[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"        "-oTLIHC-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/LIHC-TP/11541458/LIHC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/LIHC-TP/11590596/LIHC-TP.mergedcluster.txt"

nPatients in clinical file=317, in cluster file=377, common to both=317
[1]   8 317
[1] "CN_CNMF"
[1] 3
  1   2   3 
 93 106 112 
  1   2   3 
 93 106 112 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 59 108  76 
  1   2   3 
 59 108  76 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5  6 
28 58 43 25 41 39 
 1  2  3  4  5  6 
28 58 43 25 41 39 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 85 113  36 
  1   2   3 
 85 113  36 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4 
 52 112  43 105 
  1   2   3   4 
 52 112  43 105 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
 35  82  47 105  43 
  1   2   3   4   5 
 35  82  47 105  43 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3  4 
83 72 98 38 
 1  2  3  4 
83 72 98 38 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4  5 
57 72 86 29 47 
 1  2  3  4  5 
57 72 86 29 47 
[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] "HISTOLOGICALTYPE"                      
[16] "RADIATIONS.RADIATION.REGIMENINDICATION"
[17] "COMPLETENESS.OF.RESECTION"             
[18] "RACE"                                  
[19] "ETHNICITY"                             
[20] "BATCHNUMBER"                           

Input Data has 20 rows and 317 columns.

[1] "Batch" "20"   
[1] "Last Follow UP"
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-4072 TCGA-BC-4073 
         216          328          322           20           NA          849 
TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10W 
          NA           NA           NA           NA           NA           NA 
TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A110 TCGA-BC-A112 TCGA-BC-A216 
          NA           NA           NA           NA           NA         1351 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BC-A69I 
         421            8          680          289          444          387 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-BW-A5NP TCGA-BW-A5NQ 
         227          409          146           20           NA           NA 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 TCGA-CC-5263 
           2            5           NA           12           NA           NA 
TCGA-CC-5264 TCGA-CC-A123 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MB 
          NA           NA           NA            3            2            3 
TCGA-CC-A3MC TCGA-CC-A5UC TCGA-CC-A5UE TCGA-CC-A7IE TCGA-CC-A7IF TCGA-CC-A7IG 
           4           NA           NA           NA           NA           NA 
TCGA-CC-A7IH TCGA-CC-A7II TCGA-CC-A7IJ TCGA-CC-A7IK TCGA-CC-A7IL TCGA-CC-A8HS 
          NA           NA           NA           NA           NA           NA 
TCGA-CC-A8HT TCGA-CC-A8HU TCGA-CC-A8HV TCGA-CC-A9FU TCGA-DD-A113 TCGA-DD-A114 
          NA           NA           NA           NA         2425           NA 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B 
          NA           NA         3437           NA           79           NA 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1E9 TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
         662           NA           NA         2415         2017          602 
TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EF TCGA-DD-A1EG TCGA-DD-A1EH TCGA-DD-A1EI 
        2301          204           NA           NA         1495          183 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39X TCGA-DD-A39Y 
         887           NA           NA           NA           NA           NA 
TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 
          NA           NA           NA           NA           NA           NA 
TCGA-DD-A3A5 TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A8 TCGA-DD-A3A9 TCGA-DD-A4NA 
          NA           NA           NA           NA           NA         1008 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NH 
         989         2232           NA          942          445          917 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO 
         816          928           NA         1711           NA         2245 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
        3308           NA           NA           NA         2398          334 
TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-A73G 
          NA          230          334           44          843         3071 
TCGA-DD-AA3A TCGA-DD-AAC8 TCGA-DD-AAC9 TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AACC 
          NA           NA          347         2000         1800           NA 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH TCGA-DD-AACI 
          NA         1931           NA           NA           NA         1618 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACP TCGA-DD-AACQ 
        1828            9           58         1769          400          436 
TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AACZ TCGA-DD-AAD0 
        1475         1240         1157          170           NA          137 
TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AAD8 
         564          658         1029         1037          672          959 
TCGA-DD-AADA TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADI 
         930          890           NA          864           NA          763 
TCGA-DD-AADJ TCGA-DD-AADK TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADO 
         730          734          636           NA          527           92 
TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AADW 
         120          161         1742          216          252          203 
TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE1 TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 
         294          300          293          288          300          259 
TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB 
         141          382          344          386          450          370 
TCGA-DD-AAED TCGA-DD-AAEE TCGA-DD-AAEG TCGA-DD-AAEH TCGA-DD-AAEK TCGA-DD-AAVP 
         470          498          476          476         1067         2405 
TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU TCGA-DD-AAVW TCGA-DD-AAVX 
        2406         2198         1823         1882         1867         1718 
TCGA-DD-AAVY TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A459 
        1788         1699         1644         1505         1451          408 
TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX 
         386          482          423          406            7            6 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 
           6            6            6          400          408            6 
TCGA-ED-A8O6 TCGA-ED-A97K TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KA TCGA-EP-A2KB 
           6            6          570          608          357          334 
TCGA-EP-A2KC TCGA-EP-A3JL TCGA-EP-A3RK TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B 
          NA          303          363           NA           NA          987 
TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A3R3 
         729           NA          848           NA           NA            4 
TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25T 
           1           10         1836           12           37         1553 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A25Z 
        1636          860          935         1779           NA          655 
TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI 
         673          780          180          594          585          447 
TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M5 
         364          744          621          520          236           NA 
TCGA-G3-A7M6 TCGA-G3-A7M7 TCGA-G3-A7M8 TCGA-G3-A7M9 TCGA-G3-AAUZ TCGA-G3-AAV0 
         366          182           NA           NA          342          260 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 TCGA-G3-AAV7 
          NA          295          279           NA           NA           92 
TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
          NA           NA           NA           NA          631          519 
TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-KR-A7K7 TCGA-KR-A7K8 TCGA-LG-A6GG 
         122           NA          360          407          741          387 
TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E TCGA-MI-A75G TCGA-MI-A75H 
         180          130          291          507          559          391 
TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-O8-A75V TCGA-PD-A5DF 
         630          330           NA          498          135           NA 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-RC-A7SF TCGA-RC-A7SH TCGA-RC-A7SK TCGA-RG-A7D4 
          62          640          579          468          472          734 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MD TCGA-UB-A7ME TCGA-UB-A7MF 
         455          526          438           NA          486           NA 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 
         253          139           31           30          122           NA 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 
         142          782          706          717           21          743 
TCGA-ZP-A9D4 TCGA-ZS-A9CD TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
         395           NA         1066         2258          250 
Variable 1:'AGE':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=91,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=192,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 6:'NEOPLASM.DISEASESTAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY.T.STAGE':	nDistinctValues=9,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.N.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.M.STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCCUPLOADDAY':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=18,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 13:'DAYSTOLASTKNOWNALIVE':	nDistinctValues=0,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 14:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'HISTOLOGICAL.TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 17:'COMPLETENESS.OF.RESECTION':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'BATCH.NUMBER':	nDistinctValues=29,	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] "HISTOLOGICAL.TYPE"         "COMPLETENESS.OF.RESECTION"
 [9] "RACE"                      "ETHNICITY"                
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "3"          
[1] "PATHOLOGY.N" "4"          
Output Data has 317 columns, 1 survival variables, and 10 non-survival variables.
AGE, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM.DISEASESTAGE, nv=9, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1 155  78  68  13 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
  156    78    68    13 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1 155  78  68  13 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
  156    78    68    13 
PATHOLOGY.N.STAGE, nv=2, binary=FALSE, numeric=TRUE
PATHOLOGY.M.STAGE, nv=3, binary=FALSE, numeric=FALSE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL.TYPE, nv=3, binary=FALSE, numeric=FALSE
COMPLETENESS.OF.RESECTION, nv=4, binary=FALSE, numeric=FALSE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 64 28
  subtype2 60 34
  subtype3 76 30
subtype1 subtype2 subtype3 
      92       94      106 
subtype1 subtype2 subtype3 
      28       34       30 
$subtype1
TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A10S TCGA-BC-A10W TCGA-BC-A216 TCGA-CC-A3MC 
       10.59        48.99        46.78         2.99        44.42         0.13 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A1E9 TCGA-DD-A1EE TCGA-DD-A1EF 
       79.73        53.33         7.33        90.71         6.71        12.95 
TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 
       45.11         6.02        21.14         5.62        19.76        17.59 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NK TCGA-DD-A4NR TCGA-DD-A73D TCGA-DD-A73G 
        0.36        30.97        39.78         0.30        10.98       100.96 
TCGA-DD-AACB TCGA-DD-AACD TCGA-DD-AACI TCGA-DD-AACJ TCGA-DD-AACM TCGA-DD-AACQ 
       59.18        12.53        53.19        60.10        58.16        14.33 
TCGA-DD-AACZ TCGA-DD-AAD0 TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD5 TCGA-DD-AADA 
        5.62         4.50        18.54        21.63        34.09        30.58 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADN TCGA-DD-AADP TCGA-DD-AADQ 
       25.08        24.13         0.39        17.33         3.95         5.29 
TCGA-DD-AADU TCGA-DD-AAE1 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEG 
        8.28         9.63        12.69        12.16        15.45        15.65 
TCGA-DD-AAEH TCGA-DD-AAVQ TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVY TCGA-DD-AAVZ 
       15.65        79.10        59.93        61.38        58.78        55.86 
TCGA-DD-AAW0 TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A8O6 
       54.05        49.48        47.70        13.35         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ 
       18.74         0.62         9.96        22.85        14.40        23.97 
TCGA-FV-A3I1 TCGA-FV-A4ZP TCGA-FV-A4ZQ TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A5SL 
        8.12        60.36         0.39        22.13        19.53        20.42 
TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV2 TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-KR-A7K2 
        5.98        11.24         9.70         2.66         4.01        11.84 
TCGA-KR-A7K7 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75H TCGA-MI-A75I 
       13.38         5.92         4.27         9.57        12.85        20.71 
TCGA-O8-A75V TCGA-RC-A7SF TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV TCGA-ZP-A9D4 
        4.44        19.04         4.01        13.55         4.67        12.99 
TCGA-ZS-A9CD TCGA-ZS-A9CG 
       45.57         8.22 

$subtype2
TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A112 
       10.13        27.52        27.52        23.34         1.12         5.03 
TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A69H TCGA-BW-A5NO 
       13.84         0.26        22.36         9.50        14.60         0.66 
TCGA-CC-5258 TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A118 
        0.07         0.39         4.24         0.07         0.10       113.00 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A3A7 
        2.60        21.76        49.15        29.16        13.64        13.78 
TCGA-DD-A3A9 TCGA-DD-A4NJ TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B TCGA-DD-AA3A 
       30.61        30.51        29.56        73.81         9.30        13.48 
TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACG TCGA-DD-AACH 
        0.53        65.75        63.48        12.00        15.42         6.41 
TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACU TCGA-DD-AAD3 TCGA-DD-AAD6 TCGA-DD-AAD8 
       13.15        48.49        40.77        33.83        22.09        31.53 
TCGA-DD-AADB TCGA-DD-AADC TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AADO 
       29.26        13.97        28.41         3.78        20.91         3.02 
TCGA-DD-AADR TCGA-DD-AADW TCGA-DD-AADY TCGA-DD-AAE0 TCGA-DD-AAE3 TCGA-DD-AAE6 
       57.27         6.67         9.67         9.86         9.86         4.64 
TCGA-DD-AAE8 TCGA-DD-AAEE TCGA-DD-AAEK TCGA-DD-AAVP TCGA-DD-AAVU TCGA-ED-A459 
       11.31        16.37        35.08        79.07        61.87        13.41 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A7XP TCGA-ED-A8O5 TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20         0.20        13.15         0.20        11.74        10.98 
TCGA-FV-A23B TCGA-FV-A2QR TCGA-FV-A3I0 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S 
       32.45        19.10        27.88         6.38         0.03         1.22 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A5SI TCGA-G3-A7M6 TCGA-G3-AAV1 TCGA-G3-AAV6 
       58.49        14.86        14.70        12.03        11.80         2.14 
TCGA-G3-AAV7 TCGA-LG-A6GG TCGA-NI-A8LF TCGA-PD-A5DF TCGA-RC-A7SH TCGA-RC-A7SK 
        3.02        12.72        16.37        21.01        15.39        15.52 
TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7MC TCGA-UB-A7ME TCGA-UB-A7MF TCGA-UB-AA0U 
       24.13        14.96        14.40        15.98         7.04         8.32 
TCGA-WJ-A86L TCGA-WQ-A9G7 TCGA-ZP-A9D2 TCGA-ZS-A9CE 
        1.02         0.99        24.43        35.05 

$subtype3
TCGA-4R-AA8I TCGA-5C-A9VG TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10X 
        7.10        10.78         0.66        27.91        37.32        25.32 
TCGA-BC-A110 TCGA-BC-A69I TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5260 
       69.57        12.72         7.46        13.45         4.80         2.86 
TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A115 TCGA-DD-A11B 
        3.39         3.32         0.10        37.78        83.57         0.46 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EK 
       51.29        79.40        66.31        19.79        75.65        18.35 
TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A4 TCGA-DD-A3A5 
       55.69        25.81         7.66        70.06        20.12       102.74 
TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NI 
      107.11        33.14        32.52        73.38        30.15        26.83 
TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A 
       56.25       108.76        12.26        80.75        78.84        10.98 
TCGA-DD-A73C TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACK 
        7.56         1.45        27.72        11.41        55.40         0.30 
TCGA-DD-AACL TCGA-DD-AACW TCGA-DD-AACX TCGA-DD-AADJ TCGA-DD-AADS TCGA-DD-AAE2 
        1.91        38.04         5.59        24.00         7.10         9.47 
TCGA-DD-AAE4 TCGA-DD-AAE7 TCGA-DD-AAEA TCGA-DD-AAVR TCGA-DD-AAVX TCGA-ED-A4XI 
        8.52        12.56        14.79        72.26        56.48        12.69 
TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K 
       15.85        13.91         0.20         0.20        13.41         0.20 
TCGA-EP-A26S TCGA-EP-A3RK TCGA-FV-A3R3 TCGA-FV-A496 TCGA-G3-A25T TCGA-G3-A25U 
       19.99        11.93         0.13         0.33        51.06        53.79 
TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A3CK 
       28.27        30.74        21.53        25.64         5.92        19.23 
TCGA-G3-A5SJ TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M9 TCGA-G3-AAV0 TCGA-G3-AAV3 
       11.97        17.10         7.76         1.84         8.55         9.17 
TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG 
        0.89         1.02         2.20        37.71        20.75        17.06 
TCGA-KR-A7K0 TCGA-KR-A7K8 TCGA-MI-A75E TCGA-MI-A75G TCGA-MR-A8JO TCGA-NI-A4U2 
        2.14        24.36        16.67        18.38        10.85        58.88 
TCGA-QA-A7B7 TCGA-RC-A7S9 TCGA-UB-A7MB TCGA-UB-A7MD TCGA-UB-AA0V TCGA-ZP-A9CY 
        2.04        21.04        17.29         1.71         4.57        25.71 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZS-A9CF 
       23.21        23.57         0.69        74.24 

subtype1 subtype2 subtype3 
    0.13     0.03     0.10 
subtype1 subtype2 subtype3 
  100.96   113.00   108.76 
subtype1 subtype2 subtype3 
  14.365   13.810   17.080 
[1] "0.1 - 101.0 (14.4)" "0.0 - 113.0 (13.8)" "0.1 - 108.8 (17.1)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      51       20         0         14          0          0        1
  subtype2      41       30         1         20          3          2        1
  subtype3      54       22         1         18          4          5        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         0
  subtype2         0         1
  subtype3         0         1
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          51       41       54
  STAGE II         20       30       22
  STAGE III         0        1        1
  STAGE IIIA       14       20       18
  STAGE IIIB        0        3        4
  STAGE IIIC        0        2        5
  STAGE IV          1        1        0
  STAGE IVA         1        0        0
  STAGE IVB         0        1        1
[1] 9 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    54 21 16  1
  subtype2    42 33 25  6
  subtype3    59 24 23  5
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       54       42       59
  T2          21       33       24
  T3          16       25       23
  T4           1        6        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V5, binary
          cls
clus        0  1
  subtype1 65  1
  subtype2 78  1
  subtype3 79  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65    1
  subtype2   78    1
  subtype3   79    1
   clus
vv  subtype1 subtype2 subtype3
  0       65       78       79
  1        1        1        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 71  1 21
  subtype2 84  2 20
  subtype3 83  1 28
D1V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       71       84       83
  M1        1        2        1
  MX       21       20       28
[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 22 71
  subtype2 38 68
  subtype3 40 72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   71
  subtype2   38   68
  subtype3   40   72
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       22       38       40
  MALE         71       68       72
[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"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       92
  subtype2                       0                      103
  subtype3                       2                      108
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                3
  subtype3                                2
D1V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 0        0        2
  HEPATOCELLULAR CARCINOMA               92      103      108
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        3        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       R0 R1 R2 RX
  subtype1 84  6  1  1
  subtype2 91  6  0  8
  subtype3 99  2  0  7
D1V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       84       91       99
  R1        6        6        2
  R2        1        0        0
  RX        1        8        7
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1    45                         4
  subtype2                                0    58                         4
  subtype3                                0    38                         7
          vv
clus       WHITE
  subtype1    39
  subtype2    43
  subtype3    63
D1V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                  45       58       38
  BLACK OR AFRICAN AMERICAN               4        4        7
  WHITE                                  39       43       63
[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   4  84
  subtype2   3 100
  subtype3   1 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   84
  subtype2    3  100
  subtype3    1  103
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        3        1
  NOT HISPANIC OR LATINO       84      100      103
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 35 18
  subtype2 62 38
  subtype3 41 28
subtype1 subtype2 subtype3 
      53      100       69 
subtype1 subtype2 subtype3 
      18       38       28 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10X TCGA-BC-A110 TCGA-BD-A3EP TCGA-CC-5258 
       48.99        27.91        25.32        69.57        13.45         0.07 
TCGA-CC-5260 TCGA-CC-5262 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-DD-A114 TCGA-DD-A1E9 
        2.86         3.39         3.32         0.10        37.78        90.71 
TCGA-DD-A1EC TCGA-DD-A1ED TCGA-DD-A1EL TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB 
       19.79        75.65        13.64       107.11        33.14        32.52 
TCGA-DD-A4ND TCGA-DD-A4NH TCGA-DD-A4NL TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR 
       73.38        30.15        56.25       108.76        12.26         0.30 
TCGA-DD-A4NS TCGA-DD-A73C TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX 
       80.75         7.56        12.69        15.85        13.91         0.20 
TCGA-ED-A7XO TCGA-ED-A97K TCGA-EP-A3RK TCGA-ES-A2HT TCGA-G3-A25T TCGA-G3-A25V 
        0.20         0.20        11.93        14.40        51.06        28.27 
TCGA-G3-A25W TCGA-G3-A3CI TCGA-G3-A7M9 TCGA-G3-AAV3 TCGA-G3-AAV7 TCGA-HP-A5MZ 
       30.74         5.92         1.84         9.17         3.02         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 TCGA-KR-A7K8 TCGA-LG-A9QC 
       37.71        20.75        17.06         4.01        24.36         5.92 
TCGA-LG-A9QD TCGA-MI-A75E TCGA-MR-A8JO TCGA-UB-AA0V TCGA-YA-A8S7 
        4.27        16.67        10.85         4.57        13.55 

$subtype2
TCGA-4R-AA8I TCGA-5C-AAPD TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
        7.10         0.66        46.78        27.52        27.52        23.34 
TCGA-BC-A10Z TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
        1.12        44.42        13.84         0.26        22.36         9.50 
TCGA-BC-A69I TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5263 TCGA-CC-A3MB TCGA-DD-A115 
       12.72         7.46         0.66         4.24         0.10        83.57 
TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A1EG 
        2.60        21.76        51.29        79.40         6.71        45.11 
TCGA-DD-A1EJ TCGA-DD-A1EK TCGA-DD-A39V TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A0 
       29.16        18.35        21.14         5.62        19.76        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG 
        7.66        70.06       102.74         0.36        30.97        14.63 
TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73D 
       26.83        30.51        39.78        78.84        10.98        10.98 
TCGA-DD-A73E TCGA-DD-A73F TCGA-DD-AADP TCGA-ED-A7PZ TCGA-EP-A12J TCGA-EP-A26S 
        1.45        27.72         3.95         0.20        18.74        19.99 
TCGA-EP-A2KA TCGA-EP-A2KC TCGA-EP-A3JL TCGA-ES-A2HS TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.74         0.62         9.96        22.85        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A3R2 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25U TCGA-G3-A25Z 
        8.12         6.38         0.03         1.22        53.79        21.53 
TCGA-G3-A3CG TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SL 
       22.13        19.53        19.23        11.97        24.46        20.42 
TCGA-G3-A5SM TCGA-G3-A6UC TCGA-G3-A7M6 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV1 
       17.10         7.76        12.03        11.24         8.55        11.80 
TCGA-G3-AAV2 TCGA-G3-AAV4 TCGA-GJ-A6C0 TCGA-GJ-A9DB TCGA-KR-A7K0 TCGA-KR-A7K2 
        9.70         0.89         1.02         2.20         2.14        11.84 
TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75G TCGA-MI-A75H TCGA-MI-A75I TCGA-NI-A4U2 
       13.38        12.72        18.38        12.85        20.71        58.88 
TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-RG-A7D4 TCGA-UB-A7MC 
       21.01         2.04        19.04        15.52        24.13        14.40 
TCGA-UB-A7MD TCGA-UB-AA0U TCGA-WJ-A86L TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9D1 
        1.71         8.32         1.02         4.67        25.71         0.69 
TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       12.99        35.05        74.24         8.22 

$subtype3
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10W TCGA-BC-A112 
       10.78        10.59        37.32        10.13         2.99         5.03 
TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5259 TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC 
       14.60         4.80         0.16         0.39         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A116 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A11B TCGA-DD-A1EB 
       79.73        53.33       113.00         7.33         0.46        66.31 
TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A39X TCGA-DD-A3A3 TCGA-DD-A3A4 
       12.95        49.15         6.02        55.69        17.59        20.12 
TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NE TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A73B 
       13.78        30.61        21.70        29.56        73.81         9.30 
TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AADW TCGA-DD-AAEG TCGA-ED-A459 TCGA-ED-A66X 
      100.96        13.48         6.67        15.65        13.41        13.35 
TCGA-ED-A66Y TCGA-ED-A7PY TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 
        0.23         0.20        13.15        13.41         0.20         0.20 
TCGA-EP-A2KB TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A496 TCGA-FV-A4ZP 
       10.98        32.45        27.88         0.13         0.33        60.36 
TCGA-FV-A4ZQ TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A5SI TCGA-G3-A7M7 
        0.39        58.49        14.86        25.64        14.70         5.98 
TCGA-G3-AAV6 TCGA-MI-A75C TCGA-NI-A8LF TCGA-O8-A75V TCGA-RC-A7S9 TCGA-RC-A7SH 
        2.14         9.57        16.37         4.44        21.04        15.39 
TCGA-UB-A7MA TCGA-UB-A7MB TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-ZP-A9CZ 
       14.96        17.29        15.98         7.04         0.99        23.21 
TCGA-ZP-A9D0 TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       23.57        24.43        45.57 

subtype1 subtype2 subtype3 
    0.07     0.03     0.07 
subtype1 subtype2 subtype3 
  108.76   102.74   113.00 
subtype1 subtype2 subtype3 
   13.91    13.61    13.48 
[1] "0.1 - 108.8 (13.9)" "0.0 - 102.7 (13.6)" "0.1 - 113.0 (13.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      24       11         0         15          3          4        0
  subtype2      42       27         1         20          3          3        0
  subtype3      25       19         1         17          1          2        2
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         1
  subtype3         0         1
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          24       42       25
  STAGE II         11       27       19
  STAGE III         0        1        1
  STAGE IIIA       15       20       17
  STAGE IIIB        3        3        1
  STAGE IIIC        4        3        2
  STAGE IV          0        0        2
  STAGE IVA         0        1        0
  STAGE IVB         0        1        1
[1] 9 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    25 12 18  3
  subtype2    48 29 23  7
  subtype3    27 22 24  3
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       25       48       27
  T2          12       29       22
  T3          18       23       24
  T4           3        7        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V5, binary
          cls
clus        0  1
  subtype1 43  1
  subtype2 60  2
  subtype3 50  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43    1
  subtype2   60    2
  subtype3   50    1
   clus
vv  subtype1 subtype2 subtype3
  0       43       60       50
  1        1        2        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 45  0 14
  subtype2 71  1 36
  subtype3 55  3 18
D2V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       45       71       55
  M1        0        1        3
  MX       14       36       18
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 20 39
  subtype2 33 75
  subtype3 35 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   39
  subtype2   33   75
  subtype3   35   41
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       20       33       35
  MALE         39       75       41
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       2                       56
  subtype2                       0                      106
  subtype3                       0                       73
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                2
  subtype3                                3
D2V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 2        0        0
  HEPATOCELLULAR CARCINOMA               56      106       73
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        2        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       R0 R1 R2 RX
  subtype1 48  2  0  6
  subtype2 92  6  0  7
  subtype3 66  5  1  4
D2V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       48       92       66
  R1        2        6        5
  R2        0        0        1
  RX        6        7        4
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    16                         6
  subtype2                                1    22                         8
  subtype3                                0    33                         1
          vv
clus       WHITE
  subtype1    34
  subtype2    74
  subtype3    39
D2V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0
  ASIAN                                  16       22       33
  BLACK OR AFRICAN AMERICAN               6        8        1
  WHITE                                  34       74       39
[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  3 52
  subtype2  2 96
  subtype3  4 70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   52
  subtype2    2   96
  subtype3    4   70
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        2        4
  NOT HISPANIC OR LATINO       52       96       70
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = MRNASEQ_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 14 10
  subtype2 34 22
  subtype3 23 12
  subtype4 14 11
  subtype5 23 15
  subtype6 24 12
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      24       56       35       25       38       36 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      10       22       12       11       15       12 
$subtype1
TCGA-BC-4073 TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
       27.91        27.52         2.99        44.42        13.84        22.36 
TCGA-BC-A8YO TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A39Y TCGA-DD-A3A1 TCGA-DD-A4NQ 
        7.46         4.24         3.32         5.62         7.66        12.26 
TCGA-ED-A459 TCGA-G3-A25S TCGA-G3-A5SJ TCGA-G3-A7M9 TCGA-G3-AAV7 TCGA-GJ-A6C0 
       13.41         1.22        11.97         1.84         3.02         1.02 
TCGA-K7-A5RG TCGA-KR-A7K7 TCGA-LG-A6GG TCGA-MI-A75I TCGA-QA-A7B7 TCGA-RG-A7D4 
       17.06        13.38        12.72        20.71         2.04        24.13 

$subtype2
TCGA-4R-AA8I TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF 
        7.10        46.78        27.52        23.34         1.12         0.26 
TCGA-BC-A5W4 TCGA-BW-A5NO TCGA-CC-A3MB TCGA-DD-A115 TCGA-DD-A11A TCGA-DD-A11B 
        9.50         0.66         0.10        83.57         2.60         0.46 
TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EK TCGA-DD-A3A2 TCGA-DD-A3A5 
       21.76        51.29        66.31        18.35        70.06       102.74 
TCGA-DD-A4NE TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK TCGA-DD-A4NL TCGA-DD-A4NV 
       21.70        26.83        30.51        39.78        56.25        78.84 
TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73F TCGA-ED-A7XO TCGA-ES-A2HS 
       10.98         9.30         7.56        27.72         0.20        22.85 
TCGA-FV-A2QR TCGA-FV-A3R2 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CG 
       19.10         6.38         0.33        53.79        21.53        22.13 
TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-AAUZ TCGA-G3-AAV0 
       25.64         5.92        14.70        24.46        11.24         8.55 
TCGA-GJ-A9DB TCGA-HP-A5N0 TCGA-KR-A7K8 TCGA-LG-A9QD TCGA-MI-A75G TCGA-NI-A4U2 
        2.20        37.71        24.36         4.27        18.38        58.88 
TCGA-PD-A5DF TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-AA0U TCGA-ZP-A9CY 
       21.01        19.04        15.52        17.29         8.32        25.71 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.05        74.24 

$subtype3
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-DD-A113 
       10.78        10.59        14.60         0.07         0.16        79.73 
TCGA-DD-A118 TCGA-DD-A1EF TCGA-DD-A1EH TCGA-DD-A1EJ TCGA-DD-A39Z TCGA-DD-A3A3 
      113.00        12.95        49.15        29.16        19.76        17.59 
TCGA-DD-A3A9 TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A73G TCGA-ED-A66X TCGA-ED-A66Y 
       30.61        30.15        29.56       100.96        13.35         0.23 
TCGA-ED-A7PY TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A23B 
        0.20         0.20         0.20         0.20        10.98        32.45 
TCGA-FV-A4ZP TCGA-G3-AAV6 TCGA-KR-A7K2 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-UB-A7MA 
       60.36         2.14        11.84        21.04        15.39        14.96 
TCGA-UB-A7ME TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-ZP-A9CZ TCGA-ZP-A9D0 
       15.98         7.04         0.99        23.21        23.57 

$subtype4
TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5262 TCGA-CC-A3MC TCGA-DD-A119 TCGA-DD-A1EG 
       13.45         4.80         3.39         0.13         7.33        45.11 
TCGA-DD-A39X TCGA-DD-A3A7 TCGA-DD-A4NO TCGA-DD-A4NR TCGA-EP-A2KA TCGA-EP-A3JL 
       55.69        13.78        73.81         0.30        11.74         9.96 
TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I1 TCGA-G3-A25V TCGA-G3-A5SM TCGA-G3-A7M7 
       14.40        23.97         8.12        28.27        17.10         5.98 
TCGA-HP-A5MZ TCGA-K7-A6G5 TCGA-MI-A75C TCGA-O8-A75V TCGA-ZP-A9CV TCGA-ZP-A9D1 
        2.66         4.01         9.57         4.44         4.67         0.69 
TCGA-ZS-A9CD 
       45.57 

$subtype5
TCGA-BC-4072 TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 
       48.99        37.32        10.13        25.32        69.57         5.03 
TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-DD-A114 TCGA-DD-A1EC 
        2.86         0.39         0.10         0.07        37.78        19.79 
TCGA-DD-A1EI TCGA-DD-A3A6 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NS 
        6.02       107.11        33.14        32.52        73.38        80.75 
TCGA-DD-AA3A TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A82E 
       13.48        12.69        15.85        13.91         0.20        13.41 
TCGA-ED-A97K TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A495 TCGA-G3-A25T TCGA-G3-A25X 
        0.20        27.88         0.13         0.03        51.06        58.49 
TCGA-G3-A25Y TCGA-G3-A7M6 TCGA-K7-A5RF TCGA-MI-A75E TCGA-MR-A8JO TCGA-UB-AA0V 
       14.86        12.03        20.75        16.67        10.85         4.57 
TCGA-YA-A8S7 TCGA-ZP-A9D2 
       13.55        24.43 

$subtype6
TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL 
       12.72        53.33        79.40        75.65         6.71        13.64 
TCGA-DD-A39V TCGA-DD-A3A4 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP 
       21.14        20.12         0.36        30.97        14.63       108.76 
TCGA-DD-A73D TCGA-DD-A73E TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC 
       10.98         1.45        13.15        18.74        19.99         0.62 
TCGA-EP-A3RK TCGA-FV-A4ZQ TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC 
       11.93         0.39        19.53        19.23        20.42         7.76 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-KR-A7K0 TCGA-LG-A9QC 
       11.80         9.70         9.17         0.89         2.14         5.92 
TCGA-MI-A75H TCGA-NI-A8LF TCGA-UB-A7MC TCGA-UB-A7MD TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       12.85        16.37        14.40         1.71        12.99         8.22 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    1.02     0.10     0.07     0.13     0.03     0.36 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   44.42   102.74   113.00    73.81   107.11   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
  12.115   21.270   14.960    9.570   14.385   12.920 
[1] "1.0 - 44.4 (12.1)"  "0.1 - 102.7 (21.3)" "0.1 - 113.0 (15.0)"
[4] "0.1 - 73.8 (9.6)"   "0.0 - 107.1 (14.4)" "0.4 - 108.8 (12.9)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1       5       10         0          7          2          1        0
  subtype2      29        9         1         12          1          0        0
  subtype3       9       13         1         11          1          3        1
  subtype4      13        4         0          2          1          1        1
  subtype5      13       10         0         10          0          3        0
  subtype6      16       10         0          9          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         0         1
  subtype3         0         1
  subtype4         1         0
  subtype5         0         0
  subtype6         0         0
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           5       29        9       13       13       16
  STAGE II         10        9       13        4       10       10
  STAGE III         0        1        1        0        0        0
  STAGE IIIA        7       12       11        2       10        9
  STAGE IIIB        2        1        1        1        0        1
  STAGE IIIC        1        0        3        1        3        1
  STAGE IV          0        0        1        1        0        0
  STAGE IVA         0        0        0        1        0        0
  STAGE IVB         0        1        1        0        0        0
[1] 9 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     5 12  8  3
  subtype2    30  9 14  4
  subtype3    12 14 15  2
  subtype4    16  4  4  1
  subtype5    14 13 12  2
  subtype6    17 10 10  1
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T0+T1        5       30       12       16       14       17
  T2          12        9       14        4       13       10
  T3           8       14       15        4       12       10
  T4           3        4        2        1        2        1
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V5, binary
          cls
clus        0  1
  subtype1 15  0
  subtype2 37  0
  subtype3 30  2
  subtype4 12  1
  subtype5 26  1
  subtype6 26  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15    0
  subtype2   37    0
  subtype3   30    2
  subtype4   12    1
  subtype5   26    1
  subtype6   26    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       15       37       30       12       26       26
  1        0        0        2        1        1        0
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 19  0  9
  subtype2 40  1 17
  subtype3 36  2  5
  subtype4 12  1 12
  subtype5 28  0 13
  subtype6 28  0 11
D3V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  M0       19       40       36       12       28       28
  M1        0        1        2        1        0        0
  MX        9       17        5       12       13       11
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1  7 21
  subtype2 19 39
  subtype3 25 18
  subtype4  6 19
  subtype5 22 19
  subtype6  5 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   21
  subtype2   19   39
  subtype3   25   18
  subtype4    6   19
  subtype5   22   19
  subtype6    5   34
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE        7       19       25        6       22        5
  MALE         21       39       18       19       19       34
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       28
  subtype2                       0                       58
  subtype3                       0                       41
  subtype4                       0                       25
  subtype5                       2                       36
  subtype6                       0                       39
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                0
  subtype2                                0
  subtype3                                2
  subtype4                                0
  subtype5                                3
  subtype6                                0
D3V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        0        2
  HEPATOCELLULAR CARCINOMA               28       58       41       25       36
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0        0        2        0        3
                                  clus
vv                                 subtype6
  FIBROLAMELLAR CARCINOMA                 0
  HEPATOCELLULAR CARCINOMA               39
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 18  4  0  5
  subtype2 48  4  0  5
  subtype3 39  2  0  2
  subtype4 20  1  1  1
  subtype5 36  2  0  3
  subtype6 37  0  0  0
D3V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       18       48       39       20       36       37
  R1        4        4        2        1        2        0
  R2        0        0        0        1        0        0
  RX        5        5        2        1        3        0
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     9                         4
  subtype2                                0    11                         2
  subtype3                                0    20                         1
  subtype4                                0     3                         2
  subtype5                                0    15                         2
  subtype6                                1     8                         4
          vv
clus       WHITE
  subtype1    14
  subtype2    41
  subtype3    21
  subtype4    17
  subtype5    24
  subtype6    26
D3V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   9       11       20        3       15
  BLACK OR AFRICAN AMERICAN               4        2        1        2        2
  WHITE                                  14       41       21       17       24
                                  clus
vv                                 subtype6
  AMERICAN INDIAN OR ALASKA NATIVE        1
  ASIAN                                   8
  BLACK OR AFRICAN AMERICAN               4
  WHITE                                  26
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, binary
          cls
clus        0  1
  subtype1  1 23
  subtype2  5 48
  subtype3  1 40
  subtype4  1 22
  subtype5  1 39
  subtype6  0 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   23
  subtype2    5   48
  subtype3    1   40
  subtype4    1   22
  subtype5    1   39
  subtype6    0   37
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        5        1        1        1        0
  NOT HISPANIC OR LATINO       23       48       40       22       39       37
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = MRNASEQ_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 40 31
  subtype2 69 40
  subtype3 23 11
subtype1 subtype2 subtype3 
      71      109       34 
subtype1 subtype2 subtype3 
      31       40       11 
$subtype1
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Q TCGA-BC-A10R 
       10.78        10.59        48.99        27.91        37.32        10.13 
TCGA-BC-A10W TCGA-BC-A112 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 
        2.99         5.03        14.60         0.07         0.16         2.86 
TCGA-CC-5261 TCGA-CC-5263 TCGA-CC-A1HT TCGA-CC-A3M9 TCGA-CC-A3MA TCGA-CC-A3MC 
        0.39         4.24         3.32         0.10         0.07         0.13 
TCGA-DD-A113 TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EH 
       79.73        37.78       113.00        19.79        12.95        49.15 
TCGA-DD-A1EJ TCGA-DD-A39Y TCGA-DD-A3A6 TCGA-DD-A3A7 TCGA-DD-A3A9 TCGA-DD-A4NA 
       29.16         5.62       107.11        13.78        30.61        33.14 
TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73G TCGA-DD-AA3A 
       30.15        29.56        12.26         0.30       100.96        13.48 
TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66X TCGA-ED-A66Y TCGA-ED-A7PX TCGA-ED-A7PY 
       13.41        15.85        13.35         0.23         0.20         0.20 
TCGA-ED-A7PZ TCGA-ED-A82E TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB 
        0.20        13.41         0.20         0.20        11.74        10.98 
TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A3R3 TCGA-FV-A4ZP TCGA-G3-A25T TCGA-G3-A25X 
       32.45        27.88         0.13        60.36        51.06        58.49 
TCGA-G3-A25Y TCGA-G3-A5SJ TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-G3-AAV6 TCGA-G3-AAV7 
       14.86        11.97        12.03         1.84         2.14         3.02 
TCGA-KR-A7K7 TCGA-RC-A7S9 TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-A7MA TCGA-UB-A7ME 
       13.38        21.04        15.39        24.13        14.96        15.98 
TCGA-UB-A7MF TCGA-WQ-A9G7 TCGA-YA-A8S7 TCGA-ZP-A9D0 TCGA-ZP-A9D2 
        7.04         0.99        13.55        23.57        24.43 

$subtype2
TCGA-4R-AA8I TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A10Y TCGA-BC-A10Z 
        7.10        46.78        27.52        25.32        23.34         1.12 
TCGA-BC-A110 TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF TCGA-BC-A3KG TCGA-BC-A5W4 
       69.57        44.42        13.84         0.26        22.36         9.50 
TCGA-BC-A8YO TCGA-BD-A3EP TCGA-BD-A3ER TCGA-BW-A5NO TCGA-CC-5262 TCGA-CC-A3MB 
        7.46        13.45         4.80         0.66         3.39         0.10 
TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A119 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
       83.57        53.33         7.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A1EG TCGA-DD-A1EI TCGA-DD-A1EK TCGA-DD-A39X 
       51.29        66.31        45.11         6.02        18.35        55.69 
TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A5 
       19.76         7.66        70.06        17.59        20.12       102.74 
TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NI TCGA-DD-A4NJ TCGA-DD-A4NK 
       32.52        73.38        21.70        26.83        30.51        39.78 
TCGA-DD-A4NL TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A4NV TCGA-DD-A73A TCGA-DD-A73B 
       56.25        73.81        80.75        78.84        10.98         9.30 
TCGA-DD-A73C TCGA-DD-A73F TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A7XO TCGA-ED-A97K 
        7.56        27.72        12.69        13.91         0.20         0.20 
TCGA-EP-A3JL TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 
        9.96        22.85        14.40        23.97        19.10         8.12 
TCGA-FV-A3R2 TCGA-FV-A495 TCGA-FV-A496 TCGA-FV-A4ZQ TCGA-G3-A25S TCGA-G3-A25U 
        6.38         0.03         0.33         0.39         1.22        53.79 
TCGA-G3-A25V TCGA-G3-A25Z TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A3CI TCGA-G3-A5SI 
       28.27        21.53        22.13        25.64         5.92        14.70 
TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-GJ-A6C0 
       24.46        17.10         5.98        11.24         8.55         1.02 
TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A5RG TCGA-K7-A6G5 
        2.20         2.66        37.71        20.75        17.06         4.01 
TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-LG-A9QD TCGA-MI-A75C TCGA-MI-A75E 
       11.84        24.36        12.72         4.27         9.57        16.67 
TCGA-MI-A75G TCGA-MI-A75I TCGA-MR-A8JO TCGA-NI-A4U2 TCGA-O8-A75V TCGA-PD-A5DF 
       18.38        20.71        10.85        58.88         4.44        21.01 
TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MB TCGA-UB-AA0U TCGA-UB-AA0V 
        2.04        19.04        15.52        17.29         8.32         4.57 
TCGA-ZP-A9CV TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CD TCGA-ZS-A9CE 
        4.67        25.71        23.21         0.69        45.57        35.05 
TCGA-ZS-A9CF 
       74.24 

$subtype3
TCGA-BC-A10U TCGA-BC-A69I TCGA-DD-A1EA TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EL 
       27.52        12.72        79.40        75.65         6.71        13.64 
TCGA-DD-A39V TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG TCGA-DD-A4NP TCGA-DD-A73D 
       21.14         0.36        30.97        14.63       108.76        10.98 
TCGA-DD-A73E TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-EP-A3RK 
        1.45        13.15        18.74        19.99         0.62        11.93 
TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV2 
       19.53        19.23        20.42         7.76        11.80         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-MI-A75H TCGA-NI-A8LF 
        9.17         0.89         2.14         5.92        12.85        16.37 
TCGA-UB-A7MC TCGA-UB-A7MD TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       14.40         1.71        12.99         8.22 

subtype1 subtype2 subtype3 
    0.07     0.03     0.36 
subtype1 subtype2 subtype3 
  113.00   102.74   108.76 
subtype1 subtype2 subtype3 
   13.38    17.10    12.92 
[1] "0.1 - 113.0 (13.4)" "0.0 - 102.7 (17.1)" "0.4 - 108.8 (12.9)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      16       25         1         25          4          5        1
  subtype2      54       21         1         20          1          3        1
  subtype3      15       10         0          6          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         1
  subtype3         0         0
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I          16       54       15
  STAGE II         25       21       10
  STAGE III         1        1        0
  STAGE IIIA       25       20        6
  STAGE IIIB        4        1        1
  STAGE IIIC        5        3        1
  STAGE IV          1        1        0
  STAGE IVA         0        1        0
  STAGE IVB         1        1        0
[1] 9 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    18 29 33  5
  subtype2    60 22 23  7
  subtype3    16 11  7  1
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       18       60       16
  T2          29       22       11
  T3          33       23        7
  T4           5        7        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"
D4V5, binary
          cls
clus        0  1
  subtype1 58  3
  subtype2 65  1
  subtype3 23  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58    3
  subtype2   65    1
  subtype3   23    0
   clus
vv  subtype1 subtype2 subtype3
  0       58       65       23
  1        3        1        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 66  2 17
  subtype2 73  2 38
  subtype3 24  0 12
D4V6, multiclass
    clus
vv   subtype1 subtype2 subtype3
  M0       66       73       24
  M1        2        2        0
  MX       17       38       12
[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 43 42
  subtype2 36 77
  subtype3  5 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   42
  subtype2   36   77
  subtype3    5   31
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       43       36        5
  MALE         42       77       31
[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"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       82
  subtype2                       2                      109
  subtype3                       0                       36
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                3
  subtype2                                2
  subtype3                                0
D4V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  FIBROLAMELLAR CARCINOMA                 0        2        0
  HEPATOCELLULAR CARCINOMA               82      109       36
  HEPATOCHOLANGIOCARCINOMA (MIXED)        3        2        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       R0 R1 R2 RX
  subtype1 71  6  0  7
  subtype2 94  6  1  9
  subtype3 33  1  0  0
D4V9, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0       71       94       33
  R1        6        6        1
  R2        0        1        0
  RX        7        9        0
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    39                         3
  subtype2                                0    21                         8
  subtype3                                1     6                         4
          vv
clus       WHITE
  subtype1    42
  subtype2    76
  subtype3    25
D4V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                  39       21        6
  BLACK OR AFRICAN AMERICAN               3        8        4
  WHITE                                  42       76       25
[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 80
  subtype2  6 95
  subtype3  0 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   80
  subtype2    6   95
  subtype3    0   34
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        6        0
  NOT HISPANIC OR LATINO       80       95       34
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MIRSEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 32 18
  subtype2 69 35
  subtype3 27  9
  subtype4 73 28
subtype1 subtype2 subtype3 subtype4 
      50      104       36      101 
subtype1 subtype2 subtype3 subtype4 
      18       35        9       28 
$subtype1
TCGA-BC-4073 TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5262 
       27.91        23.34         1.12        13.45         0.66         3.39 
TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A11D TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A39Y 
        3.32        83.57        51.29        45.11        18.35         5.62 
TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACQ TCGA-DD-AAD8 
      102.74        13.78        27.72        65.75        14.33        31.53 
TCGA-DD-AADF TCGA-DD-AADL TCGA-DD-AAE2 TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAEE 
        3.78        20.91         9.47         8.52        11.31        16.37 
TCGA-ED-A7XO TCGA-ED-A8O5 TCGA-EP-A3JL TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR 
        0.20         0.20         9.96        11.93        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
        8.12         0.03         1.22        30.74        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-GJ-A9DB TCGA-KR-A7K8 TCGA-MI-A75I 
        5.92        12.03         1.84         2.20        24.36        20.71 
TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MA TCGA-UB-A7MD TCGA-WJ-A86L TCGA-ZP-A9CY 
       19.04        15.52        14.96         1.71         1.02        25.71 
TCGA-ZS-A9CE TCGA-ZS-A9CF 
       35.05        74.24 

$subtype2
TCGA-4R-AA8I TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KF 
        7.10        27.52         2.99        44.42        13.84         0.26 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-CC-5263 TCGA-DD-A113 TCGA-DD-A116 
       22.36         9.50         7.46         4.24        79.73        53.33 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1EC 
        2.60         0.46        21.76        79.40        66.31        19.79 
TCGA-DD-A1EE TCGA-DD-A1EL TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A1 TCGA-DD-A3A2 
        6.71        13.64        21.14        19.76         7.66        70.06 
TCGA-DD-A3A3 TCGA-DD-A3A4 TCGA-DD-A3A6 TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NG 
       17.59        20.12       107.11         0.36        30.97        14.63 
TCGA-DD-A4NP TCGA-DD-A4NQ TCGA-DD-A4NR TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C 
      108.76        12.26         0.30        10.98         9.30         7.56 
TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACF 
       10.98         1.45         0.53        12.53        63.48        12.00 
TCGA-DD-AACJ TCGA-DD-AACK TCGA-DD-AACP TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AACZ 
       60.10         0.30        13.15        48.49         5.59         5.62 
TCGA-DD-AAD0 TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB TCGA-DD-AADJ TCGA-DD-AADN 
        4.50        34.09        22.09        29.26        24.00        17.33 
TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU TCGA-DD-AAE3 
        3.02         5.29        57.27         7.10         8.28         9.86 
TCGA-DD-AAE9 TCGA-DD-AAEA TCGA-DD-AAEB TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVP 
       12.69        14.79        12.16        15.45        15.65        79.07 
TCGA-DD-AAVU TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-ED-A459 TCGA-ED-A66Y TCGA-ED-A8O6 
       61.87        58.78        49.48        13.41         0.23         0.20 
TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KB TCGA-ES-A2HS TCGA-FV-A496 TCGA-FV-A4ZP 
       18.74        19.99        10.98        22.85         0.33        60.36 
TCGA-G3-A25U TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A5SL 
       53.79        19.53        19.23        14.70        11.97        20.42 
TCGA-G3-A6UC TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-G3-AAV6 
        7.76        11.80         9.70         9.17         0.89         2.14 
TCGA-GJ-A6C0 TCGA-LG-A6GG TCGA-LG-A9QC TCGA-MI-A75C TCGA-MI-A75G TCGA-MI-A75H 
        1.02        12.72         5.92         9.57        18.38        12.85 
TCGA-NI-A4U2 TCGA-NI-A8LF TCGA-QA-A7B7 TCGA-UB-A7MB TCGA-UB-A7MC TCGA-UB-A7MF 
       58.88        16.37         2.04        17.29        14.40         7.04 
TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       12.99         8.22 

$subtype3
TCGA-BC-4072 TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A69H TCGA-BC-A69I 
       48.99        27.52        25.32        69.57        14.60        12.72 
TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-A3M9 TCGA-CC-A3MB TCGA-DD-A1ED TCGA-DD-A1EH 
        0.07         0.16         0.10         0.10        75.65        49.15 
TCGA-DD-A1EJ TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL 
       29.16        13.48        59.18        55.40        15.42         1.91 
TCGA-DD-AACW TCGA-DD-AADD TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVS 
       38.04        28.41         9.63         4.64        35.08        59.93 
TCGA-DD-AAVX TCGA-DD-AAVZ TCGA-DD-AAW3 TCGA-ED-A66X TCGA-ED-A7PZ TCGA-FV-A23B 
       56.48        55.86        47.70        13.35         0.20        32.45 
TCGA-FV-A4ZQ TCGA-G3-A5SK TCGA-K7-A5RG TCGA-KR-A7K7 TCGA-RC-A7S9 TCGA-RG-A7D4 
        0.39        24.46        17.06        13.38        21.04        24.13 

$subtype4
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-5C-AAPD TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10S 
       10.78        10.59         0.66        37.32        10.13        46.78 
TCGA-BC-A112 TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-A3MA TCGA-CC-A3MC 
        5.03         4.80         2.86         0.39         0.07         0.13 
TCGA-DD-A114 TCGA-DD-A118 TCGA-DD-A119 TCGA-DD-A1EF TCGA-DD-A1EI TCGA-DD-A39X 
       37.78       113.00         7.33        12.95         6.02        55.69 
TCGA-DD-A3A0 TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE 
       25.81        30.61        33.14        32.52        73.38        21.70 
TCGA-DD-A4NH TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NS 
       30.15        26.83        56.25        29.56        73.81        80.75 
TCGA-DD-A4NV TCGA-DD-A73G TCGA-DD-AAC9 TCGA-DD-AACH TCGA-DD-AACI TCGA-DD-AACM 
       78.84       100.96        11.41         6.41        53.19        58.16 
TCGA-DD-AACU TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADC 
       40.77        18.54        21.63        33.83        30.58        13.97 
TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADM TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AADY 
       25.08        24.13         0.39         3.95         6.67         9.67 
TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVW 
        9.86        12.56        15.65        79.10        72.26        61.38 
TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A5KG TCGA-ED-A627 TCGA-ED-A7PX TCGA-ED-A7PY 
       54.05        12.69        15.85        13.91         0.20         0.20 
TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A2KA TCGA-EP-A2KC TCGA-ES-A2HT 
       13.15        13.41         0.20        11.74         0.62        14.40 
TCGA-FV-A3I0 TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
       27.88        51.06        28.27        58.49        14.86        25.64 
TCGA-G3-A5SM TCGA-G3-A7M7 TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV7 TCGA-HP-A5MZ 
       17.10         5.98        11.24         8.55         3.02         2.66 
TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-K7-A6G5 TCGA-KR-A7K0 TCGA-KR-A7K2 TCGA-LG-A9QD 
       37.71        20.75         4.01         2.14        11.84         4.27 
TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V TCGA-PD-A5DF TCGA-RC-A7SH TCGA-UB-A7ME 
       16.67        10.85         4.44        21.01        15.39        15.98 
TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-YA-A8S7 TCGA-ZP-A9CV 
        8.32         4.57         0.99         4.01        13.55         4.67 
TCGA-ZP-A9CZ TCGA-ZP-A9D0 TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CD 
       23.21        23.57         0.69        24.43        45.57 

subtype1 subtype2 subtype3 subtype4 
    0.03     0.20     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
  102.74   108.76    75.65   113.00 
subtype1 subtype2 subtype3 subtype4 
  14.645   13.070   24.295   14.860 
[1] "0.0 - 102.7 (14.6)" "0.2 - 108.8 (13.1)" "0.1 - 75.7 (24.3)" 
[4] "0.1 - 113.0 (14.9)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      29        6         1          7          3          1        0
  subtype2      52       28         0         23          2          3        0
  subtype3      17       10         1         10          0          2        1
  subtype4      46       27         0         14          2          3        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         1         1
  subtype2         0         0
  subtype3         0         0
  subtype4         0         1
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          29       52       17       46
  STAGE II          6       28       10       27
  STAGE III         1        0        1        0
  STAGE IIIA        7       23       10       14
  STAGE IIIB        3        2        0        2
  STAGE IIIC        1        3        2        3
  STAGE IV          0        0        1        1
  STAGE IVA         1        0        0        0
  STAGE IVB         1        0        0        1
[1] 9 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    31  7 11  3
  subtype2    53 29 25  4
  subtype3    19 11 11  2
  subtype4    50 30 20  4
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       31       53       19       50
  T2           7       29       11       30
  T3          11       25       11       20
  T4           3        4        2        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V5, binary
          cls
clus        0  1
  subtype1 36  1
  subtype2 80  1
  subtype3 35  1
  subtype4 71  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    1
  subtype2   80    1
  subtype3   35    1
  subtype4   71    1
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       36       80       35       71
  1        1        1        1        1
[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"
          vv
clus       M0 M1 MX
  subtype1 32  1 19
  subtype2 92  0 20
  subtype3 37  1  5
  subtype4 80  2 23
D5V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       32       92       37       80
  M1        1        0        1        2
  MX       19       20        5       23
[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"
D5V7, binary
          cls
clus        0  1
  subtype1 18 34
  subtype2 30 82
  subtype3 15 28
  subtype4 37 68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   34
  subtype2   30   82
  subtype3   15   28
  subtype4   37   68
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       18       30       15       37
  MALE         34       82       28       68
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       51
  subtype2                       0                      112
  subtype3                       0                       42
  subtype4                       2                       99
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                1
  subtype2                                0
  subtype3                                1
  subtype4                                4
D5V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  FIBROLAMELLAR CARCINOMA                 0        0        0        2
  HEPATOCELLULAR CARCINOMA               51      112       42       99
  HEPATOCHOLANGIOCARCINOMA (MIXED)        1        0        1        4
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  40   4   0   4
  subtype2 101   4   0   6
  subtype3  38   2   0   3
  subtype4  95   4   1   4
D5V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       40      101       38       95
  R1        4        4        2        4
  R2        0        0        0        1
  RX        4        6        3        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    18                         4
  subtype2                                1    51                         4
  subtype3                                0    26                         3
  subtype4                                0    49                         4
          vv
clus       WHITE
  subtype1    28
  subtype2    53
  subtype3    14
  subtype4    48
D5V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0
  ASIAN                                  18       51       26       49
  BLACK OR AFRICAN AMERICAN               4        4        3        4
  WHITE                                  28       53       14       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"
D5V11, binary
          cls
clus         0   1
  subtype1   0  49
  subtype2   2 104
  subtype3   1  40
  subtype4   6  94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   49
  subtype2    2  104
  subtype3    1   40
  subtype4    6   94
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        2        1        6
  NOT HISPANIC OR LATINO       49      104       40       94
[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(6) Variable = MIRSEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 18 14
  subtype2 54 23
  subtype3 24 19
  subtype4 73 25
  subtype5 32  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      32       77       43       98       41 
subtype1 subtype2 subtype3 subtype4 subtype5 
      14       23       19       25        9 
$subtype1
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-BD-A3EP TCGA-BW-A5NO TCGA-CC-5262 
       48.99        27.91         1.12        13.45         0.66         3.39 
TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A115 TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL 
        4.24         3.32        83.57        45.11        18.35        13.64 
TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACB TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADJ 
       27.72        65.75        59.18        28.41         3.78        24.00 
TCGA-DD-AADL TCGA-DD-AADU TCGA-ED-A7PZ TCGA-ED-A8O5 TCGA-EP-A3JL TCGA-FV-A495 
       20.91         8.28         0.20         0.20         9.96         0.03 
TCGA-G3-A25S TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-GJ-A9DB TCGA-MI-A75I TCGA-RC-A7SK 
        1.22        12.03         1.84         2.20        20.71        15.52 
TCGA-UB-A7MD TCGA-WJ-A86L 
        1.71         1.02 

$subtype2
TCGA-4R-AA8I TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10U TCGA-BC-A10Y 
        7.10        10.13        46.78        27.52        27.52        23.34 
TCGA-BC-A112 TCGA-BC-A217 TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-CC-A3MB 
        5.03        13.84        22.36         9.50         7.46         0.10 
TCGA-DD-A113 TCGA-DD-A11A TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A3A1 
       79.73         2.60        21.76        51.29        66.31         7.66 
TCGA-DD-A3A2 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NQ TCGA-DD-A4NV 
       70.06       102.74        13.78        14.63        12.26        78.84 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-AACI TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACS 
       10.98         7.56        53.19         0.30        14.33        48.49 
TCGA-DD-AACZ TCGA-DD-AAD8 TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 
        5.62        31.53         0.39        57.27         9.67         9.47 
TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAEE TCGA-DD-AAEG TCGA-EP-A2KA 
        9.86         8.52        11.31        16.37        15.65        11.74 
TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR TCGA-FV-A3I1 TCGA-FV-A496 
        0.62        11.93        23.97        19.10         8.12         0.33 
TCGA-G3-A25U TCGA-G3-A25V TCGA-G3-A25W TCGA-G3-A25X TCGA-G3-A25Z TCGA-G3-A3CG 
       53.79        28.27        30.74        58.49        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A5SJ TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-AAUZ TCGA-G3-AAV0 
        5.92        11.97        24.46        17.10        11.24         8.55 
TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG 
        3.02         1.02        17.06        11.84        24.36        12.72 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-UB-A7MA TCGA-UB-A7MB 
       58.88        21.01         2.04        19.04        14.96        17.29 
TCGA-ZP-A9CY TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-ZS-A9CF 
       25.71        23.21         0.69        35.05        74.24 

$subtype3
TCGA-5C-AAPD TCGA-BC-A216 TCGA-CC-5261 TCGA-DD-A118 TCGA-DD-A11B TCGA-DD-A1EF 
        0.66        44.42         0.39       113.00         0.46        12.95 
TCGA-DD-A39Y TCGA-DD-A39Z TCGA-DD-A3A3 TCGA-DD-A3A6 TCGA-DD-A4NR TCGA-DD-A73B 
        5.62        19.76        17.59       107.11         0.30         9.30 
TCGA-DD-AACF TCGA-DD-AACH TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AAD5 TCGA-DD-AADB 
       12.00         6.41        13.15        40.77        34.09        29.26 
TCGA-DD-AADC TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADS TCGA-DD-AAE7 TCGA-DD-AAEA 
       13.97        17.33         3.02         7.10        12.56        14.79 
TCGA-DD-AAED TCGA-DD-AAEH TCGA-DD-AAVX TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY 
       15.45        15.65        56.48        15.85         0.23         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KB TCGA-FV-A4ZP TCGA-G3-A5SI TCGA-G3-AAV6 TCGA-K7-A6G5 
        0.20        10.98        60.36        14.70         2.14         4.01 
TCGA-MI-A75C TCGA-MI-A75G TCGA-UB-A7ME TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZP-A9D0 
        9.57        18.38        15.98         7.04        13.55        23.57 
TCGA-ZP-A9D2 
       24.43 

$subtype4
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10W TCGA-BC-A10X TCGA-BC-A110 
       10.78        10.59        37.32         2.99        25.32        69.57 
TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-A3M9 
       14.60         4.80         0.07         0.16         2.86         0.10 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EC TCGA-DD-A1ED 
        0.07         0.13        37.78         7.33        19.79        75.65 
TCGA-DD-A1EH TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A0 TCGA-DD-A3A4 
       49.15         6.02        29.16        55.69        25.81        20.12 
TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4NB TCGA-DD-A4ND TCGA-DD-A4NE TCGA-DD-A4NH 
       30.61        33.14        32.52        73.38        21.70        30.15 
TCGA-DD-A4NI TCGA-DD-A4NL TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A73G 
       26.83        56.25        29.56        73.81        80.75       100.96 
TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM 
       13.48        11.41        55.40        15.42         1.91        58.16 
TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADA TCGA-DD-AADI 
       38.04        18.54        21.63        33.83        30.58        25.08 
TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADQ TCGA-DD-AADW TCGA-DD-AAE0 TCGA-DD-AAE1 
       24.13         3.95         5.29         6.67         9.86         9.63 
TCGA-DD-AAE6 TCGA-DD-AAEK TCGA-DD-AAVQ TCGA-DD-AAVR TCGA-DD-AAVS TCGA-DD-AAVU 
        4.64        35.08        79.10        72.26        59.93        61.87 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A459 TCGA-ED-A4XI TCGA-ED-A627 
       61.38        55.86        54.05        13.41        12.69        13.91 
TCGA-ED-A66X TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A7XP TCGA-ED-A82E TCGA-ED-A97K 
       13.35         0.20         0.20        13.15        13.41         0.20 
TCGA-ES-A2HS TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 TCGA-FV-A4ZQ TCGA-G3-A25T 
       22.85        14.40        32.45        27.88         0.39        51.06 
TCGA-G3-A25Y TCGA-G3-A3CH TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF 
       14.86        25.64         5.98         2.66        37.71        20.75 
TCGA-KR-A7K7 TCGA-LG-A9QD TCGA-MI-A75E TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7S9 
       13.38         4.27        16.67        10.85         4.44        21.04 
TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-A9G7 TCGA-WQ-AB4B 
       15.39        24.13         8.32         4.57         0.99         4.01 
TCGA-ZP-A9CV TCGA-ZS-A9CD 
        4.67        45.57 

$subtype5
TCGA-BC-A3KF TCGA-BC-A69I TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V 
        0.26        12.72        53.33        79.40         6.71        21.14 
TCGA-DD-A3A8 TCGA-DD-A4NF TCGA-DD-A4NP TCGA-DD-A73D TCGA-DD-A73E TCGA-DD-AAC8 
        0.36        30.97       108.76        10.98         1.45         0.53 
TCGA-DD-AACD TCGA-DD-AACE TCGA-DD-AACJ TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD6 
       12.53        63.48        60.10         5.59         4.50        22.09 
TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAVP TCGA-DD-AAVY TCGA-DD-AAW2 TCGA-DD-AAW3 
       12.69        12.16        79.07        58.78        49.48        47.70 
TCGA-EP-A12J TCGA-EP-A26S TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-A6UC 
       18.74        19.99        19.53        19.23        20.42         7.76 
TCGA-G3-AAV1 TCGA-G3-AAV2 TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-KR-A7K0 TCGA-LG-A9QC 
       11.80         9.70         9.17         0.89         2.14         5.92 
TCGA-MI-A75H TCGA-NI-A8LF TCGA-UB-A7MC TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       12.85        16.37        14.40        12.99         8.22 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.03     0.10     0.20     0.07     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
   83.57   102.74   113.00   100.96   108.76 
subtype1 subtype2 subtype3 subtype4 subtype5 
  10.995   14.960   13.550   19.165   12.850 
[1] "0.0 - 83.6 (11.0)"  "0.1 - 102.7 (15.0)" "0.2 - 113.0 (13.6)"
[4] "0.1 - 101.0 (19.2)" "0.3 - 108.8 (12.8)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      18        4         0          9          1          1        0
  subtype2      36       20         1         10          4          1        0
  subtype3      23       11         0         10          0          1        0
  subtype4      45       26         1         18          1          5        2
  subtype5      22       10         0          7          1          1        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         1
  subtype2         1         0
  subtype3         0         0
  subtype4         0         1
  subtype5         0         0
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          18       36       23       45       22
  STAGE II          4       20       11       26       10
  STAGE III         0        1        0        1        0
  STAGE IIIA        9       10       10       18        7
  STAGE IIIB        1        4        0        1        1
  STAGE IIIC        1        1        1        5        1
  STAGE IV          0        0        0        2        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         1        0        0        1        0
[1] 9 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    18  5 10  2
  subtype2    40 21 16  5
  subtype3    24 12 11  0
  subtype4    48 29 22  5
  subtype5    23 10  8  1
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       18       40       24       48       23
  T2           5       21       12       29       10
  T3          10       16       11       22        8
  T4           2        5        0        5        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V5, binary
          cls
clus        0  1
  subtype1 26  0
  subtype2 51  1
  subtype3 35  1
  subtype4 77  2
  subtype5 33  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    0
  subtype2   51    1
  subtype3   35    1
  subtype4   77    2
  subtype5   33    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       26       51       35       77       33
  1        0        1        1        2        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 23  1 11
  subtype2 58  0 24
  subtype3 39  0  8
  subtype4 86  3 16
  subtype5 35  0  8
D6V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       23       58       39       86       35
  M1        1        0        0        3        0
  MX       11       24        8       16        8
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 12 23
  subtype2 27 55
  subtype3 16 31
  subtype4 39 66
  subtype5  6 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12   23
  subtype2   27   55
  subtype3   16   31
  subtype4   39   66
  subtype5    6   37
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       12       27       16       39        6
  MALE         23       55       31       66       37
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       35
  subtype2                       0                       80
  subtype3                       0                       46
  subtype4                       2                      100
  subtype5                       0                       43
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                0
  subtype2                                2
  subtype3                                1
  subtype4                                3
  subtype5                                0
D6V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        0        2        0
  HEPATOCELLULAR CARCINOMA               35       80       46      100       43
  HEPATOCHOLANGIOCARCINOMA (MIXED)        0        2        1        3        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       R0 R1 R2 RX
  subtype1 26  3  0  3
  subtype2 70  5  0  5
  subtype3 42  1  0  4
  subtype4 94  5  1  5
  subtype5 42  0  0  0
D6V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       26       70       42       94       42
  R1        3        5        1        5        0
  R2        0        0        0        1        0
  RX        3        5        4        5        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    15                         5
  subtype2                                0    28                         4
  subtype3                                0    29                         1
  subtype4                                0    53                         4
  subtype5                                1    19                         1
          vv
clus       WHITE
  subtype1    15
  subtype2    45
  subtype3    16
  subtype4    45
  subtype5    22
D6V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  15       28       29       53       19
  BLACK OR AFRICAN AMERICAN               5        4        1        4        1
  WHITE                                  15       45       16       45       22
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, binary
          cls
clus        0  1
  subtype1  0 34
  subtype2  2 74
  subtype3  2 43
  subtype4  5 96
  subtype5  0 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   34
  subtype2    2   74
  subtype3    2   43
  subtype4    5   96
  subtype5    0   40
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        2        5        0
  NOT HISPANIC OR LATINO       34       74       43       96       40
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_MATURE_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 45 29
  subtype2 49 22
  subtype3 69 27
  subtype4 26  6
subtype1 subtype2 subtype3 subtype4 
      74       71       96       32 
subtype1 subtype2 subtype3 subtype4 
      29       22       27        6 
$subtype1
TCGA-5C-AAPD TCGA-BC-4073 TCGA-BC-A10W TCGA-BC-A216 TCGA-BC-A217 TCGA-BC-A3KG 
        0.66        27.91         2.99        44.42        13.84        22.36 
TCGA-BC-A8YO TCGA-BW-A5NO TCGA-CC-5259 TCGA-CC-5263 TCGA-CC-A1HT TCGA-DD-A113 
        7.46         0.66         0.16         4.24         3.32        79.73 
TCGA-DD-A118 TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A1EJ TCGA-DD-A1EL TCGA-DD-A39Y 
      113.00        19.79        12.95        29.16        13.64         5.62 
TCGA-DD-A3A3 TCGA-DD-A3A7 TCGA-DD-A4NA TCGA-DD-A4NE TCGA-DD-A4NG TCGA-DD-A4NH 
       17.59        13.78        33.14        21.70        14.63        30.15 
TCGA-DD-A4NN TCGA-DD-A4NO TCGA-DD-A4NQ TCGA-DD-A73G TCGA-DD-AAC8 TCGA-DD-AACD 
       29.56        73.81        12.26       100.96         0.53        12.53 
TCGA-DD-AACH TCGA-DD-AACP TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AAD6 TCGA-DD-AADB 
        6.41        13.15         5.62        34.09        22.09        29.26 
TCGA-DD-AADC TCGA-DD-AADJ TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADW TCGA-DD-AADY 
       13.97        24.00        17.33         3.02         6.67         9.67 
TCGA-DD-AAEA TCGA-DD-AAED TCGA-DD-AAVQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y 
       14.79        15.45        79.10        13.41        15.85         0.23 
TCGA-ED-A7PY TCGA-ED-A8O5 TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-EP-A3RK 
        0.20         0.20         0.20        11.74        10.98        11.93 
TCGA-FV-A4ZP TCGA-G3-A25S TCGA-G3-A25W TCGA-G3-A5SI TCGA-G3-A5SJ TCGA-G3-A7M6 
       60.36         1.22        30.74        14.70        11.97        12.03 
TCGA-G3-AAV6 TCGA-G3-AAV7 TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K7 
        2.14         3.02         1.02        17.06        11.84        13.38 
TCGA-LG-A6GG TCGA-MI-A75C TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-UB-A7MA TCGA-UB-A7ME 
       12.72         9.57        21.01         2.04        14.96        15.98 
TCGA-UB-A7MF TCGA-YA-A8S7 
        7.04        13.55 

$subtype2
TCGA-5C-A9VG TCGA-BC-A10Q TCGA-BC-A10R TCGA-BC-A10T TCGA-BC-A10X TCGA-BC-A110 
       10.78        37.32        10.13        27.52        25.32        69.57 
TCGA-BC-A112 TCGA-BD-A3EP TCGA-BD-A3ER TCGA-CC-5260 TCGA-CC-5261 TCGA-CC-5262 
        5.03        13.45         4.80         2.86         0.39         3.39 
TCGA-CC-A3MA TCGA-CC-A3MC TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1EG TCGA-DD-A1EI 
        0.07         0.13        37.78         7.33        45.11         6.02 
TCGA-DD-A39X TCGA-DD-A3A6 TCGA-DD-A3A9 TCGA-DD-A4NS TCGA-DD-AAC9 TCGA-DD-AACI 
       55.69       107.11        30.61        80.75        11.41        53.19 
TCGA-DD-AACM TCGA-DD-AACU TCGA-DD-AAD1 TCGA-DD-AAD2 TCGA-DD-AAD3 TCGA-DD-AADI 
       58.16        40.77        18.54        21.63        33.83        25.08 
TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AAE0 TCGA-DD-AAE7 TCGA-DD-AAEG TCGA-DD-AAVR 
       24.13         3.95         9.86        12.56        15.65        72.26 
TCGA-DD-AAW0 TCGA-ED-A7PX TCGA-ED-A7XO TCGA-ED-A82E TCGA-ED-A97K TCGA-EP-A3JL 
       54.05         0.20         0.20        13.41         0.20         9.96 
TCGA-ES-A2HT TCGA-FV-A2QQ TCGA-FV-A3I0 TCGA-FV-A3I1 TCGA-G3-A25T TCGA-G3-A25V 
       14.40        23.97        27.88         8.12        51.06        28.27 
TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CG TCGA-G3-A3CH TCGA-G3-A5SM TCGA-G3-A7M7 
       58.49        14.86        22.13        25.64        17.10         5.98 
TCGA-G3-AAV3 TCGA-GJ-A9DB TCGA-HP-A5MZ TCGA-K7-A5RF TCGA-KR-A7K8 TCGA-MI-A75E 
        9.17         2.20         2.66        20.75        24.36        16.67 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7SH TCGA-UB-AA0U TCGA-UB-AA0V TCGA-WQ-AB4B 
       10.85         4.44        15.39         8.32         4.57         4.01 
TCGA-ZP-A9CV TCGA-ZP-A9CZ TCGA-ZP-A9D1 TCGA-ZP-A9D2 TCGA-ZS-A9CD 
        4.67        23.21         0.69        24.43        45.57 

$subtype3
TCGA-4R-AA8I TCGA-BC-A10S TCGA-BC-A10U TCGA-BC-A10Y TCGA-BC-A10Z TCGA-BC-A3KF 
        7.10        46.78        27.52        23.34         1.12         0.26 
TCGA-BC-A5W4 TCGA-DD-A115 TCGA-DD-A116 TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C 
        9.50        83.57        53.33         2.60         0.46        21.76 
TCGA-DD-A11D TCGA-DD-A1EA TCGA-DD-A1EB TCGA-DD-A1ED TCGA-DD-A1EE TCGA-DD-A1EK 
       51.29        79.40        66.31        75.65         6.71        18.35 
TCGA-DD-A39V TCGA-DD-A39Z TCGA-DD-A3A0 TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A4NF 
       21.14        19.76        25.81         7.66       102.74        30.97 
TCGA-DD-A4NI TCGA-DD-A4NP TCGA-DD-A73A TCGA-DD-A73B TCGA-DD-A73C TCGA-DD-A73D 
       26.83       108.76        10.98         9.30         7.56        10.98 
TCGA-DD-A73F TCGA-DD-AACA TCGA-DD-AACE TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACK 
       27.72        65.75        63.48        12.00        60.10         0.30 
TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD8 TCGA-DD-AADF 
       14.33        48.49         5.59         4.50        31.53         3.78 
TCGA-DD-AADL TCGA-DD-AADM TCGA-DD-AADQ TCGA-DD-AADR TCGA-DD-AADS TCGA-DD-AADU 
       20.91         0.39         5.29        57.27         7.10         8.28 
TCGA-DD-AAE2 TCGA-DD-AAE3 TCGA-DD-AAE4 TCGA-DD-AAE8 TCGA-DD-AAE9 TCGA-DD-AAEB 
        9.47         9.86         8.52        11.31        12.69        12.16 
TCGA-DD-AAEE TCGA-DD-AAEH TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW2 
       16.37        15.65        79.07        61.87        56.48        49.48 
TCGA-DD-AAW3 TCGA-ED-A7XP TCGA-EP-A12J TCGA-EP-A26S TCGA-EP-A2KC TCGA-FV-A2QR 
       47.70        13.15        18.74        19.99         0.62        19.10 
TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25Z TCGA-G3-A3CI TCGA-G3-A3CJ TCGA-G3-A3CK 
        0.33        53.79        21.53         5.92        19.53        19.23 
TCGA-G3-A5SK TCGA-G3-A5SL TCGA-G3-AAUZ TCGA-G3-AAV0 TCGA-G3-AAV2 TCGA-G3-AAV4 
       24.46        20.42        11.24         8.55         9.70         0.89 
TCGA-HP-A5N0 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75G TCGA-MI-A75H 
       37.71         2.14         5.92         4.27        18.38        12.85 
TCGA-MI-A75I TCGA-NI-A4U2 TCGA-RC-A7SF TCGA-RC-A7SK TCGA-UB-A7MD TCGA-WJ-A86L 
       20.71        58.88        19.04        15.52         1.71         1.02 
TCGA-ZP-A9CY TCGA-ZP-A9D0 TCGA-ZP-A9D4 TCGA-ZS-A9CE TCGA-ZS-A9CF TCGA-ZS-A9CG 
       25.71        23.57        12.99        35.05        74.24         8.22 

$subtype4
TCGA-5C-A9VH TCGA-BC-4072 TCGA-BC-A69H TCGA-CC-5258 TCGA-CC-A3M9 TCGA-CC-A3MB 
       10.59        48.99        14.60         0.07         0.10         0.10 
TCGA-DD-A1EH TCGA-DD-A4ND TCGA-DD-AA3A TCGA-DD-AACB TCGA-DD-AACC TCGA-DD-AACG 
       49.15        73.38        13.48        59.18        55.40        15.42 
TCGA-DD-AACL TCGA-DD-AACW TCGA-DD-AADA TCGA-DD-AADD TCGA-DD-AAE1 TCGA-DD-AAE6 
        1.91        38.04        30.58        28.41         9.63         4.64 
TCGA-DD-AAEK TCGA-DD-AAVS TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-ED-A4XI TCGA-ED-A627 
       35.08        59.93        61.38        55.86        12.69        13.91 
TCGA-ED-A66X TCGA-ED-A7PZ TCGA-FV-A23B TCGA-FV-A495 TCGA-FV-A4ZQ TCGA-G3-A7M9 
       13.35         0.20        32.45         0.03         0.39         1.84 
TCGA-RG-A7D4 TCGA-WQ-A9G7 
       24.13         0.99 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.07     0.26     0.03 
subtype1 subtype2 subtype3 subtype4 
  113.00   107.11   108.76    73.38 
subtype1 subtype2 subtype3 subtype4 
  13.395   15.390   18.365   14.255 
[1] "0.2 - 113.0 (13.4)" "0.1 - 107.1 (15.4)" "0.3 - 108.8 (18.4)"
[4] "0.0 - 73.4 (14.3)" 
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      30       20         0         22          5          5        0
  subtype2      29       18         0         10          0          3        1
  subtype3      56       21         1         10          0          0        0
  subtype4      17       10         1          7          1          0        1
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         1
  subtype3         0         1
  subtype4         0         0
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I          30       29       56       17
  STAGE II         20       18       21       10
  STAGE III         0        0        1        1
  STAGE IIIA       22       10       10        7
  STAGE IIIB        5        0        0        1
  STAGE IIIC        5        3        0        0
  STAGE IV          0        1        0        1
  STAGE IVA         0        1        0        0
  STAGE IVB         0        1        1        0
[1] 9 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    31 21 26  5
  subtype2    34 20 13  5
  subtype3    59 23 12  2
  subtype4    17 11 10  0
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       31       34       59       17
  T2          21       20       23       11
  T3          26       13       12       10
  T4           5        5        2        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"
D7V5, binary
          cls
clus        0  1
  subtype1 60  3
  subtype2 46  1
  subtype3 70  0
  subtype4 30  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   60    3
  subtype2   46    1
  subtype3   70    0
  subtype4   30    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       60       46       70       30
  1        3        1        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 69  0 14
  subtype2 47  2 23
  subtype3 77  1 20
  subtype4 34  1  3
D7V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  M0       69       47       77       34
  M1        0        2        1        1
  MX       14       23       20        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"
D7V7, binary
          cls
clus        0  1
  subtype1 35 48
  subtype2 24 48
  subtype3 25 73
  subtype4 13 25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   48
  subtype2   24   48
  subtype3   25   73
  subtype4   13   25
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       35       24       25       13
  MALE         48       48       73       25
[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"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       80
  subtype2                       1                       69
  subtype3                       0                       98
  subtype4                       0                       37
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                3
  subtype2                                2
  subtype3                                0
  subtype4                                1
D7V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  FIBROLAMELLAR CARCINOMA                 0        1        0        0
  HEPATOCELLULAR CARCINOMA               80       69       98       37
  HEPATOCHOLANGIOCARCINOMA (MIXED)        3        2        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       R0 R1 R2 RX
  subtype1 70  5  0  5
  subtype2 60  6  1  3
  subtype3 92  2  0  3
  subtype4 33  1  0  4
D7V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       70       60       92       33
  R1        5        6        2        1
  R2        0        1        0        0
  RX        5        3        3        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    42                         4
  subtype2                                0    32                         4
  subtype3                                1    41                         6
  subtype4                                0    23                         1
          vv
clus       WHITE
  subtype1    36
  subtype2    33
  subtype3    45
  subtype4    14
D7V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0
  ASIAN                                  42       32       41       23
  BLACK OR AFRICAN AMERICAN               4        4        6        1
  WHITE                                  36       33       45       14
[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"
D7V11, binary
          cls
clus        0  1
  subtype1  3 75
  subtype2  2 67
  subtype3  3 88
  subtype4  1 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   75
  subtype2    2   67
  subtype3    3   88
  subtype4    1   37
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        3        1
  NOT HISPANIC OR LATINO       75       67       88       37
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 28 21
  subtype2 49 20
  subtype3 61 21
  subtype4 14 13
  subtype5 37  9
subtype1 subtype2 subtype3 subtype4 subtype5 
      49       69       82       27       46 
subtype1 subtype2 subtype3 subtype4 subtype5 
      21       20       21       13        9 
$subtype1
TCGA-5C-AAPD TCGA-BC-A10U TCGA-BC-A10W TCGA-BC-A216 TCGA-CC-5263 TCGA-CC-A3M9 
        0.66        27.52         2.99        44.42         4.24         0.10 
TCGA-CC-A3MC TCGA-DD-A1EC TCGA-DD-A1EF TCGA-DD-A39Y TCGA-DD-A3A3 TCGA-DD-A3A6 
        0.13        19.79        12.95         5.62        17.59       107.11 
TCGA-DD-A4NE TCGA-DD-A4NH TCGA-DD-A4NN TCGA-DD-A4NQ TCGA-DD-AACD TCGA-DD-AACH 
       21.70        30.15        29.56        12.26        12.53         6.41 
TCGA-DD-AACI TCGA-DD-AACP TCGA-DD-AACU TCGA-DD-AACZ TCGA-DD-AAD5 TCGA-DD-AADB 
       53.19        13.15        40.77         5.62        34.09        29.26 
TCGA-DD-AADC TCGA-DD-AADN TCGA-DD-AADO TCGA-DD-AADQ TCGA-DD-AAEA TCGA-DD-AAED 
       13.97        17.33         3.02         5.29        14.79        15.45 
TCGA-DD-AAEG TCGA-DD-AAVQ TCGA-ED-A459 TCGA-ED-A5KG TCGA-ED-A66Y TCGA-ED-A7PY 
       15.65        79.10        13.41        15.85         0.23         0.20 
TCGA-ED-A8O6 TCGA-EP-A2KA TCGA-EP-A2KB TCGA-FV-A4ZP TCGA-G3-A5SJ TCGA-G3-AAV6 
        0.20        11.74        10.98        60.36        11.97         2.14 
TCGA-G3-AAV7 TCGA-UB-A7MA TCGA-UB-A7ME TCGA-UB-A7MF TCGA-YA-A8S7 TCGA-ZP-A9CV 
        3.02        14.96        15.98         7.04        13.55         4.67 
TCGA-ZP-A9D0 
       23.57 

$subtype2
TCGA-4R-AA8I TCGA-BC-A10R TCGA-BC-A10S TCGA-BC-A10T TCGA-BC-A10Y TCGA-BC-A217 
        7.10        10.13        46.78        27.52        23.34        13.84 
TCGA-BC-A3KG TCGA-BC-A5W4 TCGA-BC-A8YO TCGA-BW-A5NO TCGA-DD-A113 TCGA-DD-A118 
       22.36         9.50         7.46         0.66        79.73       113.00 
TCGA-DD-A11A TCGA-DD-A11B TCGA-DD-A11C TCGA-DD-A11D TCGA-DD-A1EB TCGA-DD-A3A0 
        2.60         0.46        21.76        51.29        66.31        25.81 
TCGA-DD-A3A1 TCGA-DD-A3A5 TCGA-DD-A3A7 TCGA-DD-A4NG TCGA-DD-A4NI TCGA-DD-A4NP 
        7.66       102.74        13.78        14.63        26.83       108.76 
TCGA-DD-A73A TCGA-DD-A73C TCGA-DD-AACK TCGA-DD-AACQ TCGA-DD-AACS TCGA-DD-AAD3 
       10.98         7.56         0.30        14.33        48.49        33.83 
TCGA-DD-AAD8 TCGA-DD-AADM TCGA-DD-AADR TCGA-DD-AADY TCGA-DD-AAE2 TCGA-DD-AAE4 
       31.53         0.39        57.27         9.67         9.47         8.52 
TCGA-DD-AAE8 TCGA-ED-A7XO TCGA-EP-A2KC TCGA-EP-A3RK TCGA-FV-A2QQ TCGA-FV-A2QR 
       11.31         0.20         0.62        11.93        23.97        19.10 
TCGA-FV-A3I1 TCGA-FV-A496 TCGA-G3-A25U TCGA-G3-A25W TCGA-G3-A25Z TCGA-G3-A3CG 
        8.12         0.33        53.79        30.74        21.53        22.13 
TCGA-G3-A3CI TCGA-G3-A5SI TCGA-G3-A5SK TCGA-G3-A5SM TCGA-G3-AAUZ TCGA-G3-AAV0 
        5.92        14.70        24.46        17.10        11.24         8.55 
TCGA-GJ-A6C0 TCGA-K7-A5RG TCGA-KR-A7K2 TCGA-KR-A7K8 TCGA-LG-A6GG TCGA-MI-A75I 
        1.02        17.06        11.84        24.36        12.72        20.71 
TCGA-NI-A4U2 TCGA-PD-A5DF TCGA-QA-A7B7 TCGA-RC-A7SF TCGA-ZP-A9CY TCGA-ZP-A9CZ 
       58.88        21.01         2.04        19.04        25.71        23.21 
TCGA-ZP-A9D1 TCGA-ZS-A9CE TCGA-ZS-A9CF 
        0.69        35.05        74.24 

$subtype3
TCGA-5C-A9VG TCGA-5C-A9VH TCGA-BC-A10Q TCGA-BC-A10X TCGA-BC-A110 TCGA-BC-A112 
       10.78        10.59        37.32        25.32        69.57         5.03 
TCGA-BC-A69H TCGA-BD-A3ER TCGA-CC-5258 TCGA-CC-5259 TCGA-CC-5260 TCGA-CC-5261 
       14.60         4.80         0.07         0.16         2.86         0.39 
TCGA-CC-A3MA TCGA-CC-A3MB TCGA-DD-A114 TCGA-DD-A119 TCGA-DD-A1ED TCGA-DD-A1EH 
        0.07         0.10        37.78         7.33        75.65        49.15 
TCGA-DD-A1EI TCGA-DD-A1EJ TCGA-DD-A39X TCGA-DD-A3A9 TCGA-DD-A4NA TCGA-DD-A4ND 
        6.02        29.16        55.69        30.61        33.14        73.38 
TCGA-DD-A4NO TCGA-DD-A4NS TCGA-DD-A73G TCGA-DD-AA3A TCGA-DD-AAC9 TCGA-DD-AACC 
       73.81        80.75       100.96        13.48        11.41        55.40 
TCGA-DD-AACG TCGA-DD-AACL TCGA-DD-AACM TCGA-DD-AACW TCGA-DD-AAD1 TCGA-DD-AAD2 
       15.42         1.91        58.16        38.04        18.54        21.63 
TCGA-DD-AADA TCGA-DD-AADI TCGA-DD-AADK TCGA-DD-AADP TCGA-DD-AADW TCGA-DD-AAE0 
       30.58        25.08        24.13         3.95         6.67         9.86 
TCGA-DD-AAE1 TCGA-DD-AAE6 TCGA-DD-AAE7 TCGA-DD-AAEK TCGA-DD-AAVR TCGA-DD-AAVS 
        9.63         4.64        12.56        35.08        72.26        59.93 
TCGA-DD-AAVW TCGA-DD-AAVZ TCGA-DD-AAW0 TCGA-ED-A4XI TCGA-ED-A627 TCGA-ED-A66X 
       61.38        55.86        54.05        12.69        13.91        13.35 
TCGA-ED-A7PX TCGA-ED-A82E TCGA-ED-A97K TCGA-ES-A2HT TCGA-FV-A23B TCGA-FV-A3I0 
        0.20        13.41         0.20        14.40        32.45        27.88 
TCGA-FV-A4ZQ TCGA-G3-A25T TCGA-G3-A25V TCGA-G3-A25X TCGA-G3-A25Y TCGA-G3-A3CH 
        0.39        51.06        28.27        58.49        14.86        25.64 
TCGA-G3-A7M7 TCGA-HP-A5MZ TCGA-HP-A5N0 TCGA-K7-A5RF TCGA-KR-A7K7 TCGA-MI-A75E 
        5.98         2.66        37.71        20.75        13.38        16.67 
TCGA-MR-A8JO TCGA-O8-A75V TCGA-RC-A7SH TCGA-RG-A7D4 TCGA-UB-AA0U TCGA-UB-AA0V 
       10.85         4.44        15.39        24.13         8.32         4.57 
TCGA-WQ-A9G7 TCGA-WQ-AB4B TCGA-ZP-A9D2 TCGA-ZS-A9CD 
        0.99         4.01        24.43        45.57 

$subtype4
TCGA-BC-4072 TCGA-BC-4073 TCGA-BC-A10Z TCGA-BD-A3EP TCGA-CC-5262 TCGA-CC-A1HT 
       48.99        27.91         1.12        13.45         3.39         3.32 
TCGA-DD-A115 TCGA-DD-A1EG TCGA-DD-A1EK TCGA-DD-A1EL TCGA-DD-A73F TCGA-DD-AACB 
       83.57        45.11        18.35        13.64        27.72        59.18 
TCGA-DD-AADD TCGA-DD-AADF TCGA-DD-AADJ TCGA-DD-AADL TCGA-ED-A7PZ TCGA-ED-A8O5 
       28.41         3.78        24.00        20.91         0.20         0.20 
TCGA-EP-A3JL TCGA-FV-A495 TCGA-G3-A25S TCGA-G3-A7M6 TCGA-G3-A7M9 TCGA-GJ-A9DB 
        9.96         0.03         1.22        12.03         1.84         2.20 
TCGA-RC-A7SK TCGA-UB-A7MD TCGA-WJ-A86L 
       15.52         1.71         1.02 

$subtype5
TCGA-BC-A3KF TCGA-DD-A116 TCGA-DD-A1EA TCGA-DD-A1EE TCGA-DD-A39V TCGA-DD-A39Z 
        0.26        53.33        79.40         6.71        21.14        19.76 
TCGA-DD-A4NF TCGA-DD-A73B TCGA-DD-A73D TCGA-DD-AAC8 TCGA-DD-AACA TCGA-DD-AACE 
       30.97         9.30        10.98         0.53        65.75        63.48 
TCGA-DD-AACF TCGA-DD-AACJ TCGA-DD-AACX TCGA-DD-AAD0 TCGA-DD-AAD6 TCGA-DD-AADS 
       12.00        60.10         5.59         4.50        22.09         7.10 
TCGA-DD-AADU TCGA-DD-AAE3 TCGA-DD-AAE9 TCGA-DD-AAEB TCGA-DD-AAEE TCGA-DD-AAEH 
        8.28         9.86        12.69        12.16        16.37        15.65 
TCGA-DD-AAVP TCGA-DD-AAVU TCGA-DD-AAVX TCGA-DD-AAW2 TCGA-DD-AAW3 TCGA-ED-A7XP 
       79.07        61.87        56.48        49.48        47.70        13.15 
TCGA-EP-A12J TCGA-EP-A26S TCGA-G3-A3CJ TCGA-G3-A3CK TCGA-G3-A5SL TCGA-G3-AAV2 
       18.74        19.99        19.53        19.23        20.42         9.70 
TCGA-G3-AAV3 TCGA-G3-AAV4 TCGA-KR-A7K0 TCGA-LG-A9QC TCGA-LG-A9QD TCGA-MI-A75C 
        9.17         0.89         2.14         5.92         4.27         9.57 
TCGA-MI-A75G TCGA-MI-A75H TCGA-ZP-A9D4 TCGA-ZS-A9CG 
       18.38        12.85        12.99         8.22 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.10     0.20     0.07     0.03     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
  107.11   113.00   100.96    83.57    79.40 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.410   17.060   15.405   12.030   13.070 
[1] "0.1 - 107.1 (13.4)" "0.2 - 113.0 (17.1)" "0.1 - 101.0 (15.4)"
[4] "0.0 - 83.6 (12.0)"  "0.3 - 79.4 (13.1)" 
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1      21       13         0         17          1          1        0
  subtype2      31       16         1         10          4          1        0
  subtype3      38       22         1         11          0          5        2
  subtype4      17        3         0          6          1          1        0
  subtype5      25       15         0          5          0          0        0
          vv
clus       STAGE IVA STAGE IVB
  subtype1         0         0
  subtype2         1         0
  subtype3         0         1
  subtype4         0         1
  subtype5         0         0
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          21       31       38       17       25
  STAGE II         13       16       22        3       15
  STAGE III         0        1        1        0        0
  STAGE IIIA       17       10       11        6        5
  STAGE IIIB        1        4        0        1        0
  STAGE IIIC        1        1        5        1        0
  STAGE IV          0        0        2        0        0
  STAGE IVA         0        1        0        0        0
  STAGE IVB         0        0        1        1        0
[1] 9 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    23 14 19  1
  subtype2    35 17 15  5
  subtype3    40 26 15  4
  subtype4    17  3  7  2
  subtype5    26 15  5  0
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       23       35       40       17       26
  T2          14       17       26        3       15
  T3          19       15       15        7        5
  T4           1        5        4        2        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V5, binary
          cls
clus        0  1
  subtype1 42  1
  subtype2 44  1
  subtype3 61  2
  subtype4 22  0
  subtype5 37  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42    1
  subtype2   44    1
  subtype3   61    2
  subtype4   22    0
  subtype5   37    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       42       44       61       22       37
  1        1        1        2        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 MX
  subtype1 47  0 10
  subtype2 52  0 20
  subtype3 68  3 15
  subtype4 19  1  9
  subtype5 41  0  6
D8V6, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  M0       47       52       68       19       41
  M1        0        0        3        1        0
  MX       10       20       15        9        6
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus        0  1
  subtype1 20 37
  subtype2 23 49
  subtype3 33 53
  subtype4 12 17
  subtype5  9 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   37
  subtype2   23   49
  subtype3   33   53
  subtype4   12   17
  subtype5    9   38
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       20       23       33       12        9
  MALE         37       49       53       17       38
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       FIBROLAMELLAR CARCINOMA HEPATOCELLULAR CARCINOMA
  subtype1                       0                       55
  subtype2                       0                       71
  subtype3                       1                       82
  subtype4                       0                       29
  subtype5                       0                       47
          vv
clus       HEPATOCHOLANGIOCARCINOMA (MIXED)
  subtype1                                2
  subtype2                                1
  subtype3                                3
  subtype4                                0
  subtype5                                0
D8V8, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  FIBROLAMELLAR CARCINOMA                 0        0        1        0        0
  HEPATOCELLULAR CARCINOMA               55       71       82       29       47
  HEPATOCHOLANGIOCARCINOMA (MIXED)        2        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       R0 R1 R2 RX
  subtype1 51  4  0  2
  subtype2 61  3  0  6
  subtype3 75  4  1  6
  subtype4 22  3  0  1
  subtype5 46  0  0  0
D8V9, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       51       61       75       22       46
  R1        4        3        4        3        0
  R2        0        0        1        0        0
  RX        2        6        6        1        0
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0    38                         1
  subtype2                                0    21                         6
  subtype3                                0    43                         4
  subtype4                                0    11                         3
  subtype5                                1    25                         1
          vv
clus       WHITE
  subtype1    18
  subtype2    40
  subtype3    36
  subtype4    15
  subtype5    19
D8V10, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        1
  ASIAN                                  38       21       43       11       25
  BLACK OR AFRICAN AMERICAN               1        6        4        3        1
  WHITE                                  18       40       36       15       19
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V11, binary
          cls
clus        0  1
  subtype1  3 53
  subtype2  1 65
  subtype3  3 79
  subtype4  0 28
  subtype5  2 42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   53
  subtype2    1   65
  subtype3    3   79
  subtype4    0   28
  subtype5    2   42
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        1        3        0        2
  NOT HISPANIC OR LATINO       53       65       79       28       42
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
