKINGONSET"             
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCHNUMBER"                           

Input Data has 22 rows and 202 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
TCGA-A4-7286 TCGA-A4-7287 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7584 TCGA-A4-7585 
         554           21          493            3           NA           NA 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7828 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
         582           27           NA            7           49            2 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8311 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
         140          780          729           NA          709           23 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A4ZT TCGA-A4-A57E 
         597          600          436          379          516           NA 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-A4-A6HP TCGA-A4-A772 
          NA            2          118           87            4           NA 
TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AL-3473 
          NA         1778         1636          412          923          763 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A47M 
        1357           26           67          595          223          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-3925 TCGA-B3-3926 
         747          108          510           14         1029          307 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 
         930         1049          379           85         1536          857 
TCGA-B9-4115 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
         803          627           14           35          460         1338 
TCGA-B9-7268 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E 
         671           64          585          207            5          102 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
         167           52         2639          586          270         1938 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
          NA           NA         1454           NA         1242          792 
TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5890 
         921          792          771          403           NA          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7045 
          29          364           NA           84         3760           NA 
TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
        2948         2839           NA         1864         1533         1516 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
         799          612           NA          232          214          218 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 
         116          353          414         3950         1093         1142 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 
         744          419          114          445           92         1240 
TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6133 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        2429         2460           NA         1856         1670         1040 
TCGA-EV-5902 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         578          757           97           10            7           36 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6793 TCGA-G7-6795 
          13          208         1575         1479           NA         1194 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LD 
        1059          765          446          786          279           NA 
TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM TCGA-GL-A59R 
        5925          393          112          841           32          178 
TCGA-GL-A59T TCGA-HE-7128 TCGA-HE-7129 TCGA-HE-7130 TCGA-HE-A5NF TCGA-HE-A5NH 
          91           NA           NA           NA         2072          408 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
         360         1726          167          511          608           62 
TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 TCGA-J7-6720 TCGA-J7-8537 
         677          649          146            2           NA            4 
TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 
         160          885          161         1043          391          543 
TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 
         438          292           11          541          148         3035 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 
        2653           NA           NA         2584         2816          391 
TCGA-PJ-A5Z9 TCGA-PJ-A8JU TCGA-Q2-A5QZ TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U 
         174           84           57         1079         1199          994 
TCGA-SX-A71V TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO 
         508          760          423           NA          102          925 
TCGA-SX-A7SP TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 
          NA          494          335         1247          847          224 
TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 TCGA-Y8-A8RZ 
           2          186          181          205 
Variable 1:'AGE':	nDistinctValues=51,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=164,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=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=16,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAROFTOBACCOSMOKINGONSET':	nDistinctValues=17,	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=16,	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 202 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=51, 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 
132  19  49   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  132    19    51 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T1  T2  T3  T4 
132  19  49   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  132    19    51 
PATHOLOGY.N.STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
34 20  4 
[1] "table(vv)"
vv
N0 N1 N2 
34 20  4 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
N0 N1 N2 
34 20  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
34 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=16, 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 69  1
  subtype2 72  5
  subtype3 25  1
subtype1 subtype2 subtype3 
      70       77       26 
subtype1 subtype2 subtype3 
       1        5        1 
$subtype1
TCGA-A4-7288 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
         493          582           27           49            2          780 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A6HP TCGA-AL-3468 
         729          709          597          436            4         1636 
TCGA-AL-3472 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-4103 
         923          659          747          108         1029          930 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
        1536          857          803           35          460         1338 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5891 
         671          585          167         1454          792           29 
TCGA-BQ-7051 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 
        1533          214          116          353         3950         1093 
TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7842 TCGA-DW-7963 TCGA-DZ-6134 
        1142          114          445           92         1240         1856 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A7VF TCGA-G7-A4TM TCGA-GL-6846 TCGA-GL-A59R 
        1040          757            7          279         5925          178 
TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IZ-8195 TCGA-IZ-8196 TCGA-IZ-A6M8 
         408         1726          167          677          649          146 
TCGA-IZ-A6M9 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A560 TCGA-MH-A562 TCGA-O9-A75Z 
           2         1043          391          543          292          148 
TCGA-P4-A5E7 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN 
        2653         1079         1199          994          423          102 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A895 TCGA-Y8-A898 
        1247          847            2          181 

$subtype2
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A48D TCGA-A4-A5Y0 
          21            3            7          140          379          118 
TCGA-A4-A5Y1 TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-5398 
          87         1778          763         1357           26          595 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4116 TCGA-B9-A5W8 
         510           14         1049          379          627          207 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
           5          102           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
        1938         1242          792          921          771          403 
TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 
         233          364           84         3760         2839         1864 
TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-5561 
        1516          799          612          232          218          414 
TCGA-DW-7838 TCGA-DW-7839 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5902 
         744          419         2429         2460         1670          578 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6796 TCGA-G7-6797 
          97           36         1479         1194         1059          765 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-7773 TCGA-GL-7966 TCGA-GL-8500 TCGA-GL-A4EM 
         446         1967          393          112          841           32 
TCGA-IA-A40U TCGA-IA-A40X TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A561 TCGA-MH-A854 
         511          608            4          160          438           11 
TCGA-MH-A856 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Q2-A5QZ 
         541         3035         2584         2816          391           57 
TCGA-SX-A7SM TCGA-SX-A7SO TCGA-Y8-A894 TCGA-Y8-A896 TCGA-Y8-A8RZ 
        1973          925          224          186          205 

$subtype3
TCGA-A4-7286 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-A4ZT TCGA-A4-A5XZ TCGA-AL-3471 
         554           23          600          516            2          412 
TCGA-AT-A5NU TCGA-B1-7332 TCGA-B3-3926 TCGA-B3-A6W5 TCGA-B9-4117 TCGA-B9-A44B 
          67          223          307           85           14           64 
TCGA-BQ-7046 TCGA-F9-A7Q0 TCGA-G7-6789 TCGA-G7-6790 TCGA-G7-7502 TCGA-GL-A59T 
        2948           10          208         1575          786           91 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40Y TCGA-KV-A6GE TCGA-KV-A74V TCGA-PJ-A5Z9 
        2072          360           62          885          161          174 
TCGA-SX-A71V TCGA-SX-A7SQ 
         508          494 

subtype1 subtype2 subtype3 
       2        3        2 
subtype1 subtype2 subtype3 
    5925     3760     2948 
subtype1 subtype2 subtype3 
     623      510      265 
[1] "2.0 - 5925.0 (623.0)" "3.0 - 3760.0 (510.0)" "2.0 - 2948.0 (265.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      57        4         7        1
  subtype2      45        5        31       10
  subtype3      20        2         4        1
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         57       45       20
  STAGE II         4        5        2
  STAGE III        7       31        4
  STAGE IV         1       10        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 60  8     8
  subtype2 50  7    36
  subtype3 20  3     6
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          60       50       20
  T2           8        7        3
  T3+T4        8       36        6
[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 11  1  0
  subtype2 21 18  3
  subtype3  1  1  1
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       11       21        1
  N1        1       18        1
  N2        0        3        1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 30  0 39
  subtype2 42  8 41
  subtype3  9  0 16
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       30       42        9
  M1        0        8        0
  MX       39       41       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"
D1V7, binary
          cls
clus        0  1
  subtype1 12 64
  subtype2 34 59
  subtype3 12 17
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   64
  subtype2   34   59
  subtype3   12   17
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       34       12
  MALE         64       59       17
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, continuous
D1V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     1                        22
  subtype2                                0     2                        23
  subtype3                                0     1                         4
          vv
clus       WHITE
  subtype1    45
  subtype2    63
  subtype3    21
D1V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0
  ASIAN                                   1        2        1
  BLACK OR AFRICAN AMERICAN              22       23        4
  WHITE                                  45       63       21
[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"
D1V11, binary
          cls
clus        0  1
  subtype1  2 63
  subtype2  6 67
  subtype3  1 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   63
  subtype2    6   67
  subtype3    1   23
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        6        1
  NOT HISPANIC OR LATINO       63       67       23
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 36  0
  subtype2 38  6
  subtype3 82  0
subtype1 subtype2 subtype3 
      36       44       82 
subtype1 subtype2 subtype3 
       0        6        0 
$subtype1
TCGA-A4-7286 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-7173 TCGA-B1-5398 TCGA-B1-A655 
         554          600          379         1357          595          510 
TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A5W8 TCGA-B9-A69E TCGA-BQ-5881 TCGA-BQ-5883 
          14          379          207          102         1454         1242 
TCGA-BQ-5884 TCGA-BQ-5888 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 
         792          403          799          232          214          116 
TCGA-DW-7838 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 
         744          445         1240         2460         1856          757 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6796 TCGA-GL-A4EM TCGA-HE-A5NF TCGA-IZ-A6M8 
          10           13         1059           32         2072          146 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A560 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-Y8-A896 
           4          160          543         2816          391          186 

$subtype2
TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-A5DJ 
          21            7          140          118           87           26 
TCGA-B9-A44B TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 
          64            5           52         2639          586          270 
TCGA-BQ-5878 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
        1938          792          771          233           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 
          84         3760         2839         1864         1533         1516 
TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 
         612          218         2429           97           36          208 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-IA-A40X TCGA-IA-A40Y 
         446         1967         5925          112          608           62 
TCGA-IZ-8195 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-PJ-A8JU TCGA-Q2-A5QZ TCGA-SX-A7SM 
         677         3035         2584           84           57         1973 
TCGA-SX-A7SO TCGA-Y8-A8RZ 
         925          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-B3-A6W5 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 
         747          108           85          460         1338          671 
TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5885 TCGA-BQ-7046 TCGA-DW-5560 TCGA-DW-5561 
         585          167          921         2948          353          414 
TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 
        3950         1093         1142          419          114           92 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 
        1670         1040          578            7         1575         1479 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-7773 TCGA-GL-8500 
        1194          765          786          279          393          841 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL 
         178           91          408          360         1726          167 
TCGA-IA-A40U TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         511          649            2          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z 
         391          438          292           11          541          148 
TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V 
        2653          174         1079         1199          994          508 
TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
         760          423          102          494          335         1247 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A898 
         847          224            2          181 

subtype1 subtype2 subtype3 
       4        5        2 
subtype1 subtype2 subtype3 
    2816     5925     3950 
subtype1 subtype2 subtype3 
   477.5    317.0    476.5 
[1] "4.0 - 2816.0 (477.5)" "5.0 - 5925.0 (317.0)" "2.0 - 3950.0 (476.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      33        2         6        2
  subtype2      14        3        28        9
  subtype3      72        4         8        0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         33       14       72
  STAGE II         2        3        4
  STAGE III        6       28        8
  STAGE IV         2        9        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 34  1     9
  subtype2 16  5    33
  subtype3 75  6     7
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          34       16       75
  T2           1        5        6
  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  9  2  1
  subtype2 13 17  3
  subtype3 10  0  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0        9       13       10
  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 24  1 16
  subtype2 22  6 25
  subtype3 28  0 56
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       24       22       28
  M1        1        6        0
  MX       16       25       56
[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 12 32
  subtype2 24 30
  subtype3 19 69
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   32
  subtype2   24   30
  subtype3   19   69
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       12       24       19
  MALE         32       30       69
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                        12
  subtype2                                0     1                        12
  subtype3                                1     1                        18
          vv
clus       WHITE
  subtype1    25
  subtype2    38
  subtype3    60
D2V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   3        1        1
  BLACK OR AFRICAN AMERICAN              12       12       18
  WHITE                                  25       38       60
[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 33
  subtype2  3 37
  subtype3  5 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   33
  subtype2    3   37
  subtype3    5   71
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        3        5
  NOT HISPANIC OR LATINO       33       37       71
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 37  0
  subtype2 46  6
  subtype3 58  1
  subtype4 24  0
subtype1 subtype2 subtype3 subtype4 
      37       52       59       24 
subtype1 subtype2 subtype3 subtype4 
       0        6        1        0 
$subtype1
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 
         554          493           49          780           23          597 
TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5XZ TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 
         600          379            2          763          595          223 
TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 TCGA-B9-5156 TCGA-B9-A5W8 TCGA-BQ-5881 
         510           14          930         1338          207         1454 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-DW-7963 
         792          233         2948         1533          214         1240 
TCGA-G7-6790 TCGA-G7-6796 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NL TCGA-IA-A40U 
        1575         1059           91         2072          167          511 
TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5EB 
         608          146          885          161         3035         2584 
TCGA-SX-A71V 
         508 

$subtype2
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-A5DJ TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W9 
          26          307         1049          627           64            5 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5883 
         102         2639          586          270         1938         1242 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5891 TCGA-BQ-5892 
         792          921          771          403           29          364 
TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
          84         3760         2839         1864         1516          799 
TCGA-BQ-7056 TCGA-BQ-7061 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
         612          218         2429           97           10           36 
TCGA-G7-6789 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM 
         208          446         1967         5925          112           32 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-8537 TCGA-MH-A560 TCGA-P4-A5ED TCGA-PJ-A5Z8 
          62          677            4          543         2816          391 
TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-Y8-A896 
          57         1973          925          186 

$subtype3
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A4ZT 
           3          582          729          709          436          516 
TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47M 
           4         1636          412          923           67          659 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4117 
         747          108           85         1536          803           14 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-DW-5560 TCGA-DW-5561 
          35          460          671          585          353          414 
TCGA-DW-7836 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-EV-5902 TCGA-F9-A7VF 
        1093          419          114           92          578            7 
TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-GL-8500 TCGA-GL-A59R 
        1194          765          786          279          841          178 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-MH-A55W 
         408          360         1726          649            2         1043 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z TCGA-PJ-A5Z9 TCGA-SX-A71R 
         391          292           11          148          174         1079 
TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ 
        1199          994          760          423          102          494 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         335         1247          847          224            2 

$subtype4
TCGA-A4-7734 TCGA-A4-7997 TCGA-AL-7173 TCGA-B3-3925 TCGA-B3-8121 TCGA-B9-4114 
          27            2         1357         1029          379          857 
TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7841 
         232          116         3950         1142          744          445 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6792 
        2460         1856         1670         1040          757         1479 
TCGA-GL-7773 TCGA-KV-A6GD TCGA-MH-A561 TCGA-MH-A856 TCGA-P4-A5E7 TCGA-Y8-A898 
         393          160          438          541         2653          181 

subtype1 subtype2 subtype3 subtype4 
       2        4        2        2 
subtype1 subtype2 subtype3 subtype4 
    3035     5925     1726     3950 
subtype1 subtype2 subtype3 subtype4 
   595.0    397.0    436.0    750.5 
[1] "2.0 - 3035.0 (595.0)" "4.0 - 5925.0 (397.0)" "2.0 - 1726.0 (436.0)"
[4] "2.0 - 3950.0 (750.5)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      25        5         9        0
  subtype2      20        4        28       11
  subtype3      50        3         4        0
  subtype4      25        0         1        1
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         25       20       50       25
  STAGE II         5        4        3        0
  STAGE III        9       28        4        1
  STAGE IV         0       11        0        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 28  5     9
  subtype2 23  6    36
  subtype3 52  7     3
  subtype4 25  1     2
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          28       23       52       25
  T2           5        6        7        1
  T3+T4        9       36        3        2
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 11  2  0
  subtype2 12 18  3
  subtype3  7  0  0
  subtype4  2  0  1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       11       12        7        2
  N1        2       18        0        0
  N2        0        3        0        1
[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 17  0 22
  subtype2 30  8 24
  subtype3 24  0 32
  subtype4 12  0 15
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       17       30       24       12
  M1        0        8        0        0
  MX       22       24       32       15
[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"
D3V7, binary
          cls
clus        0  1
  subtype1  7 35
  subtype2 32 33
  subtype3 13 49
  subtype4  6 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   35
  subtype2   32   33
  subtype3   13   49
  subtype4    6   22
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       32       13        6
  MALE         35       33       49       22
[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"
D3V8, continuous
D3V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     0                         8
  subtype2                                0     3                        14
  subtype3                                1     0                        18
  subtype4                                0     1                         7
          vv
clus       WHITE
  subtype1    31
  subtype2    45
  subtype3    37
  subtype4    17
D3V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0
  ASIAN                                   0        3        0        1
  BLACK OR AFRICAN AMERICAN               8       14       18        7
  WHITE                                  31       45       37       17
[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"
D3V11, binary
          cls
clus        0  1
  subtype1  1 34
  subtype2  4 46
  subtype3  2 53
  subtype4  2 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   34
  subtype2    4   46
  subtype3    2   53
  subtype4    2   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        4        2        2
  NOT HISPANIC OR LATINO       34       46       53       19
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 57  2
  subtype2 48  4
  subtype3 60  1
subtype1 subtype2 subtype3 
      59       52       61 
subtype1 subtype2 subtype3 
       2        4        1 
$subtype1
TCGA-A4-7286 TCGA-A4-8098 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         554          140          600          379          118           87 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 TCGA-B9-4117 
         763          595          510           14          930           14 
TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5875 
        1338           64          207            5          102         2639 
TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 
         586         1938         1454          792          921          792 
TCGA-BQ-5887 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 
         771          233           29          364         3760         2948 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7059 TCGA-BQ-7060 
        2839         1864         1516          612          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 
         218          116          744         1240         2429         1856 
TCGA-G7-6796 TCGA-G7-7501 TCGA-GL-A4EM TCGA-HE-A5NF TCGA-HE-A5NL TCGA-IA-A40U 
        1059          446           32         2072          167          511 
TCGA-IA-A40X TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A560 
         608          677          146            4          160          543 
TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO 
        3035         2584           57         1973          925 

$subtype2
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7997 TCGA-AL-3467 TCGA-AL-3472 
          21           27            7            2         1778          923 
TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 TCGA-B3-3926 
        1357           26          747          108         1029          307 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4116 TCGA-BQ-5877 TCGA-BQ-5883 TCGA-BQ-5888 
        1049          379          627          270         1242          403 
TCGA-BQ-5894 TCGA-BQ-7055 TCGA-DW-5560 TCGA-DW-7836 TCGA-DW-7839 TCGA-DW-7842 
          84          799          353         1093          419           92 
TCGA-DZ-6132 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A7Q0 
        2460         1670         1040          757           97           10 
TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6792 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-7773 
          36          208         1479          279         1967          393 
TCGA-GL-7966 TCGA-HE-A5NH TCGA-IA-A40Y TCGA-IZ-8196 TCGA-MH-A561 TCGA-MH-A854 
         112          408           62          649          438           11 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-SX-A71S 
         541          148         2653         2816          391         1199 
TCGA-SX-A7SQ TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A896 
         494          847          224          186 

$subtype3
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
         493            3          582           49          780          729 
TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5XZ 
         709           23          597          436          516            2 
TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
           4         1636          412           67          223          659 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-5155 
          85         1536          857          803           35          460 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-BQ-7051 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7837 
         671          585         1533          414         3950         1142 
TCGA-DW-7840 TCGA-DW-7841 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6795 
         114          445          578            7         1575         1194 
TCGA-G7-6797 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
         765          786         5925          841          178           91 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
         360         1726            2          885          161         1043 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V 
         391          292          174         1079          994          508 
TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SS TCGA-Y8-A895 
         760          423          102          335         1247            2 
TCGA-Y8-A898 
         181 

subtype1 subtype2 subtype3 
       4        2        2 
subtype1 subtype2 subtype3 
    3760     2816     5925 
subtype1 subtype2 subtype3 
   595.0    405.5    508.0 
[1] "4.0 - 3760.0 (595.0)" "2.0 - 2816.0 (405.5)" "2.0 - 5925.0 (508.0)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      34        3        25        2
  subtype2      38        3        11        9
  subtype3      48        6         6        1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         34       38       48
  STAGE II         3        3        6
  STAGE III       25       11        6
  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 37  5    25
  subtype2 40  5    19
  subtype3 51  9     6
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          37       40       51
  T2           5        5        9
  T3+T4       25       19        6
[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 19  7  1
  subtype2  4 12  3
  subtype3  9  1  0
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       19        4        9
  N1        7       12        1
  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 35  2 24
  subtype2 26  6 30
  subtype3 22  0 39
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       35       26       22
  M1        2        6        0
  MX       24       30       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"
D4V7, binary
          cls
clus        0  1
  subtype1 16 51
  subtype2 32 32
  subtype3 10 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   51
  subtype2   32   32
  subtype3   10   56
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       16       32       10
  MALE         51       32       56
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V8, continuous
D4V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        15
  subtype2                                0     2                        14
  subtype3                                1     1                        18
          vv
clus       WHITE
  subtype1    46
  subtype2    42
  subtype3    42
D4V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   1        2        1
  BLACK OR AFRICAN AMERICAN              15       14       18
  WHITE                                  46       42       42
[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"
D4V11, binary
          cls
clus        0  1
  subtype1  3 49
  subtype2  5 46
  subtype3  1 57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   49
  subtype2    5   46
  subtype3    1   57
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        5        1
  NOT HISPANIC OR LATINO       49       46       57
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 58  0
  subtype2 59  1
  subtype3 53  6
subtype1 subtype2 subtype3 
      58       60       59 
subtype1 subtype2 subtype3 
       0        1        6 
$subtype1
TCGA-A4-7286 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-A48D 
         554            2          140          780           23          379 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3468 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 
           2          118         1636          763          595          223 
TCGA-B1-A655 TCGA-B3-3925 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 
         510         1029          857          803           14         1338 
TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
          64          585          207          167           52         2639 
TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 
        1938         1454          792          921          792          233 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 
          29          364         3760         2948         1864         1533 
TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7837 TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 
         232          116         1142          114          445         1240 
TCGA-DZ-6135 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 TCGA-HE-A5NH 
        1670           13         1575         1479          446          408 
TCGA-HE-A5NL TCGA-IZ-A6M8 TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A560 TCGA-P4-A5E6 
         167          146          161          391          543         3035 
TCGA-P4-A5EB TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-Y8-A8RZ 
        2584           84          925          205 

$subtype2
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-A4-8630 TCGA-A4-A4ZT TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3471 
         597          436          516            4         1778          412 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B3-3926 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4116 
          26           67          307           85         1536          627 
TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5888 TCGA-BQ-7055 
          35          460          671            5          403          799 
TCGA-DW-7839 TCGA-DW-7842 TCGA-EV-5902 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-F9-A8NY 
         419           92          578           10            7           36 
TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T 
        1194          765          393          841          178           91 
TCGA-HE-A5NF TCGA-HE-A5NI TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y TCGA-IZ-A6M9 
        2072          360          511          608           62            2 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 
         885         1043          438          292           11          541 
TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SL 
        2816          174         1079          994          508          423 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-Y8-A894 TCGA-Y8-A896 
         102          494          335         1247          224          186 

$subtype3
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8518 TCGA-A4-A5Y1 TCGA-AL-3472 
          21           27            7          600           87          923 
TCGA-AL-7173 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-4103 
        1357          659          747          108           14          930 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-A69E TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5883 
        1049          379          102          586          270         1242 
TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7060 
         771           84         2839         1516          612          214 
TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7838 
         218          353          414         3950         1093          744 
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-GL-6846 
         208         1059          786          279         1967         5925 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-A5NJ TCGA-IZ-8195 TCGA-IZ-8196 TCGA-J7-8537 
         112           32         1726          677          649            4 
TCGA-KV-A6GD TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S 
         160          148         2653          391           57         1199 
TCGA-SX-A71W TCGA-SX-A7SM TCGA-SX-A7SU TCGA-Y8-A895 TCGA-Y8-A898 
         760         1973          847            2          181 

subtype1 subtype2 subtype3 
       2        2        2 
subtype1 subtype2 subtype3 
    3760     2816     5925 
subtype1 subtype2 subtype3 
   526.5    429.5    649.0 
[1] "2.0 - 3760.0 (526.5)" "2.0 - 2816.0 (429.5)" "2.0 - 5925.0 (649.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      37        6        19        1
  subtype2      48        2         8        2
  subtype3      39        4        16        9
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         37       48       39
  STAGE II         6        2        4
  STAGE III       19        8       16
  STAGE IV         1        2        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  9    19
  subtype2 51  5     9
  subtype3 42  5    23
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          39       51       42
  T2           9        5        5
  T3+T4       19        9       23
[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  4  1
  subtype2  8  3  0
  subtype3  9 13  3
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17        8        9
  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 30  1 28
  subtype2 23  2 36
  subtype3 31  5 33
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       30       23       31
  M1        1        2        5
  MX       28       36       33
[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 13 54
  subtype2 21 44
  subtype3 25 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   54
  subtype2   21   44
  subtype3   25   45
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       13       21       25
  MALE         54       44       45
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, continuous
D5V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        23
  subtype2                                1     2                        10
  subtype3                                1     2                        16
          vv
clus       WHITE
  subtype1    38
  subtype2    47
  subtype3    47
D5V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1
  ASIAN                                   1        2        2
  BLACK OR AFRICAN AMERICAN              23       10       16
  WHITE                                  38       47       47
[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  2 52
  subtype2  4 51
  subtype3  3 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   52
  subtype2    4   51
  subtype3    3   54
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        4        3
  NOT HISPANIC OR LATINO       52       51       54
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 80  3
  subtype2 42  0
  subtype3 48  4
subtype1 subtype2 subtype3 
      83       42       52 
subtype1 subtype2 subtype3 
       3        0        4 
$subtype1
TCGA-A4-7286 TCGA-A4-7732 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8516 
         554          582            2          140          780           23 
TCGA-A4-8518 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-A4-A5Y1 
         600          436          379            2          118           87 
TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-7332 
           4         1778          763           26          595          223 
TCGA-B1-A655 TCGA-B3-3925 TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4116 
         510         1029         1536          857          803          627 
TCGA-B9-4117 TCGA-B9-4617 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 TCGA-B9-A5W8 
          14           35         1338           64          585          207 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5881 
         167           52         2639          586         1938         1454 
TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
         792          921          792          233           29          364 
TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7060 
        3760         2948         1864         1533          232          214 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7839 
         218          116          414         1142          744          419 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6135 TCGA-EV-5902 TCGA-F9-A97G 
         114          445         1240         1670          578           13 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH 
        1575         1479          446           91         2072          408 
TCGA-HE-A5NL TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z 
         167          608          146          885          161          391 
TCGA-MH-A560 TCGA-MH-A562 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-PJ-A8JU TCGA-SX-A7SL 
         543          292         3035         2584           84          423 
TCGA-SX-A7SM TCGA-SX-A7SN TCGA-SX-A7SO TCGA-SX-A7SQ TCGA-Y8-A8RZ 
        1973          102          925          494          205 

$subtype2
TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
         493            3           49          729          709          597 
TCGA-A4-A4ZT TCGA-AL-3468 TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B3-3926 
         516         1636          412           67          747          307 
TCGA-B3-4103 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-7268 TCGA-BQ-5888 
         930          379           85          460          671          403 
TCGA-BQ-7055 TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 
         799           10            7         1059          765          786 
TCGA-GL-8500 TCGA-GL-A59R TCGA-HE-A5NI TCGA-IA-A40U TCGA-IZ-A6M9 TCGA-MH-A55W 
         841          178          360          511            2         1043 
TCGA-MH-A854 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SR 
          11          174         1079          994          508          335 
TCGA-SX-A7SS TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A898 
        1247          847          224            2          186          181 

$subtype3
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-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5877 
         108           14         1049            5          102          270 
TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5894 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7056 
        1242          771           84         2839         1516          612 
TCGA-DW-5560 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 
         353         3950         1093           92         2429         2460 
TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 
        1856         1040          757           97           36          208 
TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
        1194          279         1967         5925          393          112 
TCGA-GL-A4EM TCGA-HE-A5NJ TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-J7-8537 
          32         1726           62          677          649            4 
TCGA-KV-A6GD TCGA-MH-A561 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5ED 
         160          438          541          148         2653         2816 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A71W 
         391           57         1199          760 

subtype1 subtype2 subtype3 
       2        2        4 
subtype1 subtype2 subtype3 
    3760     1636     5925 
subtype1 subtype2 subtype3 
   494.0    476.5    576.5 
[1] "2.0 - 3760.0 (494.0)" "2.0 - 1636.0 (476.5)" "4.0 - 5925.0 (576.5)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      58        5        21        3
  subtype2      34        3         5        0
  subtype3      32        4        17        9
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         58       34       32
  STAGE II         5        3        4
  STAGE III       21        5       17
  STAGE IV         3        0        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 63 10    22
  subtype2 35  4     4
  subtype3 34  5    25
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          63       35       34
  T2          10        4        5
  T3+T4       22        4       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"
          vv
clus       N0 N1 N2
  subtype1 17  7  1
  subtype2  7  0  0
  subtype3 10 13  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17        7       10
  N1        7        0       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 39  3 42
  subtype2 18  0 24
  subtype3 27  5 31
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       39       18       27
  M1        3        0        5
  MX       42       24       31
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 22 73
  subtype2 11 32
  subtype3 26 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   73
  subtype2   11   32
  subtype3   26   38
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       22       11       26
  MALE         73       32       38
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        31
  subtype2                                1     1                         5
  subtype3                                0     3                        13
          vv
clus       WHITE
  subtype1    55
  subtype2    33
  subtype3    44
D6V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   1        1        3
  BLACK OR AFRICAN AMERICAN              31        5       13
  WHITE                                  55       33       44
[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"
D6V11, binary
          cls
clus        0  1
  subtype1  2 75
  subtype2  2 36
  subtype3  5 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   75
  subtype2    2   36
  subtype3    5   46
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        2        5
  NOT HISPANIC OR LATINO       75       36       46
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 61  0
  subtype2 55  1
  subtype3 54  6
subtype1 subtype2 subtype3 
      61       56       60 
subtype1 subtype2 subtype3 
       0        1        6 
$subtype1
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8310 
         554          493           49            2          140          780 
TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A48D TCGA-A4-A5XZ TCGA-A4-A5Y0 
          23          597          436          379            2          118 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B9-4114 TCGA-B9-4115 
         763          595          223          510          857          803 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A69E TCGA-B9-A8YH 
          14         1338           64          207          102          167 
TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5881 TCGA-BQ-5884 TCGA-BQ-5885 
          52         2639         1938         1454          792          921 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 
         792          233           29          364         3760         2948 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7840 TCGA-DW-7841 
        1864         1533          232          116          114          445 
TCGA-DW-7963 TCGA-DZ-6131 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 
        1240         2429           13         1575         1479          446 
TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X TCGA-IZ-A6M8 
          91         2072          167          511          608          146 
TCGA-KV-A74V TCGA-MH-A560 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-PJ-A8JU TCGA-SX-A7SO 
         161          543         3035         2584           84          925 
TCGA-Y8-A8RZ 
         205 

$subtype2
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-A4ZT TCGA-A4-A6HP 
           3          582          729          709          516            4 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B3-3926 
        1778         1636          412           26           67          307 
TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 
          85         1536          627           35          460          671 
TCGA-B9-A5W7 TCGA-B9-A5W9 TCGA-BQ-7055 TCGA-DW-7839 TCGA-DW-7842 TCGA-EV-5902 
         585            5          799          419           92          578 
TCGA-F9-A7Q0 TCGA-F9-A7VF TCGA-G7-6795 TCGA-G7-6797 TCGA-GL-7773 TCGA-GL-8500 
          10            7         1194          765          393          841 
TCGA-GL-A59R TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-IA-A40Y TCGA-IZ-A6M9 
         178          408          360         1726           62            2 
TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 
         885         1043          391          438          292           11 
TCGA-MH-A856 TCGA-P4-A5ED TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V 
         541         2816          174         1079          994          508 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-Y8-A894 
         423          102          494          335         1247          224 
TCGA-Y8-A895 TCGA-Y8-A896 
           2          186 

$subtype3
TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8518 TCGA-A4-A5Y1 TCGA-AL-3472 
          21           27            7          600           87          923 
TCGA-AL-7173 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-3925 
        1357          659          747          108           14         1029 
TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5883 
         930         1049          379          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-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
         214          218          353          414         3950         1093 
TCGA-DW-7837 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 
        1142          744         2460         1856         1670         1040 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6796 TCGA-G7-7502 
         757           97           36          208         1059          786 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IZ-8195 
         279         1967         5925          112           32          677 
TCGA-IZ-8196 TCGA-J7-8537 TCGA-KV-A6GD TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-PJ-A5Z8 
         649            4          160          148         2653          391 
TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A71W TCGA-SX-A7SM TCGA-SX-A7SU TCGA-Y8-A898 
          57         1199          760         1973          847          181 

subtype1 subtype2 subtype3 
       2        2        4 
subtype1 subtype2 subtype3 
    3760     2816     5925 
subtype1 subtype2 subtype3 
     493      421      654 
[1] "2.0 - 3760.0 (493.0)" "2.0 - 2816.0 (421.0)" "4.0 - 5925.0 (654.0)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      36        5        21        1
  subtype2      45        3         8        1
  subtype3      43        4        14       10
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         36       45       43
  STAGE II         5        3        4
  STAGE III       21        8       14
  STAGE IV         1        1       10
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 39  8    21
  subtype2 48  7     7
  subtype3 45  4    23
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          39       48       45
  T2           8        7        4
  T3+T4       21        7       23
[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  6  3  0
  subtype3 10 13  3
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       18        6       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 27  1 32
  subtype2 25  1 31
  subtype3 32  6 34
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       27       25       32
  M1        1        1        6
  MX       32       31       34
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 16 52
  subtype2 15 47
  subtype3 28 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   52
  subtype2   15   47
  subtype3   28   44
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       16       15       28
  MALE         52       47       44
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        21
  subtype2                                1     1                        11
  subtype3                                1     3                        17
          vv
clus       WHITE
  subtype1    42
  subtype2    43
  subtype3    47
D7V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1
  ASIAN                                   1        1        3
  BLACK OR AFRICAN AMERICAN              21       11       17
  WHITE                                  42       43       47
[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  1 53
  subtype2  4 49
  subtype3  4 55
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   53
  subtype2    4   49
  subtype3    4   55
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        4        4
  NOT HISPANIC OR LATINO       53       49       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(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 21  0
  subtype2 23  2
  subtype3 31  1
  subtype4 27  0
  subtype5 26  2
  subtype6 33  0
  subtype7  9  2
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      21       25       32       27       28       33       11 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       0        2        1        0        2        0        2 
$subtype1
TCGA-A4-7997 TCGA-A4-A48D TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B9-4115 
           2          379          595          223          510          803 
TCGA-B9-4117 TCGA-B9-5156 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-7046 TCGA-BQ-7059 
          14         1338          792          233         2948          232 
TCGA-BQ-7062 TCGA-DW-7963 TCGA-G7-6790 TCGA-G7-6792 TCGA-HE-A5NH TCGA-IA-A40X 
         116         1240         1575         1479          408          608 
TCGA-IZ-A6M8 TCGA-P4-A5E6 TCGA-PJ-A8JU 
         146         3035           84 

$subtype2
TCGA-A4-8098 TCGA-A4-8518 TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3473 TCGA-AL-A5DJ 
         140          600          118           87          763           26 
TCGA-B3-3925 TCGA-B9-A44B TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5884 
        1029           64           52         2639         1938          792 
TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7061 
         921           29          364         1864         1533          218 
TCGA-DZ-6131 TCGA-G7-7501 TCGA-MH-A560 TCGA-P4-A5EB TCGA-SX-A7SM TCGA-SX-A7SO 
        2429          446          543         2584         1973          925 
TCGA-Y8-A8RZ 
         205 

$subtype3
TCGA-A4-7732 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A6HP TCGA-AL-3467 
         582          709           23          436            4         1778 
TCGA-AL-3471 TCGA-B3-3926 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-A5W7 
         412          307           85         1536          627          585 
TCGA-B9-A5W8 TCGA-BQ-7044 TCGA-DW-7839 TCGA-DW-7840 TCGA-EV-5902 TCGA-F9-A7Q0 
         207         3760          419          114          578           10 
TCGA-F9-A7VF TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NI TCGA-IZ-A6M9 TCGA-MH-A55W 
           7          178           91          360            2         1043 
TCGA-MH-A55Z TCGA-MH-A562 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN 
         391          292         1079          994          423          102 
TCGA-SX-A7SR TCGA-Y8-A896 
         335          186 

$subtype4
TCGA-A4-7734 TCGA-A4-A4ZT TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N 
          27          516          923           67          659          747 
TCGA-B1-A654 TCGA-B9-A5W9 TCGA-DW-7836 TCGA-DW-7842 TCGA-EV-5901 TCGA-G7-6795 
         108            5         1093           92         1040         1194 
TCGA-GL-7773 TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A856 
         393         1726          649          438           11          541 
TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 TCGA-SX-A71S 
         148         2653         2816          391          174         1199 
TCGA-SX-A7SU TCGA-Y8-A894 TCGA-Y8-A895 
         847          224            2 

$subtype5
TCGA-AL-7173 TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5887 
        1357           14          379          102          270          771 
TCGA-BQ-5888 TCGA-BQ-7048 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 
         403         2839         1516          612          353         3950 
TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 TCGA-F9-A97G TCGA-G7-6789 
         744         2460         1856          757           13          208 
TCGA-G7-6796 TCGA-G7-7502 TCGA-GL-6846 TCGA-GL-A4EM TCGA-IZ-8195 TCGA-J7-8537 
        1059          786         5925           32          677            4 
TCGA-KV-A6GD TCGA-Q2-A5QZ TCGA-SX-A71W TCGA-Y8-A898 
         160           57          760          181 

$subtype6
TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7583 TCGA-A4-7996 TCGA-A4-8310 TCGA-A4-8311 
         554          493            3           49          780          729 
TCGA-A4-8517 TCGA-A4-A5XZ TCGA-AL-3468 TCGA-B3-4103 TCGA-B9-4114 TCGA-B9-4617 
         597            2         1636          930          857           35 
TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A8YH TCGA-BQ-5876 TCGA-BQ-5881 TCGA-BQ-7055 
         460          671          167          586         1454          799 
TCGA-BQ-7060 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7841 TCGA-DZ-6135 TCGA-G7-6797 
         214          414         1142          445         1670          765 
TCGA-GL-8500 TCGA-HE-A5NF TCGA-HE-A5NL TCGA-IA-A40U TCGA-KV-A6GE TCGA-KV-A74V 
         841         2072          167          511          885          161 
TCGA-SX-A71V TCGA-SX-A7SQ TCGA-SX-A7SS 
         508          494         1247 

$subtype7
TCGA-A4-7287 TCGA-A4-7915 TCGA-B3-4104 TCGA-BQ-5883 TCGA-BQ-5894 TCGA-F9-A4JJ 
          21            7         1049         1242           84           97 
TCGA-F9-A8NY TCGA-G7-A4TM TCGA-G7-A8LD TCGA-GL-7966 TCGA-IA-A40Y 
          36          279         1967          112           62 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       2       26        2        2        4        2        7 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    3035     2639     3760     2816     5925     2072     1967 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   510.0    600.0    375.5    516.0    644.5    586.0     97.0 
[1] "2.0 - 3035.0 (510.0)"  "26.0 - 2639.0 (600.0)" "2.0 - 3760.0 (375.5)" 
[4] "2.0 - 2816.0 (516.0)"  "4.0 - 5925.0 (644.5)"  "2.0 - 2072.0 (586.0)" 
[7] "7.0 - 1967.0 (97.0)"  
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      16        1         4        0
  subtype2      12        2        14        3
  subtype3      24        2         4        0
  subtype4      24        0         1        0
  subtype5      18        1         8        6
  subtype6      26        3         4        0
  subtype7       4        3         8        3
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I         16       12       24       24       18       26        4
  STAGE II         1        2        2        0        1        3        3
  STAGE III        4       14        4        1        8        4        8
  STAGE IV         0        3        0        0        6        0        3
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 18  2     3
  subtype2 13  3    15
  subtype3 24  5     4
  subtype4 25  1     1
  subtype5 18  1    14
  subtype6 29  4     4
  subtype7  5  3    10
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1          18       13       24       25       18       29        5
  T2           2        3        5        1        1        4        3
  T3+T4        3       15        4        1       14        4       10
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  5  1  0
  subtype2 11  6  1
  subtype3  2  0  0
  subtype4  2  0  0
  subtype5  8  4  3
  subtype6  5  0  0
  subtype7  1  9  0
D8V5, multiclass
[1] "Remove cluster labels:" "subtype3"               "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       6       18        2        2       15        5       10 
 [1] "subtype6" "subtype2" "subtype7" "subtype2" "subtype2" "subtype2"
 [7] "subtype2" "subtype5" "subtype1" "subtype1" "subtype5" "subtype6"
[13] "subtype5" "subtype2" "subtype7" "subtype2" "subtype2" "subtype2"
[19] "subtype5" "subtype5" "subtype5" "subtype1" "subtype2" "subtype2"
[25] "subtype7" "subtype7" "subtype5" "subtype5" "subtype2" "subtype2"
[31] "subtype5" "subtype2" "subtype1" "subtype2" "subtype7" "subtype5"
[37] "subtype5" "subtype5" "subtype2" "subtype7" "subtype5" "subtype7"
[43] "subtype6" "subtype7" "subtype5" "subtype5" "subtype6" "subtype1"
[49] "subtype7" "subtype7" "subtype2" "subtype1" "subtype6" "subtype2"
    clus
vv   subtype1 subtype2 subtype5 subtype6 subtype7
  N0        5       11        8        5        1
  N1        1        6        4        0        9
  N2        0        1        3        0        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1  9  0 10
  subtype2 16  3 11
  subtype3 15  0 15
  subtype4  8  0 19
  subtype5 16  2 14
  subtype6 14  0 19
  subtype7  6  3  9
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  M0        9       16       15        8       16       14        6
  M1        0        3        0        0        2        0        3
  MX       10       11       15       19       14       19        9
[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"
D8V7, binary
          cls
clus        0  1
  subtype1  6 17
  subtype2  9 22
  subtype3  7 26
  subtype4 10 17
  subtype5 11 22
  subtype6  5 32
  subtype7 11  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   17
  subtype2    9   22
  subtype3    7   26
  subtype4   10   17
  subtype5   11   22
  subtype6    5   32
  subtype7   11    7
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        6        9        7       10       11        5       11
  MALE         17       22       26       17       22       32        7
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, continuous
D8V9, continuous
[1] "Remove cluster labels:" "subtype1"               "subtype6"              
[4] "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       2        4        6        9        4        2        1 
 [1] "subtype4" "subtype2" "subtype5" "subtype5" "subtype4" "subtype3"
 [7] "subtype3" "subtype4" "subtype4" "subtype4" "subtype4" "subtype2"
[13] "subtype4" "subtype5" "subtype4" "subtype3" "subtype5" "subtype3"
[19] "subtype2" "subtype3" "subtype4" "subtype3" "subtype2"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                        10
  subtype2                                0     0                         6
  subtype3                                1     1                        10
  subtype4                                0     0                         4
  subtype5                                0     3                         5
  subtype6                                1     0                         8
  subtype7                                0     1                         6
          vv
clus       WHITE
  subtype1    11
  subtype2    24
  subtype3    18
  subtype4    21
  subtype5    24
  subtype6    25
  subtype7     9
D8V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        0
  ASIAN                                   0        0        1        0        3
  BLACK OR AFRICAN AMERICAN              10        6       10        4        5
  WHITE                                  11       24       18       21       24
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        1        0
  ASIAN                                   0        1
  BLACK OR AFRICAN AMERICAN               8        6
  WHITE                                  25        9
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
          cls
clus        0  1
  subtype1  0 19
  subtype2  1 23
  subtype3  0 28
  subtype4  5 20
  subtype5  1 25
  subtype6  1 29
  subtype7  1 13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   19
  subtype2    1   23
  subtype3    0   28
  subtype4    5   20
  subtype5    1   25
  subtype6    1   29
  subtype7    1   13
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        1        0        5        1        1
  NOT HISPANIC OR LATINO       19       23       28       20       25       29
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       13
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
