[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"        "-oTSKCM-TM"
[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/SKCM-TM/10006254/SKCM-TM.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/SKCM-TM/10668109/SKCM-TM.mergedcluster.txt"

nPatients in clinical file=295, in cluster file=361, common to both=295
[1]  10 295
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
 82  53  46 100 
  1   2   3   4 
 82  53  46 100 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
104 108  73 
  1   2   3 
104 108  73 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
47 58 26 38 
 1  2  3  4 
47 58 26 38 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4 
27 58 35 49 
 1  2  3  4 
27 58 35 49 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
 97  83 105 
  1   2   3 
 97  83 105 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
 68 170  47 
  1   2   3 
 68 170  47 
[1] "MIRSEQ_CNMF"
[1] 3
 1  2  3  4  5 
63 94 76 41 11 
 1  2  3  4  5 
63 94 76 41 11 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
76 78 36 95 
 1  2  3  4 
76 78 36 95 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
 99 101  85 
  1   2   3 
 99 101  85 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4 
119  86  55  25 
  1   2   3   4 
119  86  55  25 
[1] "terrence_modification_tag"
[1] TRUE
[1] "data2feature, selection=ALL"
 [1] "YEARSTOBIRTH"                          
 [2] "VITALSTATUS"                           
 [3] "DAYSTODEATH"                           
 [4] "DAYSTOLASTFOLLOWUP"                    
 [5] "DAYSTOSUBMITTEDSPECIMENDX"             
 [6] "PRIMARYSITEOFDESEASE"                  
 [7] "NEOPLASM.DISEASESTAGE"                 
 [8] "PATHOLOGY.T.STAGE"                     
 [9] "PATHOLOGY.N.STAGE"                     
[10] "PATHOLOGY.M.STAGE"                     
[11] "MELANOMA.ULCERATION"                   
[12] "MELANOMA.PRIMARY.KNOWN"                
[13] "BRESLOW.THICKNESS"                     
[14] "DCCUPLOADDATE"                         
[15] "GENDER"                                
[16] "DATEOFINITIALPATHOLOGICDIAGNOSIS"      
[17] "RADIATIONTHERAPY"                      
[18] "RADIATIONS.RADIATION.REGIMENINDICATION"
[19] "RACE"                                  
[20] "ETHNICITY"                             
[21] "BATCHNUMBER"                           

Input Data has 21 rows and 295 columns.

[1] "Batch" "21"   
[1] "Last Follow UP"
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q7 
          NA           NA         3408           NA           NA         4053 
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2J7 
          NA           NA         2765         2912           NA           NA 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD 
          NA           NA         3514           NA         2126           NA 
TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JN 
        1483           NA         1280           NA         5219         1709 
TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C1 TCGA-D3-A3C3 TCGA-D3-A3C6 
        2010         1372         3976           NA           NA           NA 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CC TCGA-D3-A3CE TCGA-D3-A3CF 
        1429         1409         5065         2644           NA           NA 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51E 
          NA           NA         3151         1209          653         4923 
TCGA-D3-A51F TCGA-D3-A51G TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51K TCGA-D3-A51N 
        1329           NA         1221         4012          559          305 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GR 
        1572          458         3374         4129         4195         5055 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GD TCGA-D3-A8GE 
         226         3808           NA           NA          353          462 
TCGA-D3-A8GJ TCGA-D3-A8GL TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW 
        6965           NA         2897         4609         1663          111 
TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
         195          551          345           99          338          301 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
         766         2015           NA         1487           NA         3565 
TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 
          NA         5926           NA           NA         3265         1861 
TCGA-DA-A1I8 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F2 TCGA-DA-A3F3 
          NA           NA          713           NA          870           NA 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
        6553          477          422          309          543         1372 
TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X 
        1065          108         1582          193          371           NA 
TCGA-EE-A17Y TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A182 TCGA-EE-A183 
          NA           NA           NA           NA           NA           NA 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A20H 
          NA           NA         3335           NA         2399           NA 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
          NA           NA         2452         1455           NA         1205 
TCGA-EE-A29G TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29P 
          NA          979           NA         1349           NA         1716 
TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A29W 
        1136          440         1701        10523           NA         5218 
TCGA-EE-A29X TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A5 TCGA-EE-A2A6 
          NA           NA         3130          743           NA         1787 
TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
        1446         2051         9568         4135         6328         1482 
TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GO 
        2717         1665         2423         2296         2767         3101 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 
          NA          435         1691         1365         2884           NA 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
        3932           NA           NA           NA           NA           NA 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML 
          NA           NA           NA           NA         4403         6176 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MS 
          NA           NA         7563           NA         3150         4151 
TCGA-EE-A2MT TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AD 
        1265         1620         3781         3733          786          112 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
        1658           NA          714           NA           NA           NA 
TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE 
          NA         1949           NA           NA           NA         1016 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 
        3096         4504           NA           NA           NA           NA 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E 
          NA         2365           NA           NA           NA           NA 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M 
          NA         8180           NA           NA           NA           NA 
TCGA-ER-A19N TCGA-ER-A19O TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W 
        1340           NA           NA           NA         1133           NA 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
        2433           NA           NA           NA          498          951 
TCGA-ER-A2NH TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A3YN 
         975           NA         2443         1429         1010         2828 
TCGA-FR-A3YO TCGA-FR-A44A TCGA-FR-A69P TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FR-A7U9 
          NA         5299          149         6390          461          213 
TCGA-FR-A8YC TCGA-FR-A8YD TCGA-FR-A8YE TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1YY 
          NA          896         2871           NA           NA           NA 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB 
          NA           NA           NA           NA           NA           NA 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZH 
          NA           NA         1225           NA           NA           NA 
TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZR 
          NA           NA         3080           NA           NA           NA 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
        4526         1617           NA         1505           NA           NA 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F8 TCGA-FS-A4F9 
        2367           NA           NA           NA           NA          378 
TCGA-FS-A4FB TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU 
          NA         1504         2369            6          697         1446 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 
           5           73          301          220          427         3664 
TCGA-GN-A264 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26A 
          NA         2577           NA           NA           NA           NA 
TCGA-GN-A26D TCGA-GN-A4U8 TCGA-GN-A4U9 TCGA-HR-A2OG TCGA-HR-A2OH TCGA-OD-A75X 
        1204         1410          384           NA           NA         8966 
TCGA-QB-A6FS 
         203 
Variable 1:'AGE':	nDistinctValues=68,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITALSTATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYSTODEATH':	nDistinctValues=138,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 4:'DAYSTOLASTFOLLOWUP':	nDistinctValues=156,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 5:'DAYSTOSUBMITTEDSPECIMENDX':	nDistinctValues=231,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 6:'PRIMARY.SITE.OF.DISEASE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'NEOPLASM.DISEASESTAGE':	nDistinctValues=14,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY.T.STAGE':	nDistinctValues=15,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY.N.STAGE':	nDistinctValues=10,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'PATHOLOGY.M.STAGE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'MELANOMA.ULCERATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'MELANOMA.PRIMARY.KNOWN':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'BRESLOW.THICKNESS':	nDistinctValues=118,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 14:'DCCUPLOADDAY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 15:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'DAYOFINITIALPATHOLOGICDIAGNOSIS':	nDistinctValues=29,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
Variable 17:'RADIATION.THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 18:'RADIATIONS.RADIATION.REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
Variable 19:'RACE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 20:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'BATCH.NUMBER':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "rownames(nsurv.mat)"
 [1] "AGE"                     "PRIMARY.SITE.OF.DISEASE"
 [3] "NEOPLASM.DISEASESTAGE"   "PATHOLOGY.T.STAGE"      
 [5] "PATHOLOGY.N.STAGE"       "PATHOLOGY.M.STAGE"      
 [7] "MELANOMA.ULCERATION"     "MELANOMA.PRIMARY.KNOWN" 
 [9] "BRESLOW.THICKNESS"       "GENDER"                 
[11] "RACE"                    "ETHNICITY"              
[1] "TUMOR.?STAGE"
[1] "TUMOR.?GRADE"
[1] "PATHOLOGY.T" "4"          
[1] "PATHOLOGY.N" "5"          
Output Data has 295 columns, 2 survival variables, and 12 non-survival variables.
AGE, nv=68, binary=FALSE, numeric=TRUE
PRIMARY.SITE.OF.DISEASE, nv=4, binary=FALSE, numeric=FALSE
NEOPLASM.DISEASESTAGE, nv=14, binary=FALSE, numeric=FALSE
PATHOLOGY.T.STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
T0 T1 T2 T3 T4 
22 32 61 61 60 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   54    61    61    60 
$ClinVariableName
[1] "PATHOLOGY.T.STAGE"

$Table
vv
T0 T1 T2 T3 T4 
22 32 61 61 60 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   54    61    61    60 
PATHOLOGY.N.STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
147  54  34  39 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
147  54  34  39 
$ClinVariableName
[1] "PATHOLOGY.N.STAGE"

$Table
vv
 N0  N1  N2  N3 
147  54  34  39 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
147  54  34  39 
PATHOLOGY.M.STAGE, nv=5, binary=FALSE, numeric=FALSE
MELANOMA.ULCERATION, nv=2, binary=FALSE, numeric=FALSE
MELANOMA.PRIMARY.KNOWN, nv=2, binary=FALSE, numeric=FALSE
BRESLOW.THICKNESS, nv=118, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RACE, nv=3, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2       0  1
  subtype1 37 42
  subtype2 24 28
  subtype3 22 22
  subtype4 54 41
subtype1 subtype2 subtype3 subtype4 
      79       52       44       95 
subtype1 subtype2 subtype3 subtype4 
      42       28       22       41 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3ML 
       16.47         8.52        81.24        15.25        46.98         6.31 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
        9.34        26.37        80.22        17.72        20.48        52.01 
TCGA-D3-A5GU TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1IA 
       23.11        14.60        48.79        35.80        39.19         4.93 
TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A180 
        6.64         7.00         0.20         0.00         6.31         8.12 
TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B TCGA-EE-A20I TCGA-EE-A29B 
        1.35         5.13         4.31        36.07         1.18         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V 
       11.15        38.63         1.08         8.84         9.99         2.43 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GS 
       23.90        39.39        19.43        28.31        33.83        13.02 
TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MN TCGA-EE-A2MS TCGA-EE-A2MT 
       36.33         9.53        14.56        25.08        27.16        23.05 
TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19D 
      122.73         3.68        21.60        12.95         3.78         3.52 
TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A3ET TCGA-ER-A3EV 
       11.11       114.15         9.57         1.87         6.58        22.49 
TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1ZA TCGA-FS-A1ZH TCGA-FS-A1ZJ 
       18.41         4.90        23.80         7.30        30.87        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       12.89        52.08        40.64         8.68         0.82         5.23 
TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 
       28.73         2.27         0.20        16.24        14.70        10.65 
TCGA-QB-A6FS 
        5.79 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CC 
      111.09        10.29        30.87        56.19        45.11        61.38 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1I2 
       41.10         8.84        13.94        47.87        13.22        13.68 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A181 TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29P 
       13.15         0.13         1.12         7.99         4.41        12.03 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GP TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
        8.09         9.67         5.42         7.96       111.78        26.99 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19E 
       13.81         3.22        22.92        22.22        33.60        11.90 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3PL 
        4.21        13.45        42.84        11.80        13.08         1.71 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZE 
        6.71         3.58        64.47         3.45         7.33        19.53 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FS-A4FB 
        7.17        47.38         8.65         8.81         3.22         5.98 
TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A268 TCGA-OD-A75X 
        0.13        31.33        15.42        11.05 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
       32.42        28.08        22.55        88.50        69.90        11.41 
TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z3 
       92.42        13.32         5.39         1.55         6.97         2.89 
TCGA-D9-A6EA TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       11.31        51.12         9.99        44.52        36.69        25.15 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29M TCGA-EE-A29T 
       17.56        10.55         9.21        37.97        27.12         6.48 
TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GO TCGA-EE-A2M6 TCGA-EE-A2M7 
        8.68         8.94        34.92        30.84        98.27         2.70 
TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-ER-A19B TCGA-ER-A19H 
       30.15        15.95        12.72        21.60        25.18        34.88 
TCGA-ER-A2NE TCGA-FR-A44A TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF 
        1.51        85.74        14.24        20.38         8.22        11.08 
TCGA-FS-A4F4 TCGA-GN-A26A 
        7.36        12.16 

$subtype4
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       70.16       110.79        45.83        85.32         8.38        21.14 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ 
       68.22         7.50        36.16         6.31        64.44       114.67 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H 
       46.32        82.29        24.00       103.59        42.71        15.09 
TCGA-D3-A5GL TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1I0 TCGA-DA-A1IB TCGA-DA-A3F2 
       95.38         4.01         9.90        10.03        22.36        19.36 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 
       14.83         0.00        13.22         0.20        11.57        12.20 
TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29G TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A2A0 
        4.34         5.13         8.55         9.50         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK 
       49.22        34.29        17.98        47.21        30.08        16.01 
TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       35.54         1.15        34.98         8.84         6.18        47.51 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ 
       29.46        44.25        63.42       111.91        56.02        21.60 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3J8 TCGA-EE-A3JD 
       29.65         5.56       124.31        25.84        16.14        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 
        0.46        13.94        31.40        18.61        38.40         5.72 
TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       76.41        28.60        34.68        36.07        17.72        78.44 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z4 
       12.62        11.74         9.04         5.36        11.01        15.52 
TCGA-FS-A1ZB TCGA-FS-A1ZS TCGA-FS-A1ZW TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 
        3.39        49.15        27.39        53.85        14.20        10.78 
TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
        6.41         0.99         0.16         0.43         9.90         7.23 
TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A4U8 
       12.85        24.85        84.72        10.13        11.84 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.13     1.51     0.00 
subtype1 subtype2 subtype3 subtype4 
  122.73   111.78    98.27   124.31 
subtype1 subtype2 subtype3 subtype4 
  12.950   11.965   16.755   17.980 
[1] "0.0 - 122.7 (12.9)" "0.1 - 111.8 (12.0)" "1.5 - 98.3 (16.8)" 
[4] "0.0 - 124.3 (18.0)"
D1V2, survival
          sevent
clus2       0  1
  subtype1 38 43
  subtype2 24 28
  subtype3 23 22
  subtype4 57 41
subtype1 subtype2 subtype3 subtype4 
      81       52       45       98 
subtype1 subtype2 subtype3 subtype4 
      43       28       22       41 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QB TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3ML 
       16.57        16.67        95.74        58.06        46.98        13.87 
TCGA-D3-A3MO TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A51R TCGA-D3-A5GN 
        9.34        39.75       161.85        18.38        51.68       135.75 
TCGA-D3-A5GU TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HW 
      125.19         3.65         6.41        22.95        48.89        36.03 
TCGA-DA-A1I1 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SH 
      194.83        65.92        68.09        10.49        10.16        35.01 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20B 
        8.65        94.98        14.70        68.15         4.96       109.64 
TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29L TCGA-EE-A29R 
       13.55        80.61        13.97        39.62         2.60        14.47 
TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GJ TCGA-EE-A2GM 
       55.92        25.87        24.43        47.54        89.33        75.48 
TCGA-EE-A2GN TCGA-EE-A2GS TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MI TCGA-EE-A2MN 
       90.97        55.59        94.82        47.28       204.66        47.54 
TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-ER-A197 
      136.47        41.59       122.73         3.68        64.08        13.94 
TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19Q TCGA-ER-A2ND 
       48.89        12.59        26.37       268.93        50.89        23.34 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A69P TCGA-FS-A1Z0 TCGA-FS-A1ZA 
       80.32        46.98        92.98         4.90       202.65        27.72 
TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZU 
       32.75        47.38        23.93        74.73        53.16        26.56 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-GN-A267 
       27.09        27.02        28.73        77.88         0.20        64.44 
TCGA-GN-A26D TCGA-GN-A4U9 TCGA-QB-A6FS 
       39.58        12.62         6.67 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A2J6 TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CC 
      112.04        43.43        48.76        56.19        45.11        86.93 
TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GO TCGA-D9-A6EC TCGA-DA-A1I2 
      131.90        10.03        15.06       137.92        66.25       176.55 
TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A181 TCGA-EE-A29A TCGA-EE-A29H TCGA-EE-A29P 
       13.87        17.85        33.73        63.35        32.19        56.42 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2GP TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP 
       17.92        39.29        13.91        16.96       144.76       248.65 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A19E 
       13.81       172.18       127.20        53.19       148.08        13.02 
TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A2NC TCGA-ER-A2NF TCGA-ER-A3PL 
        6.44       131.51        44.05        43.82        16.37        33.21 
TCGA-FR-A729 TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z7 TCGA-FS-A1ZE 
      210.08        15.16       216.92        48.59         7.79        40.27 
TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZR TCGA-FS-A4F2 TCGA-FS-A4FB 
        9.70       101.26       133.55        11.41        50.14        26.73 
TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A268 TCGA-OD-A75X 
       47.54       117.93        62.79       294.77 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD 
      112.57        28.08        31.59       115.53        69.90        11.87 
TCGA-D3-A2JL TCGA-D3-A3CE TCGA-D3-A3MV TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D9-A3Z3 
      171.58        60.23        21.47       166.19         7.43         3.25 
TCGA-D9-A6EA TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1I7 TCGA-DA-A1I8 
       25.18       117.21        35.93       107.34        61.18        53.92 
TCGA-DA-A3F5 TCGA-EB-A5UL TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29C TCGA-EE-A29M 
      215.44         3.55        27.22       168.26        47.84        44.35 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A6 TCGA-EE-A2GE TCGA-EE-A2GO TCGA-EE-A2M6 
      345.96       171.55        58.75       135.95       101.95       129.27 
TCGA-EE-A2M7 TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J5 TCGA-ER-A19B 
       28.83        54.51        23.47       138.81        36.95        98.40 
TCGA-ER-A19H TCGA-ER-A2NE TCGA-FR-A44A TCGA-FS-A1Z3 TCGA-FS-A1ZC TCGA-FS-A1ZD 
      152.35        20.15       174.21        20.91       357.37        53.52 
TCGA-FS-A1ZF TCGA-FS-A4F4 TCGA-GN-A26A 
       15.45        66.67        32.48 

$subtype4
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1QA TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 
       71.80       133.25        90.90       103.10        65.49        23.77 
TCGA-D3-A2JB TCGA-D3-A2JG TCGA-D3-A2JH TCGA-D3-A2JK TCGA-D3-A2JO TCGA-D3-A3BZ 
      168.00       113.52        42.08        12.10        66.08       130.72 
TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H 
       46.32       166.52        24.53       103.59        43.69        40.14 
TCGA-D3-A5GL TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A3Z1 TCGA-D9-A6E9 TCGA-DA-A1I0 
      110.93       151.53        54.67        11.34         9.90        20.38 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UN TCGA-EB-A5VV 
       23.44        28.60        15.68        45.11        52.01         6.35 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29G 
       12.20        29.82        26.89       151.27        78.87        72.07 
TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2GC TCGA-EE-A2GD 
       18.61        37.35        46.82       102.90        67.43       314.56 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT 
      208.04        48.72        54.74        79.66        14.30        44.88 
TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MJ 
       21.67        19.76        61.51       103.27       103.20        96.23 
TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
      203.05       167.90        43.23       103.56        53.26       124.31 
TCGA-EE-A3AC TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 
       25.84        34.32        27.35        33.40       101.79        31.40 
TCGA-ER-A195 TCGA-ER-A198 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A19P 
       35.44        50.76         9.17        77.75        61.05       162.08 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ES 
       37.25       148.18        79.99        31.27        32.05       247.04 
TCGA-FR-A7U9 TCGA-FS-A1YY TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZS TCGA-FS-A1ZW 
        7.00       228.59        28.08        48.85       148.80        49.48 
TCGA-FS-A4F0 TCGA-FS-A4F8 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-FW-A3TV 
       77.82       174.84        12.43        49.45        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A265 
        2.40         9.90         7.23        14.04       120.46        84.72 
TCGA-GN-A266 TCGA-GN-A4U8 
       10.13        46.36 

subtype1 subtype2 subtype3 subtype4 
    0.20     6.44     3.25     0.16 
subtype1 subtype2 subtype3 subtype4 
  268.93   294.77   357.37   314.56 
subtype1 subtype2 subtype3 subtype4 
  41.590   48.065   58.750   49.150 
[1] "0.2 - 268.9 (41.6)" "6.4 - 294.8 (48.1)" "3.2 - 357.4 (58.8)"
[4] "0.2 - 314.6 (49.2)"
D1V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 16             0
  subtype2                  9             2
  subtype3                  6             1
  subtype4                  6             1
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        14                  51
  subtype2                                        11                  31
  subtype3                                        13                  26
  subtype4                                        22                  71
D1V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                              16        9        6        6
  PRIMARY TUMOR                                    0        2        1        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       14       11       13       22
  REGIONAL LYMPH NODE                             51       31       26       71
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       1       5        3        8        5         3
  subtype2           2       0       4        2        7        4         0
  subtype3           4       2       3        2        2        4         2
  subtype4           3       3      11        3        8        4         5
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         5         4         9          5         11         14
  subtype2         2         4         7          2          1         10
  subtype3         0         1         6          2          5          6
  subtype4         7         1        10          5          6         18
          vv
clus       STAGE IV
  subtype1        3
  subtype2        3
  subtype3        4
  subtype4        2
D1V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        1        2        4        3
  STAGE 0            1        0        2        3
  STAGE I            5        4        3       11
  STAGE IA           3        2        2        3
  STAGE IB           8        7        2        8
  STAGE II           5        4        4        4
  STAGE IIA          3        0        2        5
  STAGE IIB          5        2        0        7
  STAGE IIC          4        4        1        1
  STAGE III          9        7        6       10
  STAGE IIIA         5        2        2        5
  STAGE IIIB        11        1        5        6
  STAGE IIIC        14       10        6       18
  STAGE IV           3        3        4        2
[1] 14  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    17 18 18 19
  subtype2    10 13  6 14
  subtype3    12  9  8  6
  subtype4    14 20 23 18
D1V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       17       10       12       14
  T2          18       13        9       20
  T3          18        6        8       23
  T4          19       14        6       18
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 42 16 13  9
  subtype2 28 10  3  7
  subtype3 24 10  6  5
  subtype4 47 15 10 16
D1V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       42       28       24       47
  N1       16       10       10       15
  N2       13        3        6       10
  N3        9        7        5       16
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 77  1   0   0   2
  subtype2 46  1   1   0   1
  subtype3 42  1   0   1   2
  subtype4 87  1   1   1   0
D1V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        77       46       42       87
  M1         1        1        1        1
  M1A        0        1        0        1
  M1B        0        0        1        1
  M1C        2        1        2        0
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus        0  1
  subtype1 32 25
  subtype2 17 15
  subtype3 16 10
  subtype4 39 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   25
  subtype2   17   15
  subtype3   16   10
  subtype4   39   22
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        32       17       16       39
  YES       25       15       10       22
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, binary
          cls
clus        0  1
  subtype1 10 72
  subtype2  8 45
  subtype3  6 40
  subtype4 10 90
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10   72
  subtype2    8   45
  subtype3    6   40
  subtype4   10   90
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        10        8        6       10
  YES       72       45       40       90
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
D1V12, binary
          cls
clus        0  1
  subtype1 34 48
  subtype2 23 30
  subtype3 16 30
  subtype4 35 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   34   48
  subtype2   23   30
  subtype3   16   30
  subtype4   35   65
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       34       23       16       35
  MALE         48       30       30       65
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    81
  subtype2     2                         0    51
  subtype3     1                         0    45
  subtype4     1                         1    98
D1V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        2        1        1
  BLACK OR AFRICAN AMERICAN        0        0        0        1
  WHITE                           81       51       45       98
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V14, binary
          cls
clus        0  1
  subtype1  2 80
  subtype2  0 52
  subtype3  0 44
  subtype4  1 98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   80
  subtype2    0   52
  subtype3    0   44
  subtype4    1   98
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        0        0        1
  NOT HISPANIC OR LATINO       80       52       44       98
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 48 51
  subtype2 59 42
  subtype3 31 41
subtype1 subtype2 subtype3 
      99      101       72 
subtype1 subtype2 subtype3 
      51       42       41 
$subtype1
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK 
        8.52        22.55        45.83        30.87         7.50         6.31 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
       92.42        15.25         6.31        26.37        80.22        41.10 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       20.48        13.94        95.38        52.01        47.87         6.97 
TCGA-D3-A5GU TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY 
       23.11        11.31        13.22        14.60        48.79        51.12 
TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EB-A5KH 
       39.19        36.69        25.15         6.64        13.15         0.13 
TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C 
       11.57         8.12         1.12         5.13         4.31         4.34 
TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P 
        1.18         7.99         9.90         4.41         1.08        12.03 
TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC 
        8.09         9.99         8.09        23.90        39.39        34.29 
TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2ML 
       19.43        28.31        36.33        98.27       111.78       111.91 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AD 
       56.02        25.08        26.99        21.60       122.73         3.68 
TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 
       30.15        13.81        15.95        12.72         3.22        22.92 
TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19F 
       21.60        16.14        33.60        31.40        38.40        11.11 
TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A2NE TCGA-FR-A3YN TCGA-FS-A1YW 
      114.15        34.88         4.21         1.51        18.41        64.47 
TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM 
       11.01         7.30        20.38        11.08         7.17        47.38 
TCGA-FS-A1ZQ TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 
        8.65        27.39         5.23        53.85         3.22         7.36 
TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 
       28.73        10.78         6.41         0.99        24.85        31.33 
TCGA-GN-A268 TCGA-GN-A4U8 TCGA-OD-A75X 
       15.42        11.84        11.05 

$subtype2
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       70.16       110.79        28.08        81.24        85.32         8.38 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH 
       21.14        88.50        68.22        69.90        11.41        36.16 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        64.44        45.11       114.67        46.32        82.29 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A5GR 
       24.00       103.59        42.71        15.09         8.84         1.55 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I4 
        4.01         2.89         9.90        35.80        10.03         9.99 
TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A5SG 
       44.52        22.36        19.36        17.56        14.83         0.00 
TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E 
       13.22         0.20        12.20         5.13        37.97        38.63 
TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 
        8.55        27.12         9.50         6.48         2.43        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI 
       49.22         8.94        17.98        34.92        47.21        30.08 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC 
       16.01        35.54        34.98         8.84         6.18        47.51 
TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MR 
        9.53        29.46        44.25         7.96        63.42        29.65 
TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
        5.56       124.31        21.60        27.35         0.46        13.94 
TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A19N 
       18.61        12.95         5.72        76.41        28.60        42.84 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG 
       34.68         9.57        36.07        17.72        78.44        12.62 
TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1Z4 TCGA-FS-A1ZB 
       11.74        85.74         6.71         5.36        15.52         3.39 
TCGA-FS-A1ZH TCGA-FS-A4F8 TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO 
       30.87        14.20         0.16         0.43         9.90         7.23 
TCGA-GN-A265 TCGA-GN-A266 TCGA-GN-A26A TCGA-HR-A2OH TCGA-QB-A6FS 
       84.72        10.13        12.16        15.81         5.79 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       16.47       111.09        32.42        10.29        46.98        61.38 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51K TCGA-D9-A4Z6 TCGA-DA-A1I2 
       13.32         9.34         5.39        17.72         5.72        13.68 
TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A17Z 
        4.93         7.00         0.20         0.00        10.55         6.31 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29W 
        1.35        36.07         9.21        11.15         8.84         8.68 
TCGA-EE-A2A5 TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
        9.67        33.83        30.84         5.42         1.15        13.02 
TCGA-EE-A2M7 TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JA 
        2.70        14.56        27.16        23.05        25.84        22.22 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A2NC 
       25.18         3.78         3.52        11.90        13.45        11.80 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
        1.87        13.08         9.04         6.58        22.49         1.71 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        4.90         3.58         3.45        23.80        14.24         7.33 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
        8.22        19.53        12.92        12.89        52.08         8.81 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FB TCGA-FS-A4FD 
       49.15        40.64         8.68         0.82         5.98         2.27 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 
        0.20         0.13        12.85        16.24        14.70        10.65 

subtype1 subtype2 subtype3 
    0.13     0.00     0.00 
subtype1 subtype2 subtype3 
  122.73   124.31   111.09 
subtype1 subtype2 subtype3 
   15.95    17.98    10.60 
[1] "0.1 - 122.7 (15.9)" "0.0 - 124.3 (18.0)" "0.0 - 111.1 (10.6)"
D2V2, survival
          sevent
clus2       0  1
  subtype1 50 52
  subtype2 63 42
  subtype3 31 41
subtype1 subtype2 subtype3 
     102      105       72 
subtype1 subtype2 subtype3 
      52       42       41 
$subtype1
TCGA-D3-A1Q3 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK 
       16.67        31.59        90.90        48.76       113.52        12.10 
TCGA-D3-A2JL TCGA-D3-A3C6 TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J 
      171.58        58.06        13.87        39.75       161.85       131.90 
TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GL TCGA-D3-A5GN TCGA-D3-A5GO TCGA-D3-A5GS 
       51.68        15.06       110.93       135.75       137.92         7.43 
TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JX TCGA-D9-A1X3 TCGA-D9-A6EA TCGA-D9-A6EC 
      125.19       151.53         6.41        18.12        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I7 TCGA-DA-A1I8 
       22.95        48.89       117.21       194.83        61.18        53.92 
TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A181 
       68.09        13.87        17.85        29.82        94.98        33.73 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20C TCGA-EE-A20I TCGA-EE-A29A TCGA-EE-A29B 
       68.15         4.96       151.27        13.55        63.35        80.61 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29S TCGA-EE-A29X 
       32.19         2.60        56.42        37.35        55.92        17.92 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GJ TCGA-EE-A2GM TCGA-EE-A2GU 
       24.43        47.54        67.43        89.33        75.48        94.82 
TCGA-EE-A2M6 TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
      129.27       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A3AB TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG 
       43.23       122.73         3.68        54.51        13.81        23.47 
TCGA-EE-A3AH TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-EE-A3JI 
      138.81       172.18       127.20        64.08        34.32       148.08 
TCGA-ER-A193 TCGA-ER-A198 TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19J 
       31.40        50.76        26.37       268.93       152.35         6.44 
TCGA-ER-A2NE TCGA-FR-A3YN TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZA TCGA-FS-A1ZC 
       20.15        92.98       216.92       228.59        27.72       357.37 
TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FS-A1ZW TCGA-FS-A1ZZ 
       15.45         9.70       101.26       133.55        49.48        27.02 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC 
       77.82        50.14        66.67        28.73        12.43        49.45 
TCGA-FW-A3R5 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A4U8 TCGA-OD-A75X 
       22.92       120.46       117.93        62.79        46.36       294.77 

$subtype2
TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A1QB TCGA-D3-A2J7 TCGA-D3-A2J8 
       71.80       133.25        28.08        95.74       103.10        65.49 
TCGA-D3-A2J9 TCGA-D3-A2JA TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JH 
       23.77       115.53       168.00        69.90        11.87        42.08 
TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CB 
       56.19        66.08        45.11       130.72        46.32       166.52 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51N TCGA-D3-A5GR 
       24.53       103.59        43.69        40.14        10.03       166.19 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HW 
       54.67         3.65        11.34         3.25         9.90        36.03 
TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F5 
       20.38        35.93       107.34        23.44        28.60       215.44 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5UN TCGA-EB-A5VV TCGA-EB-A6L9 
       15.68        45.11         3.55        52.01         6.35        12.20 
TCGA-EE-A183 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M 
       26.89        78.87        47.84        39.62        72.07        44.35 
TCGA-EE-A29N TCGA-EE-A29T TCGA-EE-A29V TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A6 
       18.61       345.96        25.87        46.82       102.90        58.75 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GK TCGA-EE-A2GL 
      314.56       135.95       208.04        48.72        54.74        79.66 
TCGA-EE-A2GT TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME 
       44.88        21.67        19.76        61.51        47.28       103.27 
TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
      103.20        16.96        96.23       103.56        53.26       124.31 
TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A195 TCGA-ER-A197 
       36.95        27.35        33.40       101.79        35.44        13.94 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19M TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q 
        9.17        77.75        61.05        44.05       162.08        50.89 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FR-A44A 
       37.25       148.18        79.99        31.27        32.05       174.21 
TCGA-FR-A729 TCGA-FR-A7U9 TCGA-FS-A1Z4 TCGA-FS-A1ZB TCGA-FS-A1ZH TCGA-FS-A4F8 
      210.08         7.00        28.08        48.85        32.75       174.84 
TCGA-FW-A3TV TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A266 
        0.16         2.40         9.90         7.23        84.72        10.13 
TCGA-GN-A26A TCGA-HR-A2OH TCGA-QB-A6FS 
       32.48        65.88         6.67 

$subtype3
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A2J6 TCGA-D3-A3C7 TCGA-D3-A3CC 
       16.57       112.04       112.57        43.43        46.98        86.93 
TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51K TCGA-D9-A4Z6 TCGA-DA-A1I2 
       60.23         9.34        21.47        18.38        11.11       176.55 
TCGA-DA-A1IA TCGA-DA-A3F3 TCGA-EB-A44R TCGA-EB-A5SH TCGA-EE-A17Y TCGA-EE-A17Z 
       65.92        10.49        10.16        35.01        27.22         8.65 
TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29D TCGA-EE-A29R TCGA-EE-A29W 
       14.70       109.64       168.26        13.97        14.47       171.55 
TCGA-EE-A2A5 TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GS 
       39.29        90.97       101.95        13.91        14.30        55.59 
TCGA-EE-A2M7 TCGA-EE-A2MI TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3JA 
       28.83       204.66       136.47        41.59        25.84        53.19 
TCGA-ER-A19B TCGA-ER-A19C TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A2NC 
       98.40        48.89        12.59        13.02       131.51        43.82 
TCGA-ER-A2ND TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-ER-A3PL 
       23.34        16.37       247.04        80.32        46.98        33.21 
TCGA-FR-A69P TCGA-FR-A7U8 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z7 
        4.90        15.16        48.59       202.65        20.91         7.79 
TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZR 
       53.52        40.27        47.38        23.93        74.73        11.41 
TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A4FB TCGA-FS-A4FD 
      148.80        53.16        26.56        27.09        26.73        77.88 
TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A6C8 TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U9 
        0.20        47.54        14.04        64.44        39.58        12.62 

subtype1 subtype2 subtype3 
    2.60     0.16     0.20 
subtype1 subtype2 subtype3 
  357.37   345.96   247.04 
subtype1 subtype2 subtype3 
  56.170   46.320   39.925 
[1] "2.6 - 357.4 (56.2)" "0.2 - 346.0 (46.3)" "0.2 - 247.0 (39.9)"
D2V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 16             2
  subtype2                  6             1
  subtype3                 17             1
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        25                  61
  subtype2                                        19                  81
  subtype3                                        17                  38
D2V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              16        6       17
  PRIMARY TUMOR                                    2        1        1
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       25       19       17
  REGIONAL LYMPH NODE                             61       81       38
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           6       2       7        6       10        5         5
  subtype2           3       2      12        3        8        3         3
  subtype3           1       2       4        1        7        9         2
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         7         5         9          8          7         13
  subtype2         2         1        15          4         10         22
  subtype3         5         4         8          2          7         14
          vv
clus       STAGE IV
  subtype1        3
  subtype2        6
  subtype3        3
D2V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        6        3        1
  STAGE 0            2        2        2
  STAGE I            7       12        4
  STAGE IA           6        3        1
  STAGE IB          10        8        7
  STAGE II           5        3        9
  STAGE IIA          5        3        2
  STAGE IIB          7        2        5
  STAGE IIC          5        1        4
  STAGE III          9       15        8
  STAGE IIIA         8        4        2
  STAGE IIIB         7       10        7
  STAGE IIIC        13       22       14
  STAGE IV           3        6        3
[1] 14  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    20 20 20 24
  subtype2    26 18 23 17
  subtype3     7 22 14 17
D2V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       20       26        7
  T2          20       18       22
  T3          20       23       14
  T4          24       17       17
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 59 13 15 11
  subtype2 43 24 12 19
  subtype3 39 15  7  7
D2V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       59       43       39
  N1       13       24       15
  N2       15       12        7
  N3       11       19        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       M0 M1 M1A M1B M1C
  subtype1 96  1   0   1   2
  subtype2 93  1   1   1   3
  subtype3 65  2   1   0   0
D2V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        96       93       65
  M1         1        1        2
  M1A        0        1        1
  M1B        1        1        0
  M1C        2        3        0
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus        0  1
  subtype1 43 30
  subtype2 43 22
  subtype3 18 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   30
  subtype2   43   22
  subtype3   18   22
     clus
vv    subtype1 subtype2 subtype3
  NO        43       43       18
  YES       30       22       22
[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"
D2V10, binary
          cls
clus        0  1
  subtype1  9 95
  subtype2 17 91
  subtype3  8 65
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    9   95
  subtype2   17   91
  subtype3    8   65
     clus
vv    subtype1 subtype2 subtype3
  NO         9       17        8
  YES       95       91       65
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
D2V12, binary
          cls
clus        0  1
  subtype1 38 66
  subtype2 44 64
  subtype3 28 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38   66
  subtype2   44   64
  subtype3   28   45
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       38       44       28
  MALE         66       64       45
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0   102
  subtype2     1                         1   104
  subtype3     2                         0    71
D2V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        1        2
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                          102      104       71
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
          cls
clus         0   1
  subtype1   1 100
  subtype2   1 105
  subtype3   1  71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1  100
  subtype2    1  105
  subtype3    1   71
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        1
  NOT HISPANIC OR LATINO      100      105       71
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 23 22
  subtype2 24 31
  subtype3 10 15
  subtype4 15 21
subtype1 subtype2 subtype3 subtype4 
      45       55       25       36 
subtype1 subtype2 subtype3 subtype4 
      22       31       15       21 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JO TCGA-D3-A3CB 
       16.47        70.16       110.79         8.38        64.44        82.29 
TCGA-D3-A3MR TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F3 
      103.59        10.03         9.99        25.15        19.36         7.00 
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
       17.56         5.13        37.97        38.63         8.55         8.84 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GH TCGA-EE-A2GU 
        9.99         6.48         8.68        11.31        47.21        36.33 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU 
        8.84        47.51        14.56       111.91        26.99         5.56 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M 
       27.35        13.94        76.41         3.52        11.90        28.60 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1ZA TCGA-GF-A3OT TCGA-GN-A265 
       17.72        12.62        11.74         7.30         9.90        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       10.13        16.24        12.16 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A3CE 
      111.09        32.42        28.08        22.55        45.83        13.32 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-EE-A180 TCGA-EE-A20C TCGA-EE-A29P TCGA-EE-A2A2 
        6.31         9.34         8.12         4.34        12.03        23.90 
TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD 
       34.29        16.01        35.54        13.02        98.27         9.53 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
       63.42       111.78        56.02        25.08        29.65        27.16 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA 
       23.05        25.84        15.95         3.22        21.60        22.22 
TCGA-EE-A3JE TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 
        0.46         5.72        25.18       114.15         4.21        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YW 
       11.80         1.51        13.08         9.04         1.71        64.47 
TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG 
       23.80        14.24        15.52        20.38         8.22         7.17 
TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FW-A3I3 TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       40.64         8.68         0.20        24.85        31.33        15.42 
TCGA-GN-A26D 
       14.70 

$subtype3
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-D9-A3Z1 TCGA-DA-A1IA 
       81.24        10.29        11.41         5.39         4.01         4.93 
TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A185 TCGA-EE-A29V TCGA-EE-A2A6 TCGA-EE-A2GI 
        6.64        14.83         4.31         2.43         8.94        30.08 
TCGA-EE-A2M8 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19P TCGA-ER-A19Q 
        6.18         3.68         3.78        34.88        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FS-A1ZM TCGA-FS-A1ZQ 
       36.07         1.87         6.58        18.41        47.38         8.65 
TCGA-FW-A3TV 
        0.16 

$subtype4
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       69.90        56.19        45.11        48.79        35.80        51.12 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
       13.68        44.52        22.36        11.57         1.12         1.35 
TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
        5.13         9.90         4.41         1.08        27.12         9.50 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE 
        5.42         1.15        34.98       124.31       122.73        30.15 
TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19F 
       13.81        31.40        18.61        12.95        38.40        11.11 
TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
       13.45        42.84        30.87        12.92        12.89        52.08 

subtype1 subtype2 subtype3 subtype4 
    3.52     0.20     0.16     1.08 
subtype1 subtype2 subtype3 subtype4 
  111.91   114.15    81.24   124.31 
subtype1 subtype2 subtype3 subtype4 
  14.560   20.380    8.650   20.485 
[1] "3.5 - 111.9 (14.6)" "0.2 - 114.2 (20.4)" "0.2 - 81.2 (8.7)"  
[4] "1.1 - 124.3 (20.5)"
D3V2, survival
          sevent
clus2       0  1
  subtype1 23 22
  subtype2 26 32
  subtype3 11 15
  subtype4 15 21
subtype1 subtype2 subtype3 subtype4 
      45       58       26       36 
subtype1 subtype2 subtype3 subtype4 
      22       32       15       21 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J8 TCGA-D3-A2JO TCGA-D3-A3CB 
       16.57        71.80       133.25        65.49        66.08       166.52 
TCGA-D3-A3MR TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F3 
      103.59        20.38        35.93        53.92        28.60        10.49 
TCGA-DA-A3F5 TCGA-EE-A20F TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29R 
      215.44        78.87        47.84        39.62        72.07        14.47 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GH TCGA-EE-A2GU 
       55.92       345.96       171.55        46.82       208.04        94.82 
TCGA-EE-A2M5 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MU 
       21.67        61.51       204.66       203.05       248.65        53.26 
TCGA-EE-A3JD TCGA-EE-A3JH TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19M 
       27.35       101.79        77.75        12.59        13.02        61.05 
TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A2NH TCGA-FS-A1ZA TCGA-GF-A3OT TCGA-GN-A265 
      148.18        31.27        32.05        27.72         9.90        84.72 
TCGA-GN-A266 TCGA-GN-A267 TCGA-GN-A26A 
       10.13        64.44        32.48 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A3CE 
      112.04       112.57        28.08        31.59        90.90        60.23 
TCGA-D3-A3ML TCGA-D3-A3MO TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JX TCGA-EE-A180 
       13.87         9.34       151.53        54.67         6.41        94.98 
TCGA-EE-A20C TCGA-EE-A29P TCGA-EE-A2A2 TCGA-EE-A2GC TCGA-EE-A2GK TCGA-EE-A2GL 
      151.27        56.42        24.43        67.43        54.74        79.66 
TCGA-EE-A2GS TCGA-EE-A2M6 TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MM 
       55.59       129.27        47.28        96.23       144.76       167.90 
TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AG 
       47.54       103.56       136.47        41.59        25.84        23.47 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3JA TCGA-EE-A3JE TCGA-ER-A199 TCGA-ER-A19B 
      172.18        64.08        53.19        33.40         9.17        98.40 
TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF 
      268.93         6.44        79.99        43.82        20.15        16.37 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 TCGA-FS-A1Z4 
      247.04        33.21       216.92       202.65        20.91        28.08 
TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZG TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-FW-A3I3 
      357.37        53.52         9.70        53.16        26.56         0.20 
TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 TCGA-GN-A26D 
      120.46       117.93        62.79        39.58 

$subtype3
TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MV TCGA-D9-A1JW TCGA-D9-A3Z1 
       95.74        43.43        11.87        21.47         3.65        11.34 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F8 TCGA-EE-A185 TCGA-EE-A29V TCGA-EE-A2A6 
       65.92        68.09        15.68         4.96        25.87        58.75 
TCGA-EE-A2GI TCGA-EE-A2M8 TCGA-EE-A3AD TCGA-ER-A19C TCGA-ER-A19H TCGA-ER-A19P 
       48.72        19.76         3.68        48.89       152.35       162.08 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FS-A1ZM 
       50.89        37.25        23.34        80.32        92.98       101.26 
TCGA-FS-A1ZQ TCGA-FW-A3TV 
      133.55         0.16 

$subtype4
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1HY 
       69.90        56.19        45.11        48.89        36.03       117.21 
TCGA-DA-A1I2 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-EE-A17X TCGA-EE-A181 TCGA-EE-A182 
      176.55       107.34        23.44        29.82        33.73        14.70 
TCGA-EE-A184 TCGA-EE-A29B TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N 
       68.15        80.61        32.19         2.60        44.35        18.61 
TCGA-EE-A2GP TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A3AA TCGA-EE-A3AB TCGA-EE-A3AE 
       13.91        14.30        44.88       124.31       122.73        54.51 
TCGA-EE-A3AF TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19F 
       13.81        31.40        35.44        13.94        50.76        26.37 
TCGA-ER-A19L TCGA-ER-A19N TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZP 
      131.51        44.05        32.75        47.38        23.93        74.73 

subtype1 subtype2 subtype3 subtype4 
    9.90     0.20     0.16     2.60 
subtype1 subtype2 subtype3 subtype4 
  345.96   357.37   162.08   176.55 
subtype1 subtype2 subtype3 subtype4 
  61.050   55.165   46.075   44.200 
[1] "9.9 - 346.0 (61.0)" "0.2 - 357.4 (55.2)" "0.2 - 162.1 (46.1)"
[4] "2.6 - 176.6 (44.2)"
D3V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  2             0
  subtype2                 11             1
  subtype3                  4             0
  subtype4                  5             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        14                  31
  subtype2                                         9                  37
  subtype3                                         5                  17
  subtype4                                         3                  29
D3V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                               2       11        4        5
  PRIMARY TUMOR                                    0        1        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       14        9        5        3
  REGIONAL LYMPH NODE                             31       37       17       29
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           2       1       5        2        7        1         2
  subtype2           2       2       7        1        7        2         2
  subtype3           1       0       1        2        1        0         0
  subtype4           3       0       1        3        2        4         1
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         1         0         3          3          5          9
  subtype2         2         3         8          1          2          6
  subtype3         1         0         5          1          4          5
  subtype4         2         0         4          0          4          7
          vv
clus       STAGE IV
  subtype1        2
  subtype2        5
  subtype3        0
  subtype4        2
D3V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        2        2        1        3
  STAGE 0            1        2        0        0
  STAGE I            5        7        1        1
  STAGE IA           2        1        2        3
  STAGE IB           7        7        1        2
  STAGE II           1        2        0        4
  STAGE IIA          2        2        0        1
  STAGE IIB          1        2        1        2
  STAGE IIC          0        3        0        0
  STAGE III          3        8        5        4
  STAGE IIIA         3        1        1        0
  STAGE IIIB         5        2        4        4
  STAGE IIIC         9        6        5        7
  STAGE IV           2        5        0        2
[1] 14  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     8 12 10  9
  subtype2     9 13  7 13
  subtype3     7  7  5  2
  subtype4    12  5  6  7
D3V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        8        9        7       12
  T2          12       13        7        5
  T3          10        7        5        6
  T4           9       13        2        7
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 22  7  6  8
  subtype2 36  6  6  6
  subtype3  8  6  7  3
  subtype4 19  6  6  4
D3V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       22       36        8       19
  N1        7        6        6        6
  N2        6        6        7        6
  N3        8        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       M0 M1 M1A M1B M1C
  subtype1 42  1   1   0   0
  subtype2 48  3   1   2   0
  subtype3 25  0   0   0   0
  subtype4 34  0   0   0   2
D3V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        42       48       25       34
  M1         1        3        0        0
  M1A        1        1        0        0
  M1B        0        2        0        0
  M1C        0        0        0        2
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V9, binary
          cls
clus        0  1
  subtype1 21  7
  subtype2 23 15
  subtype3 11  5
  subtype4 10 10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    7
  subtype2   23   15
  subtype3   11    5
  subtype4   10   10
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21       23       11       10
  YES        7       15        5       10
[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"
D3V10, binary
          cls
clus        0  1
  subtype1  6 41
  subtype2  8 50
  subtype3  3 23
  subtype4  8 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   41
  subtype2    8   50
  subtype3    3   23
  subtype4    8   30
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         6        8        3        8
  YES       41       50       23       30
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
D3V12, binary
          cls
clus        0  1
  subtype1 17 30
  subtype2 20 38
  subtype3 11 15
  subtype4 16 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   30
  subtype2   20   38
  subtype3   11   15
  subtype4   16   22
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       20       11       16
  MALE         30       38       15       22
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       WHITE
  subtype1    47
  subtype2    58
  subtype3    26
  subtype4    38
[1] "NOT AVAILABLE: table dimension [4x1]"
D3V14, binary
          cls
clus        0
  subtype1 47
  subtype2 58
  subtype3 26
  subtype4 37
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 11 14
  subtype2 27 30
  subtype3 14 20
  subtype4 20 25
subtype1 subtype2 subtype3 subtype4 
      25       57       34       45 
subtype1 subtype2 subtype3 subtype4 
      14       30       20       25 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A3F2 
       16.47        70.16         8.38        10.03         9.99        19.36 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
        7.00        17.56         1.35        37.97        38.63         8.55 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GP TCGA-EE-A2M5 
        8.84         2.43         8.68        11.31         5.42         8.84 
TCGA-EE-A2MC TCGA-EE-A2MU TCGA-EE-A3JH TCGA-ER-A19A TCGA-GF-A3OT TCGA-GN-A265 
       47.51         5.56        13.94        76.41         9.90        84.72 
TCGA-GN-A267 
       16.24 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3CE 
      111.09       110.79        28.08        69.90        64.44        13.32 
TCGA-D3-A3MO TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-EE-A29B TCGA-EE-A29P 
        9.34        48.79        51.12        25.15         9.90        12.03 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       23.90        16.01        35.54        34.98        36.33        98.27 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
       14.56       111.78        56.02        25.08        29.65       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J7 
      122.73        25.84        30.15        13.81        15.95        21.60 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
       22.22        27.35        31.40         5.72        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 
       11.90        11.11       114.15         4.21        42.84        78.44 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       11.80         1.51        13.08         9.04        23.80        15.52 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A264 
        7.30        20.38         8.22        40.64         8.68        31.33 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       10.13        15.42        14.70 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3ML 
       32.42        81.24        56.19        45.11        82.29         6.31 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A181 
        4.01        35.80        13.68        22.36        14.83         1.12 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
        5.13         4.34         5.13         4.41        27.12         9.50 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-ER-A195 TCGA-ER-A197 
        9.99         6.48         1.15         6.18        18.61        12.95 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3ET 
       34.88        13.45        28.60        17.72        12.62         6.58 
TCGA-FR-A3YN TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       18.41        30.87        12.92        52.08 

$subtype4
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MR TCGA-D3-A3MV 
       22.55        45.83        10.29        11.41       103.59         5.39 
TCGA-DA-A1I5 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A185 
       44.52         4.93         6.64        11.57         8.12         4.31 
TCGA-EE-A29L TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GS 
        1.08         8.94        34.29        47.21        30.08        13.02 
TCGA-EE-A2MD TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT 
        9.53        63.42       111.91        26.99        27.16        23.05 
TCGA-EE-A3AD TCGA-EE-A3J3 TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19P 
        3.68         3.22         0.46        38.40         3.78        34.68 
TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1YW 
        9.57        36.07         1.87        11.74         1.71        64.47 
TCGA-FS-A1Z3 TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 
       14.24         7.17        12.89        47.38         8.65         0.20 
TCGA-FW-A3TV TCGA-GN-A262 TCGA-GN-A26A 
        0.16        24.85        12.16 

subtype1 subtype2 subtype3 subtype4 
    1.35     1.51     1.12     0.16 
subtype1 subtype2 subtype3 subtype4 
   84.72   124.31    82.29   111.91 
subtype1 subtype2 subtype3 subtype4 
  10.030   23.900   13.565   11.740 
[1] "1.4 - 84.7 (10.0)"  "1.5 - 124.3 (23.9)" "1.1 - 82.3 (13.6)" 
[4] "0.2 - 111.9 (11.7)"
D4V2, survival
          sevent
clus2       0  1
  subtype1 11 14
  subtype2 27 30
  subtype3 14 20
  subtype4 23 26
subtype1 subtype2 subtype3 subtype4 
      25       57       34       49 
subtype1 subtype2 subtype3 subtype4 
      14       30       20       26 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q6 TCGA-D3-A2J8 TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A3F2 
       16.57        71.80        65.49        20.38        35.93        28.60 
TCGA-DA-A3F3 TCGA-DA-A3F5 TCGA-EE-A182 TCGA-EE-A29C TCGA-EE-A29E TCGA-EE-A29G 
       10.49       215.44        14.70        47.84        39.62        72.07 
TCGA-EE-A29R TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A0 TCGA-EE-A2GP TCGA-EE-A2M5 
       14.47        25.87       171.55        46.82        13.91        21.67 
TCGA-EE-A2MC TCGA-EE-A2MU TCGA-EE-A3JH TCGA-ER-A19A TCGA-GF-A3OT TCGA-GN-A265 
       61.51        53.26       101.79        77.75         9.90        84.72 
TCGA-GN-A267 
       64.44 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q7 TCGA-D3-A1Q8 TCGA-D3-A2JC TCGA-D3-A2JO TCGA-D3-A3CE 
      112.04       133.25        28.08        69.90        66.08        60.23 
TCGA-D3-A3MO TCGA-DA-A1HV TCGA-DA-A1HY TCGA-DA-A1I8 TCGA-EE-A29B TCGA-EE-A29P 
        9.34        48.89       117.21        53.92        80.61        56.42 
TCGA-EE-A2A2 TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M6 
       24.43        54.74        79.66        44.88        94.82       129.27 
TCGA-EE-A2MI TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A3AA 
      204.66       144.76       167.90        47.54       103.56       124.31 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AG TCGA-EE-A3J7 
      122.73        25.84        54.51        13.81        23.47        64.08 
TCGA-EE-A3JA TCGA-EE-A3JD TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D 
       53.19        27.35        31.40         9.17        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19J TCGA-ER-A19N TCGA-ER-A1A1 
       13.02        26.37       268.93         6.44        44.05        79.99 
TCGA-ER-A2NC TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-FS-A1Z0 TCGA-FS-A1Z4 
       43.82        20.15        16.37       247.04       202.65        28.08 
TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZT TCGA-FS-A1ZU TCGA-GN-A264 
       27.72       357.37        53.52        53.16        26.56       117.93 
TCGA-GN-A266 TCGA-GN-A268 TCGA-GN-A26D 
       10.13        62.79        39.58 

$subtype3
TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3ML 
      112.57        95.74        56.19        45.11       166.52        13.87 
TCGA-D9-A3Z1 TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IB TCGA-DA-A3F8 TCGA-EE-A181 
       11.34        36.03       176.55        23.44        15.68        33.73 
TCGA-EE-A184 TCGA-EE-A20C TCGA-EE-A20F TCGA-EE-A29H TCGA-EE-A29M TCGA-EE-A29N 
       68.15       151.27        78.87        32.19        44.35        18.61 
TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A2GR TCGA-EE-A2M8 TCGA-ER-A195 TCGA-ER-A197 
       55.92       345.96        14.30        19.76        35.44        13.94 
TCGA-ER-A19H TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NG TCGA-ER-A3ET 
      152.35       131.51        61.05       148.18        31.27        80.32 
TCGA-FR-A3YN TCGA-FS-A1ZH TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       92.98        32.75        47.38        74.73 

$subtype4
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A3MR TCGA-D3-A3MV 
       31.59        90.90        43.43        11.87       103.59        21.47 
TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-DA-A1I5 TCGA-DA-A1IA 
      151.53        54.67         3.65         6.41       107.34        65.92 
TCGA-DA-A1IC TCGA-EE-A17X TCGA-EE-A180 TCGA-EE-A185 TCGA-EE-A29L TCGA-EE-A2A6 
       68.09        29.82        94.98         4.96         2.60        58.75 
TCGA-EE-A2GC TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MJ 
       67.43       208.04        48.72        55.59        47.28        96.23 
TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD TCGA-EE-A3J3 
      203.05       248.65       136.47        41.59         3.68       172.18 
TCGA-EE-A3JE TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       33.40        50.76        48.89       162.08        50.89        37.25 
TCGA-ER-A2ND TCGA-ER-A2NH TCGA-ER-A3PL TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZG 
       23.34        32.05        33.21       216.92        20.91         9.70 
TCGA-FS-A1ZK TCGA-FS-A1ZM TCGA-FS-A1ZQ TCGA-FW-A3I3 TCGA-FW-A3TV TCGA-GN-A262 
       23.93       101.26       133.55         0.20         0.16       120.46 
TCGA-GN-A26A 
       32.48 

subtype1 subtype2 subtype3 subtype4 
    9.90     6.44    11.34     0.16 
subtype1 subtype2 subtype3 subtype4 
  215.44   357.37   345.96   248.65 
subtype1 subtype2 subtype3 subtype4 
   46.82    53.92    51.65    48.89 
[1] "9.9 - 215.4 (46.8)"  "6.4 - 357.4 (53.9)"  "11.3 - 346.0 (51.7)"
[4] "0.2 - 248.7 (48.9)" 
D4V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                  3             0
  subtype2                  9             1
  subtype3                  2             0
  subtype4                  8             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                         8                  16
  subtype2                                         8                  40
  subtype3                                         4                  28
  subtype4                                        11                  30
D4V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                               3        9        2        8
  PRIMARY TUMOR                                    0        1        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        8        8        4       11
  REGIONAL LYMPH NODE                             16       40       28       30
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       1       2        1        3        0         1
  subtype2           2       1       7        3        5        0         3
  subtype3           4       1       2        1        4        3         1
  subtype4           1       0       3        3        5        4         0
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         0         0         1          2          5          7
  subtype2         4         3        10          0          2          9
  subtype3         0         0         3          2          3          5
  subtype4         2         0         6          1          5          6
          vv
clus       STAGE IV
  subtype1        2
  subtype2        2
  subtype3        1
  subtype4        4
D4V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        1        2        4        1
  STAGE 0            1        1        1        0
  STAGE I            2        7        2        3
  STAGE IA           1        3        1        3
  STAGE IB           3        5        4        5
  STAGE II           0        0        3        4
  STAGE IIA          1        3        1        0
  STAGE IIB          0        4        0        2
  STAGE IIC          0        3        0        0
  STAGE III          1       10        3        6
  STAGE IIIA         2        0        2        1
  STAGE IIIB         5        2        3        5
  STAGE IIIC         7        9        5        6
  STAGE IV           2        2        1        4
[1] 14  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     4  6  7  7
  subtype2    16 12  4 11
  subtype3     6  9  8  3
  subtype4    10 10  9 10
D4V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        4       16        6       10
  T2           6       12        9       10
  T3           7        4        8        9
  T4           7       11        3       10
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 10  8  4  4
  subtype2 32  5  8  9
  subtype3 18  5  6  3
  subtype4 25  7  7  5
D4V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       10       32       18       25
  N1        8        5        5        7
  N2        4        8        6        7
  N3        4        9        3        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 24  1   1   0   0
  subtype2 51  1   0   1   0
  subtype3 32  0   0   0   1
  subtype4 42  2   1   1   1
D4V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        24       51       32       42
  M1         1        1        0        2
  M1A        1        0        0        1
  M1B        0        1        0        1
  M1C        0        0        1        1
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V9, binary
          cls
clus        0  1
  subtype1 11  6
  subtype2 19 14
  subtype3 12  5
  subtype4 23 12
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11    6
  subtype2   19   14
  subtype3   12    5
  subtype4   23   12
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        11       19       12       23
  YES        6       14        5       12
[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"
D4V10, binary
          cls
clus        0  1
  subtype1  3 24
  subtype2 14 44
  subtype3  3 32
  subtype4  5 44
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   24
  subtype2   14   44
  subtype3    3   32
  subtype4    5   44
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         3       14        3        5
  YES       24       44       32       44
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
D4V12, binary
          cls
clus        0  1
  subtype1  6 21
  subtype2 25 33
  subtype3 15 20
  subtype4 18 31
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   21
  subtype2   25   33
  subtype3   15   20
  subtype4   18   31
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        6       25       15       18
  MALE         21       33       20       31
[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       WHITE
  subtype1    27
  subtype2    58
  subtype3    35
  subtype4    49
[1] "NOT AVAILABLE: table dimension [4x1]"
D4V14, binary
          cls
clus        0
  subtype1 27
  subtype2 58
  subtype3 35
  subtype4 48
[1] "NOT AVAILABLE: table only has an event [0]"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 41 52
  subtype2 53 26
  subtype3 44 56
subtype1 subtype2 subtype3 
      93       79      100 
subtype1 subtype2 subtype3 
      52       26       56 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JA 
       16.47       111.09        32.42        70.16        28.08        88.50 
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       69.90        56.19        45.11        15.25        46.98        13.32 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
        9.34         5.39         8.84        20.48        52.01         1.55 
TCGA-D3-A5GS TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F3 
        6.97        51.12        13.68        36.69        25.15         7.00 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A 
       17.56        10.55        36.07         4.34         9.21         7.99 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 
        8.55         8.09         8.84         6.48         8.68         9.67 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
       17.98        34.92        33.83        30.84         5.42        13.02 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK 
        8.84        98.27         2.70        47.51        14.56       111.78 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH 
       56.02        26.99        27.16       122.73        15.95        12.72 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D 
        3.22        21.60        16.14        18.61        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC 
       11.90        34.88         4.21        13.45        28.60        11.80 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
        1.71         4.90         5.36         3.45        23.80        14.24 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.33         7.30        20.38         8.22        11.08        30.87 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FB 
       47.38         8.81        49.15         3.22        28.73         5.98 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
        6.41         2.27         9.90        12.85        24.85        10.13 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       12.16        10.65        11.05 

$subtype2
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
        8.52       110.79        85.32         8.38        21.14        68.22 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D3-A3CB 
       30.87        36.16        92.42        64.44        46.32        82.29 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51T 
       24.00       103.59        42.71        15.09        41.10        13.94 
TCGA-D3-A5GO TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 
       47.87        48.79        39.19        44.52        22.36        19.36 
TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29N 
       14.83         0.00         0.20         1.12         5.13         9.50 
TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 
       12.03         9.99        11.31        49.22        23.90         8.94 
TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT 
       47.21        30.08        19.43        16.01        35.54        34.98 
TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML 
        6.18        29.46        44.25         7.96        63.42       111.91 
TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA 
       29.65         5.56       124.31        30.15        21.60        22.22 
TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19A 
       27.35         0.46        13.94        31.40         5.72        76.41 
TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
      114.15        42.84        34.68        36.07        17.72        78.44 
TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 TCGA-FS-A1Z4 TCGA-FS-A1ZP TCGA-FS-A1ZT 
       11.74        85.74         6.71        15.52        52.08        40.64 
TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A5DY TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U8 
       27.39        14.20         0.43         7.23        84.72        11.84 
TCGA-HR-A2OH 
       15.81 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG 
       22.55        45.83        81.24        10.29        11.41         7.50 
TCGA-D3-A2JK TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E 
        6.31       114.67        61.38         6.31        26.37        80.22 
TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       17.72        95.38        23.11         4.01         2.89         5.72 
TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 
        9.90        11.31        13.22        14.60        35.80        10.03 
TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
        9.99         4.93         6.64        13.15         0.20         0.13 
TCGA-EB-A5SH TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 
        0.00        13.22        11.57         6.31         8.12         1.35 
TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C 
       12.20         5.13         4.31         1.18         9.90        37.97 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V 
       11.15        38.63         4.41         1.08        27.12         2.43 
TCGA-EE-A29X TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU 
        8.09        39.39        34.29        28.31         1.15        36.33 
TCGA-EE-A2MD TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD 
        9.53        25.08        21.60        23.05        25.84         3.68 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C 
       13.81        22.92        33.60        12.95        38.40         3.78 
TCGA-ER-A19F TCGA-ER-A19Q TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG 
       11.11         9.57         1.87         1.51        13.08        12.62 
TCGA-ER-A3ES TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FS-A1YW 
        9.04         6.58        22.49        18.41         3.58        64.47 
TCGA-FS-A1YY TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       11.01         3.39        19.53         7.17        12.92        12.89 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 
        8.65         8.68         0.82         5.23        53.85         7.36 
TCGA-FS-A4F9 TCGA-FW-A3I3 TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 
       10.78         0.20         0.99         0.13         0.16        31.33 
TCGA-GN-A267 TCGA-GN-A268 TCGA-GN-A26D TCGA-QB-A6FS 
       16.24        15.42        14.70         5.79 

subtype1 subtype2 subtype3 
    1.55     0.00     0.00 
subtype1 subtype2 subtype3 
  122.73   124.31   114.67 
subtype1 subtype2 subtype3 
   13.45    27.39    11.06 
[1] "1.6 - 122.7 (13.4)" "0.0 - 124.3 (27.4)" "0.0 - 114.7 (11.1)"
D5V2, survival
          sevent
clus2       0  1
  subtype1 41 52
  subtype2 55 27
  subtype3 48 56
subtype1 subtype2 subtype3 
      93       82      104 
subtype1 subtype2 subtype3 
      52       27       56 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JA 
       16.57       112.04       112.57        71.80        28.08       115.53 
TCGA-D3-A2JC TCGA-D3-A2JN TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3C7 TCGA-D3-A3CE 
       69.90        56.19        45.11        58.06        46.98        60.23 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A5GN TCGA-D3-A5GR 
        9.34        21.47        10.03        51.68       135.75       166.19 
TCGA-D3-A5GS TCGA-DA-A1HY TCGA-DA-A1I2 TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F3 
        7.43       117.21       176.55        61.18        53.92        10.49 
TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A 
      215.44        27.22       109.64       151.27       168.26        63.35 
TCGA-EE-A29G TCGA-EE-A29Q TCGA-EE-A29R TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A5 
       72.07        37.35        14.47       345.96       171.55        39.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GN TCGA-EE-A2GO TCGA-EE-A2GP TCGA-EE-A2GS 
      314.56       135.95        90.97       101.95        13.91        55.59 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MC TCGA-EE-A2MI TCGA-EE-A2MK 
       21.67       129.27        28.83        61.51       204.66       144.76 
TCGA-EE-A2MM TCGA-EE-A2MP TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH 
      167.90       248.65       136.47       122.73        23.47       138.81 
TCGA-EE-A3J3 TCGA-EE-A3J7 TCGA-EE-A3J8 TCGA-ER-A195 TCGA-ER-A19B TCGA-ER-A19D 
      172.18        64.08        34.32        35.44        98.40        12.59 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19J TCGA-ER-A19L TCGA-ER-A19M TCGA-ER-A2NC 
       13.02       152.35         6.44       131.51        61.05        43.82 
TCGA-ER-A3PL TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       33.21         4.90         7.00        48.59       202.65        20.91 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH 
        7.79        27.72       357.37        53.52        15.45        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZR TCGA-FS-A1ZS TCGA-FS-A4F2 TCGA-FS-A4F5 TCGA-FS-A4FB 
      101.26        11.41       148.80        50.14        28.73        26.73 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-GF-A3OT TCGA-GF-A6C8 TCGA-GN-A262 TCGA-GN-A266 
       49.45        77.88         9.90        14.04       120.46        10.13 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       32.48        12.62       294.77 

$subtype2
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB 
       16.67       133.25       103.10        65.49        23.77       168.00 
TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JO TCGA-D3-A3C8 TCGA-D3-A3CB 
       48.76        42.08       171.58        66.08        46.32       166.52 
TCGA-D3-A3CF TCGA-D3-A3MR TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51T 
       24.53       103.59        43.69        40.14       131.90        15.06 
TCGA-D3-A5GO TCGA-D9-A149 TCGA-D9-A1JX TCGA-DA-A1HV TCGA-DA-A1I1 TCGA-DA-A1I5 
      137.92        54.67         6.41        48.89       194.83       107.34 
TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F8 TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 
       23.44        28.60        15.68        45.11         6.35        12.20 
TCGA-EE-A181 TCGA-EE-A20F TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A2A0 
       33.73        78.87        18.61        56.42        55.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
      102.90        24.43        58.75       208.04        48.72        89.33 
TCGA-EE-A2GK TCGA-EE-A2GL TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MG 
       54.74        79.66        44.88        19.76       103.27       103.20 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2ML TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA 
       16.96        96.23       203.05       103.56        53.26       124.31 
TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JE TCGA-EE-A3JH 
       54.51        36.95        53.19        27.35        33.40       101.79 
TCGA-ER-A193 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19G TCGA-ER-A19N TCGA-ER-A19P 
       31.40         9.17        77.75       268.93        44.05       162.08 
TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NH TCGA-FR-A44A TCGA-FR-A729 
       37.25       148.18        79.99        32.05       174.21       210.08 
TCGA-FS-A1Z4 TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A5DY 
       28.08        74.73        53.16        49.48       174.84         2.40 
TCGA-GF-A4EO TCGA-GN-A265 TCGA-GN-A4U8 TCGA-HR-A2OH 
        7.23        84.72        46.36        65.88 

$subtype3
TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J6 TCGA-D3-A2JD TCGA-D3-A2JG 
       31.59        90.90        95.74        43.43        11.87       113.52 
TCGA-D3-A2JK TCGA-D3-A3BZ TCGA-D3-A3CC TCGA-D3-A3ML TCGA-D3-A3MU TCGA-D3-A51E 
       12.10       130.72        86.93        13.87        39.75       161.85 
TCGA-D3-A51K TCGA-D3-A5GL TCGA-D3-A5GU TCGA-D9-A148 TCGA-D9-A1JW TCGA-D9-A1X3 
       18.38       110.93       125.19       151.53         3.65        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       11.34         3.25        11.11         9.90        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IC 
       22.95        36.03        20.38        35.93        65.92        68.09 
TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       13.87        10.16        17.85        35.01         3.55        52.01 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        94.98        14.70        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29C TCGA-EE-A29D TCGA-EE-A29E 
        4.96        13.55        80.61        47.84        13.97        39.62 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2GB 
       32.19         2.60        44.35        25.87        17.92        47.54 
TCGA-EE-A2GC TCGA-EE-A2GM TCGA-EE-A2GR TCGA-EE-A2GU TCGA-EE-A2MD TCGA-EE-A2MN 
       67.43        75.48        14.30        94.82        47.28        47.54 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
       43.23        41.59        25.84         3.68        13.81       127.20 
TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19Q 
      148.08        13.94        50.76        48.89        26.37        50.89 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3ET 
       23.34        20.15        16.37        31.27       247.04        80.32 
TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1ZB 
       46.98        92.98        15.16       216.92       228.59        48.85 
TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       40.27         9.70        47.38        23.93       133.55        26.56 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F9 TCGA-FW-A3I3 
       27.09        27.02        77.82        66.67        12.43         0.20 
TCGA-FW-A3R5 TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 
       22.92        47.54         0.16       117.93        64.44        62.79 
TCGA-GN-A26D TCGA-QB-A6FS 
       39.58         6.67 

subtype1 subtype2 subtype3 
    4.90     2.40     0.16 
subtype1 subtype2 subtype3 
  357.37   268.93   247.04 
subtype1 subtype2 subtype3 
  56.190   53.885   35.980 
[1] "4.9 - 357.4 (56.2)" "2.4 - 268.9 (53.9)" "0.2 - 247.0 (36.0)"
D5V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 11             0
  subtype2                  5             0
  subtype3                 23             4
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        33                  53
  subtype2                                        13                  65
  subtype3                                        15                  62
D5V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              11        5       23
  PRIMARY TUMOR                                    0        0        4
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       33       13       15
  REGIONAL LYMPH NODE                             53       65       62
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           4       3      10        1        9        7         4
  subtype2           3       1       9        6        6        5         4
  subtype3           3       2       4        3       10        5         2
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         4         2        12          5          6         14
  subtype2         1         2        10          0          8         15
  subtype3         9         6        10          9         10         20
          vv
clus       STAGE IV
  subtype1        7
  subtype2        2
  subtype3        3
D5V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        4        3        3
  STAGE 0            3        1        2
  STAGE I           10        9        4
  STAGE IA           1        6        3
  STAGE IB           9        6       10
  STAGE II           7        5        5
  STAGE IIA          4        4        2
  STAGE IIB          4        1        9
  STAGE IIC          2        2        6
  STAGE III         12       10       10
  STAGE IIIA         5        0        9
  STAGE IIIB         6        8       10
  STAGE IIIC        14       15       20
  STAGE IV           7        2        3
[1] 14  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 17 13
  subtype2    20 13 16 14
  subtype3    15 18 24 31
D5V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       18       20       15
  T2          29       13       18
  T3          17       16       24
  T4          13       14       31
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 49 16 12 13
  subtype2 43 16  6 10
  subtype3 49 20 16 14
D5V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       49       43       49
  N1       16       16       20
  N2       12        6       16
  N3       13       10       14
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 85  2   1   1   3
  subtype2 73  1   0   0   1
  subtype3 96  1   1   1   1
D5V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        85       73       96
  M1         2        1        1
  M1A        1        0        1
  M1B        1        0        1
  M1C        3        1        1
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus        0  1
  subtype1 27 22
  subtype2 35 16
  subtype3 42 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   22
  subtype2   35   16
  subtype3   42   36
     clus
vv    subtype1 subtype2 subtype3
  NO        27       35       42
  YES       22       16       36
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V10, binary
          cls
clus        0  1
  subtype1 15 82
  subtype2 12 71
  subtype3  7 98
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   15   82
  subtype2   12   71
  subtype3    7   98
     clus
vv    subtype1 subtype2 subtype3
  NO        15       12        7
  YES       82       71       98
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
D5V12, binary
          cls
clus        0  1
  subtype1 42 55
  subtype2 31 52
  subtype3 37 68
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   55
  subtype2   31   52
  subtype3   37   68
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       42       31       37
  MALE         55       52       68
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         0    95
  subtype2     1                         1    80
  subtype3     3                         0   102
D5V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            1        1        3
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                           95       80      102
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V14, binary
          cls
clus         0   1
  subtype1   0  94
  subtype2   0  82
  subtype3   3 100
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   94
  subtype2    0   82
  subtype3    3  100
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        0        3
  NOT HISPANIC OR LATINO       94       82      100
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 26 40
  subtype2 95 66
  subtype3 17 28
subtype1 subtype2 subtype3 
      66      161       45 
subtype1 subtype2 subtype3 
      40       66       28 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3ML 
       16.47        10.29         7.50         6.31        61.38         6.31 
TCGA-D3-A51K TCGA-D3-A5GL TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-D9-A6EG 
       17.72        95.38         5.72        11.31        13.22        14.60 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH TCGA-EB-A5UN 
        4.93         6.64         0.20         0.13         0.00        13.22 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A185 TCGA-EE-A29B 
       11.57         6.31         8.12         1.35         4.31         9.90 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29Q TCGA-EE-A29V 
       11.15        38.63         8.55         1.08         8.09         2.43 
TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AD 
       28.31        33.83         1.15        27.16        23.05         3.68 
TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A2ND TCGA-ER-A2NE 
       21.60        12.95         3.78         4.21         1.87         1.51 
TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A7U8 TCGA-FS-A1Z3 
       13.08         9.04        22.49         1.71         3.58        14.24 
TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK TCGA-FS-A1ZR 
        3.39        19.53         7.17        12.92        12.89         8.81 
TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4F9 TCGA-FS-A4FC 
        8.68         0.82         5.23        28.73        10.78         6.41 
TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A268 TCGA-OD-A75X 
        2.27         0.20         0.13        31.33        15.42        11.05 

$subtype2
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
        8.52       110.79        22.55        45.83        81.24        85.32 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
        8.38        21.14        68.22        69.90        11.41        30.87 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       36.16        92.42        56.19        64.44        45.11       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR 
       46.98        46.32        82.29        13.32        24.00       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       26.37        80.22        42.71        15.09        41.10         8.84 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A3Z1 
       13.94        47.87         1.55         6.97        23.11         4.01 
TCGA-D9-A3Z3 TCGA-D9-A6E9 TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 
        2.89         9.90        48.79        35.80        10.03        39.19 
TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 
       13.68         9.99        44.52        22.36        19.36         7.00 
TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 
       14.83        13.15         0.00         0.20         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
        5.13         5.13         1.18        37.97         4.41        27.12 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
        9.50        12.03         9.99         6.48         8.09        11.31 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
       49.22        23.90         8.94        39.39        34.29        17.98 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
       34.92        47.21        30.08        19.43        16.01        35.54 
TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
        5.42        34.98        36.33         8.84        98.27         6.18 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       47.51         9.53        29.46        44.25         7.96        14.56 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       63.42       111.78       111.91        56.02        25.08        26.99 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       21.60        29.65         5.56       124.31        25.84        30.15 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       13.81         3.22        22.92        21.60        22.22        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
        0.46        13.94        33.60        31.40        18.61        38.40 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M 
        5.72        76.41        11.11       114.15        34.88        28.60 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       42.84        34.68         9.57        36.07        17.72        78.44 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
       12.62        11.74         6.58        18.41        85.74         6.71 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
        5.36        64.47        11.01        23.80        15.52         7.30 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
       47.38        52.08         8.65        49.15        40.64        27.39 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-FW-A3TV 
       53.85         3.22         7.36        14.20         0.99         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 
        0.43         9.90         7.23        12.85        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-HR-A2OH TCGA-QB-A6FS 
       16.24        14.70        11.84        15.81         5.79 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A3C6 
      111.09        32.42        70.16        28.08        88.50        15.25 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A5GN TCGA-DA-A1HY TCGA-DA-A1I7 
        9.34         5.39        20.48        52.01        51.12        36.69 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
       25.15        17.56        10.55        36.07         4.34         9.21 
TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GO TCGA-EE-A2GS 
        7.99         8.84         8.68         9.67        30.84        13.02 
TCGA-EE-A2M7 TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A19B 
        2.70       122.73        15.95        12.72        16.14        25.18 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A2NC TCGA-FR-A69P TCGA-FS-A1YX 
        3.52        11.90        13.45        11.80         4.90         3.45 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A4FB 
        7.33        20.38         8.22        11.08        30.87         5.98 
TCGA-GN-A262 TCGA-GN-A26A TCGA-GN-A4U9 
       24.85        12.16        10.65 

subtype1 subtype2 subtype3 
     0.0      0.0      2.7 
subtype1 subtype2 subtype3 
   95.38   124.31   122.73 
subtype1 subtype2 subtype3 
   8.615   21.600   13.020 
[1] "0.0 - 95.4 (8.6)"   "0.0 - 124.3 (21.6)" "2.7 - 122.7 (13.0)"
D6V2, survival
          sevent
clus2        0   1
  subtype1  27  40
  subtype2 100  67
  subtype3  17  28
subtype1 subtype2 subtype3 
      67      167       45 
subtype1 subtype2 subtype3 
      40       67       28 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A3CC TCGA-D3-A3ML 
       16.57        43.43       113.52        12.10        86.93        13.87 
TCGA-D3-A51K TCGA-D3-A5GL TCGA-D9-A1X3 TCGA-D9-A4Z6 TCGA-D9-A6EA TCGA-D9-A6EC 
       18.38       110.93        18.12        11.11        25.18        66.25 
TCGA-D9-A6EG TCGA-DA-A1IA TCGA-DA-A1IC TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SH 
       22.95        65.92        68.09        10.16        17.85        35.01 
TCGA-EB-A5UN TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A182 TCGA-EE-A185 
       52.01        29.82         8.65        94.98        14.70         4.96 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29L TCGA-EE-A29Q 
       80.61        13.97        39.62        72.07         2.60        37.35 
TCGA-EE-A29V TCGA-EE-A2GM TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MS TCGA-EE-A2MT 
       25.87        75.48        90.97        14.30       136.47        41.59 
TCGA-EE-A3AD TCGA-EE-A3J7 TCGA-ER-A197 TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A2ND 
        3.68        64.08        13.94        48.89         6.44        23.34 
TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES TCGA-ER-A3EV TCGA-ER-A3PL TCGA-FR-A7U8 
       20.15        16.37       247.04        46.98        33.21        15.16 
TCGA-FS-A1Z3 TCGA-FS-A1ZB TCGA-FS-A1ZE TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
       20.91        48.85        40.27         9.70        47.38        23.93 
TCGA-FS-A1ZR TCGA-FS-A1ZU TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F5 TCGA-FS-A4F9 
       11.41        26.56        27.09        27.02        28.73        12.43 
TCGA-FS-A4FC TCGA-FS-A4FD TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GN-A264 TCGA-GN-A268 
       49.45        77.88         0.20        47.54       117.93        62.79 
TCGA-OD-A75X 
      294.77 

$subtype2
TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A1Q9 TCGA-D3-A1QA TCGA-D3-A1QB TCGA-D3-A2J7 
       16.67       133.25        31.59        90.90        95.74       103.10 
TCGA-D3-A2J8 TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF 
       65.49        23.77       168.00        69.90        11.87        48.76 
TCGA-D3-A2JH TCGA-D3-A2JL TCGA-D3-A2JN TCGA-D3-A2JO TCGA-D3-A2JP TCGA-D3-A3BZ 
       42.08       171.58        56.19        66.08        45.11       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3CF TCGA-D3-A3MR 
       46.98        46.32       166.52        60.23        24.53       103.59 
TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N 
       39.75       161.85        43.69        40.14       131.90        10.03 
TCGA-D3-A51T TCGA-D3-A5GO TCGA-D3-A5GR TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D9-A148 
       15.06       137.92       166.19         7.43       125.19       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1JX TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A6E9 
       54.67         3.65         6.41        11.34         3.25         9.90 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I0 TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1I4 
       48.89        36.03        20.38       194.83       176.55        35.93 
TCGA-DA-A1I5 TCGA-DA-A1IB TCGA-DA-A3F2 TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q 
      107.34        23.44        28.60        10.49        15.68        13.87 
TCGA-EB-A5SG TCGA-EB-A5UL TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A181 TCGA-EE-A183 
       45.11         3.55         6.35        12.20        33.73        26.89 
TCGA-EE-A184 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29C TCGA-EE-A29H TCGA-EE-A29M 
       68.15        78.87        13.55        47.84        32.19        44.35 
TCGA-EE-A29N TCGA-EE-A29P TCGA-EE-A29S TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A0 
       18.61        56.42        55.92       345.96        17.92        46.82 
TCGA-EE-A2A1 TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GC TCGA-EE-A2GD 
      102.90        24.43        58.75        47.54        67.43       314.56 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GK TCGA-EE-A2GL 
      135.95       208.04        48.72        89.33        54.74        79.66 
TCGA-EE-A2GP TCGA-EE-A2GT TCGA-EE-A2GU TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2M8 
       13.91        44.88        94.82        21.67       129.27        19.76 
TCGA-EE-A2MC TCGA-EE-A2MD TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MH TCGA-EE-A2MI 
       61.51        47.28       103.27       103.20        16.96       204.66 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP 
       96.23       144.76       203.05       167.90        47.54       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MR TCGA-EE-A2MU TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AE 
       43.23       103.56        53.26       124.31        25.84        54.51 
TCGA-EE-A3AF TCGA-EE-A3J3 TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD 
       13.81       172.18       127.20        36.95        53.19        27.35 
TCGA-EE-A3JE TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A198 
       33.40       101.79       148.08        31.40        35.44        50.76 
TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19F TCGA-ER-A19G TCGA-ER-A19H TCGA-ER-A19M 
        9.17        77.75        26.37       268.93       152.35        61.05 
TCGA-ER-A19N TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A19W TCGA-ER-A1A1 
       44.05       162.08        50.89        37.25       148.18        79.99 
TCGA-ER-A2NG TCGA-ER-A2NH TCGA-ER-A3ET TCGA-FR-A3YN TCGA-FR-A44A TCGA-FR-A729 
       31.27        32.05        80.32        92.98       174.21       210.08 
TCGA-FR-A7U9 TCGA-FS-A1YW TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA 
        7.00       216.92       228.59       202.65        28.08        27.72 
TCGA-FS-A1ZM TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZS TCGA-FS-A1ZT TCGA-FS-A1ZW 
      101.26        74.73       133.55       148.80        53.16        49.48 
TCGA-FS-A4F0 TCGA-FS-A4F2 TCGA-FS-A4F4 TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-FW-A3TV 
       77.82        50.14        66.67       174.84        22.92         0.16 
TCGA-FW-A5DY TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GF-A6C8 TCGA-GN-A265 TCGA-GN-A266 
        2.40         9.90         7.23        14.04        84.72        10.13 
TCGA-GN-A267 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-HR-A2OH TCGA-QB-A6FS 
       64.44        39.58        46.36        65.88         6.67 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1Q8 TCGA-D3-A2JA TCGA-D3-A3C6 
      112.04       112.57        71.80        28.08       115.53        58.06 
TCGA-D3-A3MO TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A5GN TCGA-DA-A1HY TCGA-DA-A1I7 
        9.34        21.47        51.68       135.75       117.21        61.18 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20C TCGA-EE-A20H 
       53.92       215.44        27.22       109.64       151.27       168.26 
TCGA-EE-A29A TCGA-EE-A29R TCGA-EE-A29W TCGA-EE-A2A5 TCGA-EE-A2GO TCGA-EE-A2GS 
       63.35        14.47       171.55        39.29       101.95        55.59 
TCGA-EE-A2M7 TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-ER-A19B 
       28.83       122.73        23.47       138.81        34.32        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A2NC TCGA-FR-A69P TCGA-FS-A1YX 
       12.59        13.02       131.51        43.82         4.90        48.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZC TCGA-FS-A1ZD TCGA-FS-A1ZF TCGA-FS-A1ZH TCGA-FS-A4FB 
        7.79       357.37        53.52        15.45        32.75        26.73 
TCGA-GN-A262 TCGA-GN-A26A TCGA-GN-A4U9 
      120.46        32.48        12.62 

subtype1 subtype2 subtype3 
    0.20     0.16     4.90 
subtype1 subtype2 subtype3 
  294.77   345.96   357.37 
subtype1 subtype2 subtype3 
   28.73    50.89    53.92 
[1] "0.2 - 294.8 (28.7)" "0.2 - 346.0 (50.9)" "4.9 - 357.4 (53.9)"
D6V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 22             3
  subtype2                 11             1
  subtype3                  6             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        14                  28
  subtype2                                        29                 129
  subtype3                                        18                  23
D6V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              22       11        6
  PRIMARY TUMOR                                    3        1        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       14       29       18
  REGIONAL LYMPH NODE                             28      129       23
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       1       3        1        3        5         2
  subtype2           6       2      17        9       16        8         6
  subtype3           3       3       3        0        6        4         2
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         7         5         5          5          6         15
  subtype2         7         4        22          5         15         26
  subtype3         0         1         5          4          3          8
          vv
clus       STAGE IV
  subtype1        4
  subtype2        6
  subtype3        2
D6V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        1        6        3
  STAGE 0            1        2        3
  STAGE I            3       17        3
  STAGE IA           1        9        0
  STAGE IB           3       16        6
  STAGE II           5        8        4
  STAGE IIA          2        6        2
  STAGE IIB          7        7        0
  STAGE IIC          5        4        1
  STAGE III          5       22        5
  STAGE IIIA         5        5        4
  STAGE IIIB         6       15        3
  STAGE IIIC        15       26        8
  STAGE IV           4        6        2
[1] 14  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     5 11 17 25
  subtype2    42 34 30 28
  subtype3     6 15 10  5
D6V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1        5       42        6
  T2          11       34       15
  T3          17       30       10
  T4          25       28        5
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 32 12  8 10
  subtype2 86 30 20 21
  subtype3 23 10  6  6
D6V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       32       86       23
  N1       12       30       10
  N2        8       20        6
  N3       10       21        6
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1  60   3   1   0   0
  subtype2 152   1   1   1   4
  subtype3  42   0   0   1   1
D6V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        60      152       42
  M1         3        1        0
  M1A        1        1        0
  M1B        0        1        1
  M1C        0        4        1
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V9, binary
          cls
clus        0  1
  subtype1 23 26
  subtype2 67 37
  subtype3 14 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   26
  subtype2   67   37
  subtype3   14   11
     clus
vv    subtype1 subtype2 subtype3
  NO        23       67       14
  YES       26       37       11
[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"
D6V10, binary
          cls
clus         0   1
  subtype1   5  63
  subtype2  24 146
  subtype3   5  42
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   63
  subtype2   24  146
  subtype3    5   42
     clus
vv    subtype1 subtype2 subtype3
  NO         5       24        5
  YES       63      146       42
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
D6V12, binary
          cls
clus         0   1
  subtype1  23  45
  subtype2  69 101
  subtype3  18  29
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23   45
  subtype2   69  101
  subtype3   18   29
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       23       69       18
  MALE         45      101       29
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         0    66
  subtype2     2                         1   165
  subtype3     1                         0    46
D6V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            2        2        1
  BLACK OR AFRICAN AMERICAN        0        1        0
  WHITE                           66      165       46
[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"
D6V14, binary
          cls
clus         0   1
  subtype1   2  65
  subtype2   1 166
  subtype3   0  45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   65
  subtype2    1  166
  subtype3    0   45
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            2        1        0
  NOT HISPANIC OR LATINO       65      166       45
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 32 28
  subtype2 38 51
  subtype3 37 36
  subtype4 23 16
  subtype5  6  5
subtype1 subtype2 subtype3 subtype4 subtype5 
      60       89       73       39       11 
subtype1 subtype2 subtype3 subtype4 subtype5 
      28       51       36       16        5 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       16.47        32.42        81.24        21.14        68.22        69.90 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A51H TCGA-D3-A8GD TCGA-D9-A6E9 
       11.41        30.87        82.29        15.09        10.22         9.90 
TCGA-D9-A6EA TCGA-DA-A1IB TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A6L9 TCGA-EE-A17X 
       11.31        22.36        13.15         0.13         0.20        11.57 
TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29X 
       12.20         4.34         9.50         8.09         6.48         8.09 
TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GT TCGA-EE-A2M6 
        8.94        16.01        28.31        30.84        34.98        98.27 
TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A2MT 
       44.25        56.02        25.08        29.65        27.16        23.05 
TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A199 TCGA-ER-A19E 
       25.84        30.15        21.60        27.35         5.72        11.90 
TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF TCGA-FR-A8YE 
       13.45        42.84        78.44         1.51        13.08         3.29 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZK TCGA-FS-A1ZQ 
       23.80        15.52         7.30        19.53        12.89         8.65 
TCGA-FS-A1ZU TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A262 TCGA-OD-A75X 
        8.68        14.20         0.13         7.23        24.85        11.05 

$subtype2
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
        8.52        45.83        10.29         7.50         6.31        92.42 
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL 
       15.25        24.00         6.31        80.22        17.72        95.38 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A3Z1 
        6.97        23.11        22.06       142.45        75.65         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 
        2.89         5.72        13.22        48.79        35.80        13.68 
TCGA-DA-A1IA TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Z 
        4.93         6.64         7.00         0.00         0.00         6.31 
TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I 
        8.12         1.12         5.13         4.31         5.13         1.18 
TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M 
        9.90        11.15        38.63         4.41         1.08        27.12 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR 
       34.29        30.08        19.43        35.54        33.83         1.15 
TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AD 
        7.96        63.42       111.78        21.60       124.31         3.68 
TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 
       13.81        22.92        22.22        33.60        12.95        38.40 
TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND 
        3.78         4.21        34.68         9.57        36.07         1.87 
TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD 
       12.62         9.04         1.71        18.41         3.58         4.70 
TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP 
       64.47        14.24        11.08         7.17        12.92        52.08 
TCGA-FS-A1ZR TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 
        8.81        27.39         5.23        53.85         7.36        28.73 
TCGA-GN-A264 TCGA-GN-A267 TCGA-GN-A268 TCGA-HR-A2OH TCGA-QB-A6FS 
       31.33        16.24        15.42        15.81         5.79 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
      111.09        70.16       110.79        85.32         8.38        88.50 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51F 
       56.19       114.67        46.32        61.38         9.34        42.71 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GL TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 
       29.72        15.19        38.93        51.12         9.99        44.52 
TCGA-DA-A1I7 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       36.69        13.22        10.55         9.21         7.99        37.97 
TCGA-EE-A29G TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A5 
        8.55         9.99         2.43         8.68        49.22         9.67 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 
       17.98        34.92        47.21         5.42        13.02         8.84 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 
        6.18        47.51        29.46        14.56         5.56         3.22 
TCGA-EE-A3J7 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
       21.60         0.46        13.94        31.40        18.61        76.41 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NH 
        3.52        34.88        28.60        17.72        11.80        11.74 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY 
        6.58        22.49         4.90         5.36         3.45        11.01 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.33         3.39         8.22        47.38        49.15        40.64 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A26A 
        2.27         0.99         0.16         9.90        10.13        12.16 
TCGA-GN-A4U9 
       10.65 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3MR 
       28.08        22.55        36.16        64.44        13.32       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-DA-A1I0 
       26.37         5.39        20.48        13.94        52.01        10.03 
TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A182 TCGA-EE-A20B 
       19.36        17.56        14.83         0.20         1.35        36.07 
TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 
       12.03        11.31        23.90        39.39        36.33         2.70 
TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 
        9.53       111.91        26.99       122.73        15.95        16.14 
TCGA-ER-A19F TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 
       11.11       114.15         2.20        20.38        30.87         0.20 
TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 
       84.72        14.70        11.84 

$subtype5
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A51J TCGA-D3-A51N TCGA-DA-A1I1 TCGA-DA-A1I8 
       45.11        46.98        41.10         8.84        39.19        25.15 
TCGA-EE-A29R TCGA-EE-A3AH TCGA-ER-A19B TCGA-FS-A1ZY TCGA-FS-A4FB 
        8.84        12.72        25.18         0.82         5.98 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.13     0.00     0.16     0.20     0.82 
subtype1 subtype2 subtype3 subtype4 subtype5 
   98.27   142.45   114.67   122.73    46.98 
subtype1 subtype2 subtype3 subtype4 subtype5 
  15.305   12.950   13.220   19.360   25.150 
[1] "0.1 - 98.3 (15.3)"  "0.0 - 142.4 (12.9)" "0.2 - 114.7 (13.2)"
[4] "0.2 - 122.7 (19.4)" "0.8 - 47.0 (25.1)" 
D7V2, survival
          sevent
clus2       0  1
  subtype1 33 28
  subtype2 43 51
  subtype3 37 36
  subtype4 23 17
  subtype5  6  5
subtype1 subtype2 subtype3 subtype4 subtype5 
      61       94       73       40       11 
subtype1 subtype2 subtype3 subtype4 subtype5 
      28       51       36       17        5 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1QB TCGA-D3-A2J9 TCGA-D3-A2JB TCGA-D3-A2JC 
       16.57       112.57        95.74        23.77       168.00        69.90 
TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A3CB TCGA-D3-A51H TCGA-D3-A8GD TCGA-D9-A6E9 
       11.87        48.76       166.52        40.14        11.61         9.90 
TCGA-D9-A6EA TCGA-DA-A1IB TCGA-EB-A44Q TCGA-EB-A5KH TCGA-EB-A5VV TCGA-EB-A6L9 
       25.18        23.44        13.87        17.85         6.35        12.20 
TCGA-EE-A17X TCGA-EE-A183 TCGA-EE-A20C TCGA-EE-A29N TCGA-EE-A29Q TCGA-EE-A29T 
       29.82        26.89       151.27        18.61        37.35       345.96 
TCGA-EE-A29X TCGA-EE-A2A6 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GT 
       17.92        58.75        54.74        75.48       101.95        44.88 
TCGA-EE-A2M6 TCGA-EE-A2MG TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
      129.27       103.20       167.90        47.54       103.56       136.47 
TCGA-EE-A2MT TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3J5 TCGA-EE-A3JD TCGA-ER-A199 
       41.59        25.84        54.51        36.95        27.35         9.17 
TCGA-ER-A19E TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NE TCGA-ER-A2NF 
       13.02       131.51        44.05        79.99        20.15        16.37 
TCGA-FR-A8YE TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZE TCGA-FS-A1ZK 
       94.39       202.65        28.08        27.72        40.27        23.93 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A4F8 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A262 
      133.55        26.56       174.84        47.54         7.23       120.46 
TCGA-OD-A75X 
      294.77 

$subtype2
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
       16.67        90.90        43.43       113.52        12.10       171.58 
TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E TCGA-D3-A51K TCGA-D3-A5GL 
       58.06        24.53        13.87       161.85        18.38       110.93 
TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A148 
        7.43       125.19        79.59       228.99        95.24       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65        18.12        11.34         3.25        11.11 
TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IC 
       66.25        48.89        36.03       176.55        65.92        68.09 
TCGA-DA-A3F3 TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EE-A17Z TCGA-EE-A180 
       10.49        45.11        35.01         3.55         8.65        94.98 
TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B 
       33.73        68.15         4.96        78.87        13.55        80.61 
TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A2GC 
       13.97        39.62        32.19         2.60        44.35        67.43 
TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2MH 
       48.72        89.33        79.66        90.97        14.30        16.96 
TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MQ TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF 
       96.23       144.76        43.23       124.31         3.68        13.81 
TCGA-EE-A3J4 TCGA-EE-A3JA TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 TCGA-ER-A19C 
      127.20        53.19       148.08        13.94        50.76        48.89 
TCGA-ER-A19J TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND TCGA-ER-A2NG 
        6.44       162.08        50.89        37.25        23.34        31.27 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YW 
      247.04        33.21        92.98        15.16        29.46       216.92 
TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZR 
       20.91        15.45         9.70        47.38        74.73        11.41 
TCGA-FS-A1ZW TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F4 TCGA-FS-A4F5 TCGA-GN-A264 
       49.48        27.02        77.82        66.67        28.73       117.93 
TCGA-GN-A267 TCGA-GN-A268 TCGA-HR-A2OH TCGA-QB-A6FS 
       64.44        62.79        65.88         6.67 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
      112.04        71.80       133.25       103.10        65.49       115.53 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51F 
       56.19       130.72        46.32        86.93         9.34        43.69 
TCGA-D3-A8GB TCGA-D3-A8GE TCGA-D3-A8GL TCGA-DA-A1HY TCGA-DA-A1I4 TCGA-DA-A1I5 
       30.84        15.19        89.13       117.21        35.93       107.34 
TCGA-DA-A1I7 TCGA-EB-A5UN TCGA-EE-A17Y TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
       61.18        52.01        27.22       168.26        63.35        47.84 
TCGA-EE-A29G TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2A5 
       72.07        55.92        25.87       171.55       102.90        39.29 
TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 
      314.56       135.95       208.04        13.91        55.59        21.67 
TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2ME TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 
       19.76        61.51       103.27       204.66        53.26       172.18 
TCGA-EE-A3J7 TCGA-EE-A3JE TCGA-EE-A3JH TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A 
       64.08        33.40       101.79        31.40        35.44        77.75 
TCGA-ER-A19D TCGA-ER-A19H TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NH 
       12.59       152.35        61.05       148.18        43.82        32.05 
TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY 
       80.32        46.98         4.90         7.00        48.59       228.59 
TCGA-FS-A1Z7 TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A1ZT 
        7.79        48.85        53.52       101.26       148.80        53.16 
TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A3OT TCGA-GN-A266 TCGA-GN-A26A 
       77.88        22.92         0.16         9.90        10.13        32.48 
TCGA-GN-A4U9 
       12.62 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3CE TCGA-D3-A3MR 
       28.08        31.59        42.08        66.08        60.23       103.59 
TCGA-D3-A3MU TCGA-D3-A3MV TCGA-D3-A51R TCGA-D3-A51T TCGA-D3-A5GN TCGA-D9-A1JX 
       39.75        21.47        51.68        15.06       135.75         6.41 
TCGA-DA-A1I0 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A182 
       20.38        28.60       215.44        15.68        10.16        14.70 
TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU 
      109.64        56.42        46.82        24.43        47.54        94.82 
TCGA-EE-A2M7 TCGA-EE-A2MD TCGA-EE-A2ML TCGA-EE-A2MP TCGA-EE-A3AB TCGA-EE-A3AG 
       28.83        47.28       203.05       248.65       122.73        23.47 
TCGA-EE-A3J8 TCGA-ER-A19F TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FS-A1ZH 
       34.32        26.37       268.93        34.82       357.37        32.75 
TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 
        0.20        84.72        39.58        46.36 

$subtype5
TCGA-D3-A2JP TCGA-D3-A3C7 TCGA-D3-A51J TCGA-D3-A51N TCGA-DA-A1I1 TCGA-DA-A1I8 
       45.11        46.98       131.90        10.03       194.83        53.92 
TCGA-EE-A29R TCGA-EE-A3AH TCGA-ER-A19B TCGA-FS-A1ZY TCGA-FS-A4FB 
       14.47       138.81        98.40        27.09        26.73 

subtype1 subtype2 subtype3 subtype4 subtype5 
    6.35     2.60     0.16     0.20    10.03 
subtype1 subtype2 subtype3 subtype4 subtype5 
  345.96   247.04   314.56   357.37   194.83 
subtype1 subtype2 subtype3 subtype4 subtype5 
  41.590   48.050   55.920   40.915   46.980 
[1] "6.3 - 346.0 (41.6)"  "2.6 - 247.0 (48.0)"  "0.2 - 314.6 (55.9)" 
[4] "0.2 - 357.4 (40.9)"  "10.0 - 194.8 (47.0)"
D7V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 11             3
  subtype2                 13             1
  subtype3                 12             0
  subtype4                  4             0
  subtype5                  1             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                         6                  43
  subtype2                                        14                  65
  subtype3                                        27                  37
  subtype4                                         9                  28
  subtype5                                         4                   6
D7V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                              11       13       12        4
  PRIMARY TUMOR                                    3        1        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        6       14       27        9
  REGIONAL LYMPH NODE                             43       65       37       28
                                           clus
vv                                          subtype5
  DISTANT METASTASIS                               1
  PRIMARY TUMOR                                    0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE        4
  REGIONAL LYMPH NODE                              6
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           5       5       8        6        3        3         1
  subtype2           2       0       4        3       10        6         3
  subtype3           2       1       8        1       11        2         3
  subtype4           1       0       2        1        1        4         2
  subtype5           0       0       0        0        0        1         0
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         1         3         6          1          2         12
  subtype2         8         3         8          5         11         15
  subtype3         4         2         9          5          6         14
  subtype4         1         2         4          2          7          5
  subtype5         1         0         3          0          0          4
          vv
clus       STAGE IV
  subtype1        0
  subtype2        5
  subtype3        3
  subtype4        4
  subtype5        1
D7V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4 subtype5
  I OR II NOS        5        2        2        1        0
  STAGE 0            5        0        1        0        0
  STAGE I            8        4        8        2        0
  STAGE IA           6        3        1        1        0
  STAGE IB           3       10       11        1        0
  STAGE II           3        6        2        4        1
  STAGE IIA          1        3        3        2        0
  STAGE IIB          1        8        4        1        1
  STAGE IIC          3        3        2        2        0
  STAGE III          6        8        9        4        3
  STAGE IIIA         1        5        5        2        0
  STAGE IIIB         2       11        6        7        0
  STAGE IIIC        12       15       14        5        4
  STAGE IV           0        5        3        4        1
[1] 14  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    16  9  6 12
  subtype2    16 18 22 21
  subtype3     6 29 16 12
  subtype4     9  4 10 10
  subtype5     5  1  3  1
D7V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1       16       16        6        9        5
  T2           9       18       29        4        1
  T3           6       22       16       10        3
  T4          12       21       12       10        1
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 35  5  6 10
  subtype2 48 16 12 12
  subtype3 39 18  7  8
  subtype4 17  8  9  4
  subtype5  3  4  0  4
D7V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       35       48       39       17        3
  N1        5       16       18        8        4
  N2        6       12        7        9        0
  N3       10       12        8        4        4
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 58  0   0   0   0
  subtype2 83  2   1   1   2
  subtype3 69  1   0   1   1
  subtype4 34  1   1   1   1
  subtype5 10  0   0   0   1
D7V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  M0        58       83       69       34       10
  M1         0        2        1        1        0
  M1A        0        1        0        1        0
  M1B        0        1        1        1        0
  M1C        0        2        1        1        1
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus        0  1
  subtype1 20 14
  subtype2 42 27
  subtype3 30 17
  subtype4 11 13
  subtype5  1  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   14
  subtype2   42   27
  subtype3   30   17
  subtype4   11   13
  subtype5    1    3
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        20       42       30       11        1
  YES       14       27       17       13        3
[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"
D7V10, binary
          cls
clus        0  1
  subtype1  7 56
  subtype2 11 83
  subtype3  6 70
  subtype4  7 34
  subtype5  5  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   56
  subtype2   11   83
  subtype3    6   70
  subtype4    7   34
  subtype5    5    6
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         7       11        6        7        5
  YES       56       83       70       34        6
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
D7V12, binary
          cls
clus        0  1
  subtype1 26 37
  subtype2 37 57
  subtype3 21 55
  subtype4 16 25
  subtype5  5  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26   37
  subtype2   37   57
  subtype3   21   55
  subtype4   16   25
  subtype5    5    6
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       26       37       21       16        5
  MALE         37       57       55       25        6
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     3                         1    59
  subtype2     0                         0    93
  subtype3     1                         0    74
  subtype4     1                         0    40
  subtype5     0                         0    11
D7V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                            3        0        1        1        0
  BLACK OR AFRICAN AMERICAN        1        0        0        0        0
  WHITE                           59       93       74       40       11
[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"
D7V14, binary
          cls
clus        0  1
  subtype1  0 62
  subtype2  2 90
  subtype3  2 71
  subtype4  0 41
  subtype5  0 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   62
  subtype2    2   90
  subtype3    2   71
  subtype4    0   41
  subtype5    0   11
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        2        2        0        0
  NOT HISPANIC OR LATINO       62       90       71       41       11
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 32 41
  subtype2 36 37
  subtype3 20 14
  subtype4 48 44
subtype1 subtype2 subtype3 subtype4 
      73       73       34       92 
subtype1 subtype2 subtype3 subtype4 
      41       37       14       44 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB 
       16.47         8.52       110.79        10.29        85.32        68.22 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A5GL TCGA-D3-A8GB TCGA-D3-A8GM 
       61.38        24.00         6.31        95.38        29.72        75.65 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1I2 TCGA-DA-A1I4 TCGA-DA-A1IA 
        2.89         5.72         9.90        13.68         9.99         4.93 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-EB-A5UN TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A183 
       22.36         6.64        13.22         0.20         8.12        12.20 
TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29V 
        9.90        38.63         8.55        27.12         9.50         2.43 
TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 TCGA-EE-A2GD TCGA-EE-A2GL TCGA-EE-A2GR 
        8.09         9.67         8.94        17.98        35.54         1.15 
TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN 
       34.98         6.18        29.46        63.42        56.02        25.08 
TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF 
       21.60        27.16        23.05       124.31        25.84        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19C 
       22.92        21.60        21.60        27.35        38.40         3.78 
TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES 
       13.45         1.87         1.51        13.08        12.62         9.04 
TCGA-ER-A3PL TCGA-FS-A1YY TCGA-FS-A1Z0 TCGA-FS-A1ZK TCGA-FS-A1ZR TCGA-FS-A1ZT 
        1.71        11.01        23.80        12.89         8.81        40.64 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TU TCGA-FW-A3TV TCGA-GN-A267 TCGA-GN-A26D 
        7.36         2.27         0.13         0.16        16.24        14.70 
TCGA-QB-A6FS 
        5.79 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      111.09        32.42        70.16        81.24         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 
       88.50        69.90        11.41        56.19       114.67        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A8GD 
       46.32        13.32         9.34        42.71        15.09        10.22 
TCGA-D3-A8GE TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-EB-A5KH TCGA-EE-A17X 
       15.19        51.12        36.69        25.15         0.13        11.57 
TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29Q TCGA-EE-A29T 
        4.34         9.21         7.99        37.97         8.09         6.48 
TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2M5 
        8.68        49.22        16.01        28.31        30.84         8.84 
TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR TCGA-EE-A3J3 
       98.27        47.51        44.25        14.56        29.65         3.22 
TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B TCGA-ER-A19D 
       31.40        18.61         5.72        76.41        25.18         3.52 
TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 TCGA-ER-A2NC 
       11.90        34.88        42.84        17.72        78.44        11.80 
TCGA-ER-A2NH TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1Z4 TCGA-FS-A1Z7 
       11.74         4.90         5.36         3.29        15.52         7.33 
TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZM TCGA-FS-A1ZS 
        7.30         3.39         8.22        19.53        47.38        49.15 
TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A266 TCGA-GN-A26A 
       14.20         0.99         9.90         7.23        10.13        12.16 
TCGA-GN-A4U9 
       10.65 

$subtype3
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A3MV 
       28.08        22.55        36.16        64.44       103.59         5.39 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-DA-A1I0 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-DA-A3F8 
       20.48        52.01        10.03        19.36        17.56        14.83 
TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 
        0.20        10.55         1.35        36.07        12.03        11.31 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A3AB 
       23.90        39.39        36.33         2.70       111.91       122.73 
TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC 
       15.95        16.14         0.46       114.15         2.20        20.38 
TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U8 
       30.87         0.20        84.72        11.84 

$subtype4
TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       45.83        30.87         7.50         6.31        92.42        45.11 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
       15.25        82.29        26.37        80.22        41.10        17.72 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ 
        8.84        13.94         6.97        23.11        22.06       142.45 
TCGA-D3-A8GL TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
       38.93         4.01        11.31        13.22        48.79        35.80 
TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F3 TCGA-EB-A44Q TCGA-EB-A5SG TCGA-EB-A5SH 
       39.19        44.52         7.00        13.15         0.00         0.00 
TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I 
        6.31         1.12         5.13         4.31         5.13         1.18 
TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A2GC 
       11.15         4.41         1.08         8.84         9.99        34.29 
TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GN TCGA-EE-A2GP 
       34.92        47.21        30.08        19.43        33.83         5.42 
TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK TCGA-EE-A2MP TCGA-EE-A2MU 
       13.02         9.53         7.96       111.78        26.99         5.56 
TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI 
        3.68        30.15        12.72        22.22        13.94        33.60 
TCGA-ER-A197 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q 
       12.95        11.11         4.21        28.60        34.68         9.57 
TCGA-ER-A19S TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD 
       36.07         6.58        22.49        18.41         3.58         4.70 
TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
       64.47         3.45        14.24        11.08         7.17        12.92 
TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ 
       52.08         8.65         8.68        27.39         0.82         5.23 
TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-GN-A262 TCGA-GN-A264 TCGA-GN-A268 
       53.85        28.73         5.98        24.85        31.33        15.42 
TCGA-HR-A2OH TCGA-OD-A75X 
       15.81        11.05 

subtype1 subtype2 subtype3 subtype4 
    0.13     0.13     0.20     0.00 
subtype1 subtype2 subtype3 subtype4 
  124.31   114.67   122.73   142.45 
subtype1 subtype2 subtype3 subtype4 
   13.22    15.19    19.87    13.58 
[1] "0.1 - 124.3 (13.2)" "0.1 - 114.7 (15.2)" "0.2 - 122.7 (19.9)"
[4] "0.0 - 142.4 (13.6)"
D8V2, survival
          sevent
clus2       0  1
  subtype1 35 41
  subtype2 37 37
  subtype3 20 15
  subtype4 50 44
subtype1 subtype2 subtype3 subtype4 
      76       74       35       94 
subtype1 subtype2 subtype3 subtype4 
      41       37       15       44 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1Q7 TCGA-D3-A2J6 TCGA-D3-A2J7 TCGA-D3-A2JB 
       16.57        16.67       133.25        43.43       103.10       168.00 
TCGA-D3-A3CC TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A5GL TCGA-D3-A8GB TCGA-D3-A8GM 
       86.93        24.53        13.87       110.93        30.84        95.24 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-DA-A1I2 
       54.67         3.65         3.25        11.11         9.90       176.55 
TCGA-DA-A1I4 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-EB-A5UL TCGA-EB-A5UN 
       35.93        65.92        23.44        68.09         3.55        52.01 
TCGA-EB-A6L9 TCGA-EE-A180 TCGA-EE-A183 TCGA-EE-A29B TCGA-EE-A29E TCGA-EE-A29G 
       12.20        94.98        26.89        80.61        39.62        72.07 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29V TCGA-EE-A29X TCGA-EE-A2A5 TCGA-EE-A2A6 
       44.35        18.61        25.87        17.92        39.29        58.75 
TCGA-EE-A2GD TCGA-EE-A2GL TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2ME 
      314.56        79.66        14.30        44.88        19.76       103.27 
TCGA-EE-A2MJ TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
       96.23       167.90        47.54        43.23       136.47        41.59 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AF TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3J7 
      124.31        25.84        13.81       127.20        36.95        64.08 
TCGA-EE-A3JD TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19L TCGA-ER-A2ND TCGA-ER-A2NE 
       27.35        50.76        48.89       131.51        23.34        20.15 
TCGA-ER-A2NF TCGA-ER-A2NG TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FS-A1YY TCGA-FS-A1Z0 
       16.37        31.27       247.04        33.21       228.59       202.65 
TCGA-FS-A1ZK TCGA-FS-A1ZR TCGA-FS-A1ZT TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TU 
       23.93        11.41        53.16        66.67        77.88        47.54 
TCGA-FW-A3TV TCGA-GN-A267 TCGA-GN-A26D TCGA-QB-A6FS 
        0.16        64.44        39.58         6.67 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      112.04       112.57        71.80        95.74        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C7 
      115.53        69.90        11.87        56.19       130.72        46.98 
TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A51F TCGA-D3-A51H TCGA-D3-A8GD 
       46.32        60.23         9.34        43.69        40.14        11.61 
TCGA-D3-A8GE TCGA-DA-A1HY TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-EB-A5KH TCGA-EB-A5VV 
       15.19       117.21        61.18        53.92        17.85         6.35 
TCGA-EE-A17X TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29Q 
       29.82       151.27       168.26        63.35        47.84        37.35 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO 
      345.96       171.55       102.90        54.74        75.48       101.95 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR 
       21.67       129.27        61.51       103.20       204.66       103.56 
TCGA-EE-A3J3 TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 TCGA-ER-A19A TCGA-ER-A19B 
      172.18        31.40        35.44         9.17        77.75        98.40 
TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A19W TCGA-ER-A1A1 
       12.59        13.02       152.35        44.05       148.18        79.99 
TCGA-ER-A2NC TCGA-ER-A2NH TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1Z4 
       43.82        32.05         4.90         7.00        94.39        28.08 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZM 
        7.79        27.72        48.85        53.52        40.27       101.26 
TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A266 
      148.80       174.84        22.92         9.90         7.23        10.13 
TCGA-GN-A26A TCGA-GN-A4U9 
       32.48        12.62 

$subtype3
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MR TCGA-D3-A3MV 
       28.08        31.59        42.08        66.08       103.59        21.47 
TCGA-D3-A51R TCGA-D3-A5GN TCGA-D9-A1JX TCGA-DA-A1I0 TCGA-DA-A3F2 TCGA-DA-A3F5 
       51.68       135.75         6.41        20.38        28.60       215.44 
TCGA-DA-A3F8 TCGA-EB-A44R TCGA-EE-A17Y TCGA-EE-A182 TCGA-EE-A20B TCGA-EE-A29P 
       15.68        10.16        27.22        14.70       109.64        56.42 
TCGA-EE-A2A0 TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML 
       46.82        24.43        47.54        94.82        28.83       203.05 
TCGA-EE-A3AB TCGA-EE-A3AG TCGA-EE-A3J8 TCGA-EE-A3JE TCGA-ER-A19G TCGA-FR-A8YC 
      122.73        23.47        34.32        33.40       268.93        34.82 
TCGA-FS-A1ZC TCGA-FS-A1ZH TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U8 
      357.37        32.75         0.20        84.72        46.36 

$subtype4
TCGA-D3-A1QA TCGA-D3-A2JF TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL TCGA-D3-A2JP 
       90.90        48.76       113.52        12.10       171.58        45.11 
TCGA-D3-A3C6 TCGA-D3-A3CB TCGA-D3-A3MU TCGA-D3-A51E TCGA-D3-A51J TCGA-D3-A51K 
       58.06       166.52        39.75       161.85       131.90        18.38 
TCGA-D3-A51N TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GJ 
       10.03        15.06         7.43       125.19        79.59       228.99 
TCGA-D3-A8GL TCGA-D9-A148 TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A6EA TCGA-D9-A6EC 
       89.13       151.53        18.12        11.34        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I5 TCGA-DA-A3F3 TCGA-EB-A44Q 
       48.89        36.03       194.83       107.34        10.49        13.87 
TCGA-EB-A5SG TCGA-EB-A5SH TCGA-EE-A17Z TCGA-EE-A181 TCGA-EE-A184 TCGA-EE-A185 
       45.11        35.01         8.65        33.73        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29R 
       78.87        13.55        13.97        32.19         2.60        14.47 
TCGA-EE-A29S TCGA-EE-A2GC TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GI TCGA-EE-A2GJ 
       55.92        67.43       135.95       208.04        48.72        89.33 
TCGA-EE-A2GN TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MK 
       90.97        13.91        55.59        47.28        16.96       144.76 
TCGA-EE-A2MP TCGA-EE-A2MU TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AH TCGA-EE-A3JA 
      248.65        53.26         3.68        54.51       138.81        53.19 
TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A19F TCGA-ER-A19J TCGA-ER-A19M 
      101.79       148.08        13.94        26.37         6.44        61.05 
TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A3YN 
      162.08        50.89        37.25        80.32        46.98        92.98 
TCGA-FR-A7U8 TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1YX TCGA-FS-A1Z3 TCGA-FS-A1ZF 
       15.16        29.46       216.92        48.59        20.91        15.45 
TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW 
        9.70        47.38        74.73       133.55        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-GN-A262 
       27.09        27.02        77.82        28.73        26.73       120.46 
TCGA-GN-A264 TCGA-GN-A268 TCGA-HR-A2OH TCGA-OD-A75X 
      117.93        62.79        65.88       294.77 

subtype1 subtype2 subtype3 subtype4 
    0.16     4.90     0.20     2.60 
subtype1 subtype2 subtype3 subtype4 
  314.56   345.96   357.37   294.77 
subtype1 subtype2 subtype3 subtype4 
  43.890   53.720   34.820   49.185 
[1] "0.2 - 314.6 (43.9)" "4.9 - 346.0 (53.7)" "0.2 - 357.4 (34.8)"
[4] "2.6 - 294.8 (49.2)"
D8V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 13             2
  subtype2                  8             0
  subtype3                  4             0
  subtype4                 16             2
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        15                  46
  subtype2                                        20                  50
  subtype3                                        11                  21
  subtype4                                        14                  62
D8V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                              13        8        4       16
  PRIMARY TUMOR                                    2        0        0        2
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       15       20       11       14
  REGIONAL LYMPH NODE                             46       50       21       62
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           1       3       5        2        6        5         4
  subtype2           3       3       9        2        7        3         1
  subtype3           1       0       1        1        1        3         2
  subtype4           5       0       7        6       11        5         2
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         4         4        10          5          5         15
  subtype2         4         2        10          3          3         17
  subtype3         1         1         3          1          9          4
  subtype4         6         3         7          4          9         14
          vv
clus       STAGE IV
  subtype1        1
  subtype2        2
  subtype3        4
  subtype4        6
D8V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        1        3        1        5
  STAGE 0            3        3        0        0
  STAGE I            5        9        1        7
  STAGE IA           2        2        1        6
  STAGE IB           6        7        1       11
  STAGE II           5        3        3        5
  STAGE IIA          4        1        2        2
  STAGE IIB          4        4        1        6
  STAGE IIC          4        2        1        3
  STAGE III         10       10        3        7
  STAGE IIIA         5        3        1        4
  STAGE IIIB         5        3        9        9
  STAGE IIIC        15       17        4       14
  STAGE IV           1        2        4        6
[1] 14  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    11 16 22 15
  subtype2    14 19  9 14
  subtype3     8  3 10  8
  subtype4    19 23 16 19
D8V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       11       14        8       19
  T2          16       19        3       23
  T3          22        9       10       16
  T4          15       14        8       19
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 35 15 11  9
  subtype2 39 13  7 13
  subtype3 13  8  8  4
  subtype4 55 15  8 12
D8V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       35       39       13       55
  N1       15       13        8       15
  N2       11        7        8        8
  N3        9       13        4       12
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 71  0   1   0   0
  subtype2 70  1   0   1   0
  subtype3 30  1   1   1   1
  subtype4 83  2   0   1   4
D8V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0        71       70       30       83
  M1         0        1        1        2
  M1A        1        0        1        0
  M1B        0        1        1        1
  M1C        0        0        1        4
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus        0  1
  subtype1 33 22
  subtype2 22 17
  subtype3 10 12
  subtype4 39 23
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   22
  subtype2   22   17
  subtype3   10   12
  subtype4   39   23
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        33       22       10       39
  YES       22       17       12       23
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V10, binary
          cls
clus        0  1
  subtype1  5 71
  subtype2 13 65
  subtype3  6 30
  subtype4 12 83
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   71
  subtype2   13   65
  subtype3    6   30
  subtype4   12   83
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO         5       13        6       12
  YES       71       65       30       83
[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"
D8V11, continuous
D8V12, binary
          cls
clus        0  1
  subtype1 25 51
  subtype2 27 51
  subtype3 12 24
  subtype4 41 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   25   51
  subtype2   27   51
  subtype3   12   24
  subtype4   41   54
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       25       27       12       41
  MALE         51       51       24       54
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     1                         1    74
  subtype2     1                         0    76
  subtype3     2                         0    34
  subtype4     1                         0    93
D8V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            1        1        2        1
  BLACK OR AFRICAN AMERICAN        1        0        0        0
  WHITE                           74       76       34       93
[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"
D8V14, binary
          cls
clus        0  1
  subtype1  0 75
  subtype2  2 73
  subtype3  0 35
  subtype4  2 92
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   75
  subtype2    2   73
  subtype3    0   35
  subtype4    2   92
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            0        2        0        2
  NOT HISPANIC OR LATINO       75       73       35       92
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 55 39
  subtype2 41 55
  subtype3 40 42
subtype1 subtype2 subtype3 
      94       96       82 
subtype1 subtype2 subtype3 
      39       55       42 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J9 
       16.47        32.42        28.08        22.55        81.24        21.14 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JO 
       68.22        69.90        11.41        30.87        36.16        64.44 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       46.98        82.29        13.32       103.59        26.37         5.39 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
       80.22        15.09        41.10         8.84        20.48        13.94 
TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D9-A6EA TCGA-DA-A1I0 TCGA-DA-A1I8 
       52.01        10.22        38.93        11.31        10.03        25.15 
TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH TCGA-EB-A5SG 
       17.56        14.83        13.15         0.20         0.13         0.00 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20C TCGA-EE-A29E TCGA-EE-A29P 
        0.20        11.57         1.35         4.34        38.63        12.03 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A2 TCGA-EE-A2A6 TCGA-EE-A2GB 
        8.09         6.48         8.09        23.90         8.94        39.39 
TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GU TCGA-EE-A2M6 TCGA-EE-A2M7 
       16.01        28.31        30.84        36.33        98.27         2.70 
TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MR TCGA-EE-A2MS 
        7.96       111.91        56.02        25.08        29.65        27.16 
TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG TCGA-EE-A3AH TCGA-EE-A3J8 
      122.73        25.84        30.15        15.95        12.72        16.14 
TCGA-EE-A3JD TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E TCGA-ER-A19G TCGA-ER-A19L 
       27.35         5.72        25.18        11.90       114.15        13.45 
TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A2NH TCGA-FR-A8YC TCGA-FR-A8YE 
       42.84        78.44        13.08        11.74         2.20         3.29 
TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       23.80        15.52         7.30        20.38         8.65         8.68 
TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A3TU TCGA-GF-A4EO TCGA-GN-A262 
       27.39        14.20         0.20         0.13         7.23        24.85 
TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X 
       84.72        14.70        11.84        11.05 

$subtype2
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
        8.52        45.83        10.29         7.50         6.31        92.42 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51K TCGA-D3-A5GS 
       45.11        15.25        24.00         6.31        17.72         6.97 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A3Z1 
       23.11        29.72        22.06       142.45        75.65         4.01 
TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW 
        2.89         5.72         9.90        13.22        48.79        35.80 
TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A5SH 
       13.68         4.93        22.36         6.64         7.00         0.00 
TCGA-EB-A5UN TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       13.22         6.31         8.12         1.12        12.20         5.13 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H 
        4.31         5.13         1.18         9.90        11.15         4.41 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ 
        1.08        27.12         9.50        34.29        30.08        19.43 
TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2MJ TCGA-EE-A2MK 
       35.54        33.83         1.15        34.98        63.42       111.78 
TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF 
       26.99        21.60        23.05       124.31         3.68        13.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 
       22.92        21.60        22.22        13.94        33.60        12.95 
TCGA-ER-A198 TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S 
       38.40         3.78        11.11        34.68         9.57        36.07 
TCGA-ER-A2ND TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 
        1.87         1.51         9.04         1.71        18.41         3.58 
TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ 
        4.70        64.47        14.24        11.08         7.17        12.92 
TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 
       12.89        52.08        40.64         0.82         5.23        53.85 
TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-GN-A267 TCGA-GN-A268 TCGA-HR-A2OH TCGA-QB-A6FS 
       28.73         5.98        16.24        15.42        15.81         5.79 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
      111.09        70.16       110.79        85.32         8.38        88.50 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51F 
       56.19       114.67        46.32        61.38         9.34        42.71 
TCGA-D3-A5GL TCGA-D3-A8GE TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
       95.38        15.19        51.12        39.19         9.99        44.52 
TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       36.69        19.36        10.55        36.07         9.21         7.99 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       37.97         8.55         8.84         9.99         2.43         8.68 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       11.31        49.22         9.67        17.98        34.92        47.21 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
        5.42        13.02         8.84         6.18        47.51         9.53 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J7 
       29.46        44.25        14.56         5.56         3.22        21.60 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19H 
        0.46        31.40        18.61        76.41         3.52        34.88 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ET 
        4.21        28.60        17.72        11.80        12.62         6.58 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       22.49         4.90         5.36         3.45        11.01         7.33 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
        3.39         8.22        19.53        30.87        47.38         8.81 
TCGA-FS-A1ZS TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A3OT 
       49.15         7.36         2.27         0.99         0.16         9.90 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 
       31.33        10.13        12.16        10.65 

subtype1 subtype2 subtype3 
    0.00     0.00     0.16 
subtype1 subtype2 subtype3 
  122.73   142.45   114.67 
subtype1 subtype2 subtype3 
  16.305   13.220   12.820 
[1] "0.0 - 122.7 (16.3)" "0.0 - 142.4 (13.2)" "0.2 - 114.7 (12.8)"
D9V2, survival
          sevent
clus2       0  1
  subtype1 56 40
  subtype2 46 55
  subtype3 40 42
subtype1 subtype2 subtype3 
      96      101       82 
subtype1 subtype2 subtype3 
      40       55       42 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q5 TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A1QB TCGA-D3-A2J9 
       16.57       112.57        28.08        31.59        95.74        23.77 
TCGA-D3-A2JB TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JH TCGA-D3-A2JO 
      168.00        69.90        11.87        48.76        42.08        66.08 
TCGA-D3-A3C7 TCGA-D3-A3CB TCGA-D3-A3CE TCGA-D3-A3MR TCGA-D3-A3MU TCGA-D3-A3MV 
       46.98       166.52        60.23       103.59        39.75        21.47 
TCGA-D3-A51E TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A51R TCGA-D3-A51T 
      161.85        40.14       131.90        10.03        51.68        15.06 
TCGA-D3-A5GN TCGA-D3-A8GD TCGA-D3-A8GL TCGA-D9-A1JX TCGA-D9-A6EA TCGA-DA-A1I0 
      135.75        11.61        89.13         6.41        25.18        20.38 
TCGA-DA-A1I8 TCGA-DA-A3F5 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A44R TCGA-EB-A5KH 
       53.92       215.44        15.68        13.87        10.16        17.85 
TCGA-EB-A5SG TCGA-EB-A5VV TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A182 TCGA-EE-A20C 
       45.11         6.35        12.20        29.82        14.70       151.27 
TCGA-EE-A29E TCGA-EE-A29P TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29X TCGA-EE-A2A2 
       39.62        56.42        37.35       345.96        17.92        24.43 
TCGA-EE-A2A6 TCGA-EE-A2GB TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO TCGA-EE-A2GU 
       58.75        47.54        54.74        75.48       101.95        94.82 
TCGA-EE-A2M6 TCGA-EE-A2M7 TCGA-EE-A2MH TCGA-EE-A2ML TCGA-EE-A2MM TCGA-EE-A2MN 
      129.27        28.83        16.96       203.05       167.90        47.54 
TCGA-EE-A2MR TCGA-EE-A2MS TCGA-EE-A3AB TCGA-EE-A3AC TCGA-EE-A3AE TCGA-EE-A3AG 
      103.56       136.47       122.73        25.84        54.51        23.47 
TCGA-EE-A3AH TCGA-EE-A3J8 TCGA-EE-A3JD TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19E 
      138.81        34.32        27.35         9.17        98.40        13.02 
TCGA-ER-A19G TCGA-ER-A19L TCGA-ER-A19N TCGA-ER-A1A1 TCGA-ER-A2NF TCGA-ER-A2NH 
      268.93       131.51        44.05        79.99        16.37        32.05 
TCGA-FR-A8YC TCGA-FR-A8YE TCGA-FS-A1Z0 TCGA-FS-A1Z4 TCGA-FS-A1ZA TCGA-FS-A1ZC 
       34.82        94.39       202.65        28.08        27.72       357.37 
TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW TCGA-FS-A4F8 TCGA-FW-A3I3 TCGA-FW-A3TU 
      133.55        26.56        49.48       174.84         0.20        47.54 
TCGA-GF-A4EO TCGA-GN-A262 TCGA-GN-A265 TCGA-GN-A26D TCGA-GN-A4U8 TCGA-OD-A75X 
        7.23       120.46        84.72        39.58        46.36       294.77 

$subtype2
TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JG TCGA-D3-A2JK TCGA-D3-A2JL 
       16.67        90.90        43.43       113.52        12.10       171.58 
TCGA-D3-A2JP TCGA-D3-A3C6 TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51K TCGA-D3-A5GS 
       45.11        58.06        24.53        13.87        18.38         7.43 
TCGA-D3-A5GU TCGA-D3-A8GB TCGA-D3-A8GC TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A148 
      125.19        30.84        79.59       228.99        95.24       151.53 
TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 
       54.67         3.65        18.12        11.34         3.25        11.11 
TCGA-D9-A6E9 TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I2 TCGA-DA-A1IA 
        9.90        66.25        48.89        36.03       176.55        65.92 
TCGA-DA-A1IB TCGA-DA-A1IC TCGA-DA-A3F3 TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A5UN 
       23.44        68.09        10.49        35.01         3.55        52.01 
TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 TCGA-EE-A185 
        8.65        94.98        33.73        26.89        68.15         4.96 
TCGA-EE-A20F TCGA-EE-A20I TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29H TCGA-EE-A29L 
       78.87        13.55        80.61        13.97        32.19         2.60 
TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL 
       44.35        18.61        67.43        48.72        89.33        79.66 
TCGA-EE-A2GN TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2MJ TCGA-EE-A2MK TCGA-EE-A2MP 
       90.97        14.30        44.88        96.23       144.76       248.65 
TCGA-EE-A2MQ TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AD TCGA-EE-A3AF TCGA-EE-A3J4 
       43.23        41.59       124.31         3.68        13.81       127.20 
TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JH TCGA-EE-A3JI TCGA-ER-A197 TCGA-ER-A198 
       36.95        53.19       101.79       148.08        13.94        50.76 
TCGA-ER-A19C TCGA-ER-A19F TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19S TCGA-ER-A2ND 
       48.89        26.37       162.08        50.89        37.25        23.34 
TCGA-ER-A2NE TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A7U8 TCGA-FR-A8YD 
       20.15       247.04        33.21        92.98        15.16        29.46 
TCGA-FS-A1YW TCGA-FS-A1Z3 TCGA-FS-A1ZF TCGA-FS-A1ZG TCGA-FS-A1ZJ TCGA-FS-A1ZK 
      216.92        20.91        15.45         9.70        47.38        23.93 
TCGA-FS-A1ZP TCGA-FS-A1ZT TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 
       74.73        53.16        27.09        27.02        77.82        28.73 
TCGA-FS-A4FB TCGA-GN-A267 TCGA-GN-A268 TCGA-HR-A2OH TCGA-QB-A6FS 
       26.73        64.44        62.79        65.88         6.67 

$subtype3
TCGA-D3-A1Q4 TCGA-D3-A1Q6 TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2J8 TCGA-D3-A2JA 
      112.04        71.80       133.25       103.10        65.49       115.53 
TCGA-D3-A2JN TCGA-D3-A3BZ TCGA-D3-A3C8 TCGA-D3-A3CC TCGA-D3-A3MO TCGA-D3-A51F 
       56.19       130.72        46.32        86.93         9.34        43.69 
TCGA-D3-A5GL TCGA-D3-A8GE TCGA-DA-A1HY TCGA-DA-A1I1 TCGA-DA-A1I4 TCGA-DA-A1I5 
      110.93        15.19       117.21       194.83        35.93       107.34 
TCGA-DA-A1I7 TCGA-DA-A3F2 TCGA-EE-A17Y TCGA-EE-A20B TCGA-EE-A20H TCGA-EE-A29A 
       61.18        28.60        27.22       109.64       168.26        63.35 
TCGA-EE-A29C TCGA-EE-A29G TCGA-EE-A29R TCGA-EE-A29S TCGA-EE-A29V TCGA-EE-A29W 
       47.84        72.07        14.47        55.92        25.87       171.55 
TCGA-EE-A2A0 TCGA-EE-A2A1 TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH 
       46.82       102.90        39.29       314.56       135.95       208.04 
TCGA-EE-A2GP TCGA-EE-A2GS TCGA-EE-A2M5 TCGA-EE-A2M8 TCGA-EE-A2MC TCGA-EE-A2MD 
       13.91        55.59        21.67        19.76        61.51        47.28 
TCGA-EE-A2ME TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MU TCGA-EE-A3J3 TCGA-EE-A3J7 
      103.27       103.20       204.66        53.26       172.18        64.08 
TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A19A TCGA-ER-A19D TCGA-ER-A19H 
       33.40        31.40        35.44        77.75        12.59       152.35 
TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19W TCGA-ER-A2NC TCGA-ER-A2NG TCGA-ER-A3ET 
        6.44        61.05       148.18        43.82        31.27        80.32 
TCGA-ER-A3EV TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FS-A1YX TCGA-FS-A1YY TCGA-FS-A1Z7 
       46.98         4.90         7.00        48.59       228.59         7.79 
TCGA-FS-A1ZB TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM TCGA-FS-A1ZR 
       48.85        53.52        40.27        32.75       101.26        11.41 
TCGA-FS-A1ZS TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3R5 TCGA-FW-A3TV TCGA-GF-A3OT 
      148.80        66.67        77.88        22.92         0.16         9.90 
TCGA-GN-A264 TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 
      117.93        10.13        32.48        12.62 

subtype1 subtype2 subtype3 
    0.20     2.60     0.16 
subtype1 subtype2 subtype3 
  357.37   248.65   314.56 
subtype1 subtype2 subtype3 
  47.260   43.430   55.755 
[1] "0.2 - 357.4 (47.3)" "2.6 - 248.7 (43.4)" "0.2 - 314.6 (55.8)"
D9V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 12             2
  subtype2                 18             2
  subtype3                 11             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        17                  68
  subtype2                                        12                  68
  subtype3                                        31                  43
D9V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3
  DISTANT METASTASIS                              12       18       11
  PRIMARY TUMOR                                    2        2        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       17       12       31
  REGIONAL LYMPH NODE                             68       68       43
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           6       3       8        7        3        5         1
  subtype2           2       2       5        3       11        6         3
  subtype3           2       1       9        1       11        5         5
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         2         4        12          2         11         18
  subtype2         9         4        10          6         10         16
  subtype3         4         2         8          5          5         16
          vv
clus       STAGE IV
  subtype1        4
  subtype2        4
  subtype3        5
D9V5, multiclass
             clus
vv            subtype1 subtype2 subtype3
  I OR II NOS        6        2        2
  STAGE 0            3        2        1
  STAGE I            8        5        9
  STAGE IA           7        3        1
  STAGE IB           3       11       11
  STAGE II           5        6        5
  STAGE IIA          1        3        5
  STAGE IIB          2        9        4
  STAGE IIC          4        4        2
  STAGE III         12       10        8
  STAGE IIIA         2        6        5
  STAGE IIIB        11       10        5
  STAGE IIIC        18       16       16
  STAGE IV           4        4        5
[1] 14  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    28 12 12 21
  subtype2    17 19 24 23
  subtype3     7 30 21 12
D9V6, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       28       17        7
  T2          12       19       30
  T3          12       24       21
  T4          21       23       12
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 43 16 12 17
  subtype2 53 19 13 11
  subtype3 46 16  9 10
D9V7, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       43       53       46
  N1       16       19       16
  N2       12       13        9
  N3       17       11       10
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       M0 M1 M1A M1B M1C
  subtype1 86  1   1   1   1
  subtype2 93  1   1   1   2
  subtype3 75  2   0   1   2
D9V8, multiclass
     clus
vv    subtype1 subtype2 subtype3
  M0        86       93       75
  M1         1        1        2
  M1A        1        1        0
  M1B        1        1        1
  M1C        1        2        2
[1] 5 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V9, binary
          cls
clus        0  1
  subtype1 31 25
  subtype2 42 27
  subtype3 31 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   25
  subtype2   42   27
  subtype3   31   22
     clus
vv    subtype1 subtype2 subtype3
  NO        31       42       31
  YES       25       27       22
[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"
D9V10, binary
          cls
clus        0  1
  subtype1 17 82
  subtype2 11 90
  subtype3  8 77
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   82
  subtype2   11   90
  subtype3    8   77
     clus
vv    subtype1 subtype2 subtype3
  NO        17       11        8
  YES       82       90       77
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V11, continuous
D9V12, binary
          cls
clus        0  1
  subtype1 41 58
  subtype2 38 63
  subtype3 26 59
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   41   58
  subtype2   38   63
  subtype3   26   59
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       41       38       26
  MALE         58       63       59
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     4                         1    94
  subtype2     0                         0   100
  subtype3     1                         0    83
D9V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                            4        0        1
  BLACK OR AFRICAN AMERICAN        1        0        0
  WHITE                           94      100       83
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V14, binary
          cls
clus        0  1
  subtype1  0 98
  subtype2  2 98
  subtype3  2 79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   98
  subtype2    2   98
  subtype3    2   79
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            0        2        2
  NOT HISPANIC OR LATINO       98       98       79
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2       0  1
  subtype1 57 57
  subtype2 44 37
  subtype3 21 32
  subtype4 14 10
subtype1 subtype2 subtype3 subtype4 
     114       81       53       24 
subtype1 subtype2 subtype3 subtype4 
      57       37       32       10 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JG 
       16.47         8.52        45.83        10.29        68.22         7.50 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E 
       92.42        45.11        82.29        24.00         6.31        80.22 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       17.72        13.94         6.97        23.11        22.06        10.22 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 
      142.45        75.65         4.01         2.89         5.72         9.90 
TCGA-D9-A6EA TCGA-D9-A6EC TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 
       11.31        13.22        48.79        35.80        39.19        13.68 
TCGA-DA-A1IA TCGA-DA-A1IB TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SH 
        4.93        22.36         7.00        14.83        13.15         0.00 
TCGA-EB-A6L9 TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 
        0.20        11.57         6.31         8.12         1.12        12.20 
TCGA-EE-A184 TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E 
        5.13         4.31         5.13         9.90        11.15        38.63 
TCGA-EE-A29H TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29X 
        4.41         1.08        27.12         9.50         8.84         8.09 
TCGA-EE-A2A6 TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN 
        8.94        34.29        30.08        19.43        35.54        33.83 
TCGA-EE-A2GR TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MJ 
        1.15        34.98         6.18         9.53         7.96        63.42 
TCGA-EE-A2MK TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS 
      111.78        56.02        25.08        26.99        21.60        27.16 
TCGA-EE-A2MT TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF 
       23.05       124.31        25.84         3.68        30.15        13.81 
TCGA-EE-A3AH TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JI 
       12.72        22.92        21.60        22.22        27.35        33.60 
TCGA-ER-A198 TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A2NE TCGA-ER-A2NF 
       38.40        11.11        13.45        36.07         1.51        13.08 
TCGA-ER-A3ES TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 
        9.04         1.71        18.41         4.70        64.47        23.80 
TCGA-FS-A1Z3 TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU 
       14.24         7.17        12.89        52.08         8.65         8.68 
TCGA-FS-A1ZW TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB 
       27.39         0.82         5.23        53.85        28.73         5.98 
TCGA-FW-A3TU TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26D TCGA-HR-A2OH TCGA-QB-A6FS 
        0.13        24.85        15.42        14.70        15.81         5.79 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      111.09        32.42        70.16        81.24         8.38        21.14 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A3BZ 
       88.50        69.90        11.41        30.87        56.19       114.67 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51F 
       46.98        46.32        13.32         9.34       103.59        42.71 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A8GE TCGA-D3-A8GL TCGA-DA-A1HY 
       15.09        41.10         8.84        15.19        38.93        51.12 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SG 
       36.69        25.15        19.36        17.56         0.13         0.00 
TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C TCGA-EE-A29Q 
       10.55         4.34         9.21         7.99        37.97         8.09 
TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GM TCGA-EE-A2GO 
        6.48         8.68        49.22        16.01        28.31        30.84 
TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI TCGA-EE-A2MR 
        8.84        98.27        47.51        44.25        14.56        29.65 
TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 TCGA-ER-A199 
      122.73         3.22         0.46        31.40        18.61         5.72 
TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19N TCGA-ER-A1A1 
       25.18         3.52        11.90        34.88        42.84        78.44 
TCGA-ER-A2NC TCGA-ER-A2NH TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE TCGA-FS-A1Z4 
       11.80        11.74         4.90         5.36         3.29        15.52 
TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH TCGA-FS-A1ZM 
        7.33         7.30         8.22        19.53        30.87        47.38 
TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GF-A4EO TCGA-GN-A266 
       49.15        14.20         0.99         9.90         7.23        10.13 
TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       12.16        10.65        11.05 

$subtype3
TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU 
      110.79        85.32         6.31        15.25        61.38        26.37 
TCGA-D3-A5GL TCGA-D3-A8GB TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC 
       95.38        29.72        10.03         9.99        44.52         6.64 
TCGA-EB-A5UN TCGA-EE-A182 TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29S TCGA-EE-A29V 
       13.22         1.35         1.18         8.55         9.99         2.43 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS 
        9.67        17.98        34.92        47.21         5.42        13.02 
TCGA-EE-A2ME TCGA-EE-A2MU TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19A 
       29.46         5.56        21.60        13.94        12.95        76.41 
TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
        3.78         4.21        28.60        34.68         9.57        17.72 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YX 
        1.87        12.62         6.58        22.49         3.58         3.45 
TCGA-FS-A1YY TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZR TCGA-FS-A1ZT 
       11.01         3.39        11.08        12.92         8.81        40.64 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 
        7.36         2.27         0.16        31.33        16.24 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MV TCGA-D3-A51R 
       28.08        22.55        36.16        64.44         5.39        20.48 
TCGA-D3-A5GN TCGA-EB-A44R TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 TCGA-EE-A2A2 
       52.01         0.20        36.07        12.03        11.31        23.90 
TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A3AG TCGA-EE-A3J8 
       39.39        36.33         2.70       111.91        15.95        16.14 
TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FW-A3I3 TCGA-GN-A265 TCGA-GN-A4U8 
      114.15         2.20        20.38         0.20        84.72        11.84 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.00     0.16     0.20 
subtype1 subtype2 subtype3 subtype4 
  142.45   122.73   110.79   114.15 
subtype1 subtype2 subtype3 subtype4 
  13.875   16.010   12.620   21.515 
[1] "0.0 - 142.4 (13.9)" "0.0 - 122.7 (16.0)" "0.2 - 110.8 (12.6)"
[4] "0.2 - 114.2 (21.5)"
D10V2, survival
          sevent
clus2       0  1
  subtype1 62 57
  subtype2 45 37
  subtype3 21 32
  subtype4 14 11
subtype1 subtype2 subtype3 subtype4 
     119       82       53       25 
subtype1 subtype2 subtype3 subtype4 
      57       37       32       11 
$subtype1
TCGA-D3-A1Q1 TCGA-D3-A1Q3 TCGA-D3-A1QA TCGA-D3-A2J6 TCGA-D3-A2JB TCGA-D3-A2JG 
       16.57        16.67        90.90        43.43       168.00       113.52 
TCGA-D3-A2JL TCGA-D3-A2JP TCGA-D3-A3CB TCGA-D3-A3CF TCGA-D3-A3ML TCGA-D3-A51E 
      171.58        45.11       166.52        24.53        13.87       161.85 
TCGA-D3-A51K TCGA-D3-A51T TCGA-D3-A5GS TCGA-D3-A5GU TCGA-D3-A8GC TCGA-D3-A8GD 
       18.38        15.06         7.43       125.19        79.59        11.61 
TCGA-D3-A8GJ TCGA-D3-A8GM TCGA-D9-A148 TCGA-D9-A149 TCGA-D9-A1JW TCGA-D9-A1X3 
      228.99        95.24       151.53        54.67         3.65        18.12 
TCGA-D9-A3Z1 TCGA-D9-A3Z3 TCGA-D9-A4Z6 TCGA-D9-A6E9 TCGA-D9-A6EA TCGA-D9-A6EC 
       11.34         3.25        11.11         9.90        25.18        66.25 
TCGA-DA-A1HV TCGA-DA-A1HW TCGA-DA-A1I1 TCGA-DA-A1I2 TCGA-DA-A1IA TCGA-DA-A1IB 
       48.89        36.03       194.83       176.55        65.92        23.44 
TCGA-DA-A3F3 TCGA-DA-A3F8 TCGA-EB-A44Q TCGA-EB-A5SH TCGA-EB-A5UL TCGA-EB-A6L9 
       10.49        15.68        13.87        35.01         3.55        12.20 
TCGA-EE-A17X TCGA-EE-A17Z TCGA-EE-A180 TCGA-EE-A181 TCGA-EE-A183 TCGA-EE-A184 
       29.82         8.65        94.98        33.73        26.89        68.15 
TCGA-EE-A185 TCGA-EE-A20F TCGA-EE-A29B TCGA-EE-A29D TCGA-EE-A29E TCGA-EE-A29H 
        4.96        78.87        80.61        13.97        39.62        32.19 
TCGA-EE-A29L TCGA-EE-A29M TCGA-EE-A29N TCGA-EE-A29R TCGA-EE-A29X TCGA-EE-A2A6 
        2.60        44.35        18.61        14.47        17.92        58.75 
TCGA-EE-A2GC TCGA-EE-A2GI TCGA-EE-A2GJ TCGA-EE-A2GL TCGA-EE-A2GN TCGA-EE-A2GR 
       67.43        48.72        89.33        79.66        90.97        14.30 
TCGA-EE-A2GT TCGA-EE-A2M8 TCGA-EE-A2MD TCGA-EE-A2MH TCGA-EE-A2MJ TCGA-EE-A2MK 
       44.88        19.76        47.28        16.96        96.23       144.76 
TCGA-EE-A2MM TCGA-EE-A2MN TCGA-EE-A2MP TCGA-EE-A2MQ TCGA-EE-A2MS TCGA-EE-A2MT 
      167.90        47.54       248.65        43.23       136.47        41.59 
TCGA-EE-A3AA TCGA-EE-A3AC TCGA-EE-A3AD TCGA-EE-A3AE TCGA-EE-A3AF TCGA-EE-A3AH 
      124.31        25.84         3.68        54.51        13.81       138.81 
TCGA-EE-A3J4 TCGA-EE-A3J5 TCGA-EE-A3JA TCGA-EE-A3JD TCGA-EE-A3JI TCGA-ER-A198 
      127.20        36.95        53.19        27.35       148.08        50.76 
TCGA-ER-A19F TCGA-ER-A19L TCGA-ER-A19S TCGA-ER-A2NE TCGA-ER-A2NF TCGA-ER-A3ES 
       26.37       131.51        37.25        20.15        16.37       247.04 
TCGA-ER-A3PL TCGA-FR-A3YN TCGA-FR-A8YD TCGA-FS-A1YW TCGA-FS-A1Z0 TCGA-FS-A1Z3 
       33.21        92.98        29.46       216.92       202.65        20.91 
TCGA-FS-A1ZG TCGA-FS-A1ZK TCGA-FS-A1ZP TCGA-FS-A1ZQ TCGA-FS-A1ZU TCGA-FS-A1ZW 
        9.70        23.93        74.73       133.55        26.56        49.48 
TCGA-FS-A1ZY TCGA-FS-A1ZZ TCGA-FS-A4F0 TCGA-FS-A4F5 TCGA-FS-A4FB TCGA-FW-A3TU 
       27.09        27.02        77.82        28.73        26.73        47.54 
TCGA-GN-A262 TCGA-GN-A268 TCGA-GN-A26D TCGA-HR-A2OH TCGA-QB-A6FS 
      120.46        62.79        39.58        65.88         6.67 

$subtype2
TCGA-D3-A1Q4 TCGA-D3-A1Q5 TCGA-D3-A1Q6 TCGA-D3-A1QB TCGA-D3-A2J8 TCGA-D3-A2J9 
      112.04       112.57        71.80        95.74        65.49        23.77 
TCGA-D3-A2JA TCGA-D3-A2JC TCGA-D3-A2JD TCGA-D3-A2JF TCGA-D3-A2JN TCGA-D3-A3BZ 
      115.53        69.90        11.87        48.76        56.19       130.72 
TCGA-D3-A3C7 TCGA-D3-A3C8 TCGA-D3-A3CE TCGA-D3-A3MO TCGA-D3-A3MR TCGA-D3-A51F 
       46.98        46.32        60.23         9.34       103.59        43.69 
TCGA-D3-A51H TCGA-D3-A51J TCGA-D3-A51N TCGA-D3-A8GE TCGA-D3-A8GL TCGA-DA-A1HY 
       40.14       131.90        10.03        15.19        89.13       117.21 
TCGA-DA-A1I7 TCGA-DA-A1I8 TCGA-DA-A3F2 TCGA-DA-A3F5 TCGA-EB-A5KH TCGA-EB-A5SG 
       61.18        53.92        28.60       215.44        17.85        45.11 
TCGA-EB-A5VV TCGA-EE-A17Y TCGA-EE-A20C TCGA-EE-A20H TCGA-EE-A29A TCGA-EE-A29C 
        6.35        27.22       151.27       168.26        63.35        47.84 
TCGA-EE-A29Q TCGA-EE-A29T TCGA-EE-A29W TCGA-EE-A2A1 TCGA-EE-A2GK TCGA-EE-A2GM 
       37.35       345.96       171.55       102.90        54.74        75.48 
TCGA-EE-A2GO TCGA-EE-A2M5 TCGA-EE-A2M6 TCGA-EE-A2MC TCGA-EE-A2MG TCGA-EE-A2MI 
      101.95        21.67       129.27        61.51       103.20       204.66 
TCGA-EE-A2MR TCGA-EE-A3AB TCGA-EE-A3J3 TCGA-EE-A3JE TCGA-ER-A193 TCGA-ER-A195 
      103.56       122.73       172.18        33.40        31.40        35.44 
TCGA-ER-A199 TCGA-ER-A19B TCGA-ER-A19D TCGA-ER-A19E TCGA-ER-A19H TCGA-ER-A19N 
        9.17        98.40        12.59        13.02       152.35        44.05 
TCGA-ER-A1A1 TCGA-ER-A2NC TCGA-ER-A2NH TCGA-FR-A69P TCGA-FR-A7U9 TCGA-FR-A8YE 
       79.99        43.82        32.05         4.90         7.00        94.39 
TCGA-FS-A1Z4 TCGA-FS-A1Z7 TCGA-FS-A1ZA TCGA-FS-A1ZD TCGA-FS-A1ZE TCGA-FS-A1ZH 
       28.08         7.79        27.72        53.52        40.27        32.75 
TCGA-FS-A1ZM TCGA-FS-A1ZS TCGA-FS-A4F8 TCGA-FW-A3R5 TCGA-GF-A3OT TCGA-GF-A4EO 
      101.26       148.80       174.84        22.92         9.90         7.23 
TCGA-GN-A266 TCGA-GN-A26A TCGA-GN-A4U9 TCGA-OD-A75X 
       10.13        32.48        12.62       294.77 

$subtype3
TCGA-D3-A1Q7 TCGA-D3-A2J7 TCGA-D3-A2JK TCGA-D3-A3C6 TCGA-D3-A3CC TCGA-D3-A3MU 
      133.25       103.10        12.10        58.06        86.93        39.75 
TCGA-D3-A5GL TCGA-D3-A8GB TCGA-DA-A1I0 TCGA-DA-A1I4 TCGA-DA-A1I5 TCGA-DA-A1IC 
      110.93        30.84        20.38        35.93       107.34        68.09 
TCGA-EB-A5UN TCGA-EE-A182 TCGA-EE-A20I TCGA-EE-A29G TCGA-EE-A29S TCGA-EE-A29V 
       52.01        14.70        13.55        72.07        55.92        25.87 
TCGA-EE-A2A5 TCGA-EE-A2GD TCGA-EE-A2GE TCGA-EE-A2GH TCGA-EE-A2GP TCGA-EE-A2GS 
       39.29       314.56       135.95       208.04        13.91        55.59 
TCGA-EE-A2ME TCGA-EE-A2MU TCGA-EE-A3J7 TCGA-EE-A3JH TCGA-ER-A197 TCGA-ER-A19A 
      103.27        53.26        64.08       101.79        13.94        77.75 
TCGA-ER-A19C TCGA-ER-A19J TCGA-ER-A19M TCGA-ER-A19P TCGA-ER-A19Q TCGA-ER-A19W 
       48.89         6.44        61.05       162.08        50.89       148.18 
TCGA-ER-A2ND TCGA-ER-A2NG TCGA-ER-A3ET TCGA-ER-A3EV TCGA-FR-A7U8 TCGA-FS-A1YX 
       23.34        31.27        80.32        46.98        15.16        48.59 
TCGA-FS-A1YY TCGA-FS-A1ZB TCGA-FS-A1ZF TCGA-FS-A1ZJ TCGA-FS-A1ZR TCGA-FS-A1ZT 
      228.59        48.85        15.45        47.38        11.41        53.16 
TCGA-FS-A4F4 TCGA-FS-A4FD TCGA-FW-A3TV TCGA-GN-A264 TCGA-GN-A267 
       66.67        77.88         0.16       117.93        64.44 

$subtype4
TCGA-D3-A1Q8 TCGA-D3-A1Q9 TCGA-D3-A2JH TCGA-D3-A2JO TCGA-D3-A3MV TCGA-D3-A51R 
       28.08        31.59        42.08        66.08        21.47        51.68 
TCGA-D3-A5GN TCGA-D9-A1JX TCGA-EB-A44R TCGA-EE-A20B TCGA-EE-A29P TCGA-EE-A2A0 
      135.75         6.41        10.16       109.64        56.42        46.82 
TCGA-EE-A2A2 TCGA-EE-A2GB TCGA-EE-A2GU TCGA-EE-A2M7 TCGA-EE-A2ML TCGA-EE-A3AG 
       24.43        47.54        94.82        28.83       203.05        23.47 
TCGA-EE-A3J8 TCGA-ER-A19G TCGA-FR-A8YC TCGA-FS-A1ZC TCGA-FW-A3I3 TCGA-GN-A265 
       34.32       268.93        34.82       357.37         0.20        84.72 
TCGA-GN-A4U8 
       46.36 

subtype1 subtype2 subtype3 subtype4 
    2.60     4.90     0.16     0.20 
subtype1 subtype2 subtype3 subtype4 
  248.65   345.96   314.56   357.37 
subtype1 subtype2 subtype3 subtype4 
   41.59    53.72    53.26    46.36 
[1] "2.6 - 248.7 (41.6)" "4.9 - 346.0 (53.7)" "0.2 - 314.6 (53.3)"
[4] "0.2 - 357.4 (46.4)"
D10V3, continuous
          vv
clus       DISTANT METASTASIS PRIMARY TUMOR
  subtype1                 17             4
  subtype2                  9             0
  subtype3                 12             0
  subtype4                  3             0
          vv
clus       REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE REGIONAL LYMPH NODE
  subtype1                                        13                  85
  subtype2                                        24                  53
  subtype3                                        17                  25
  subtype4                                         6                  16
D10V4, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  DISTANT METASTASIS                              17        9       12        3
  PRIMARY TUMOR                                    4        0        0        0
  REGIONAL CUTANEOUS OR SUBCUTANEOUS TISSUE       13       24       17        6
  REGIONAL LYMPH NODE                             85       53       25       16
[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       I OR II NOS STAGE 0 STAGE I STAGE IA STAGE IB STAGE II STAGE IIA
  subtype1           5       3       5        7       10        9         3
  subtype2           3       3       9        2        7        2         1
  subtype3           1       0       7        1        7        2         3
  subtype4           1       0       1        1        1        3         2
          vv
clus       STAGE IIB STAGE IIC STAGE III STAGE IIIA STAGE IIIB STAGE IIIC
  subtype1         9         4        13          5         10         22
  subtype2         4         2        13          3          7         17
  subtype3         1         3         3          4          5          9
  subtype4         1         1         1          1          4          2
          vv
clus       STAGE IV
  subtype1        3
  subtype2        3
  subtype3        5
  subtype4        2
D10V5, multiclass
             clus
vv            subtype1 subtype2 subtype3 subtype4
  I OR II NOS        5        3        1        1
  STAGE 0            3        3        0        0
  STAGE I            5        9        7        1
  STAGE IA           7        2        1        1
  STAGE IB          10        7        7        1
  STAGE II           9        2        2        3
  STAGE IIA          3        1        3        2
  STAGE IIB          9        4        1        1
  STAGE IIC          4        2        3        1
  STAGE III         13       13        3        1
  STAGE IIIA         5        3        4        1
  STAGE IIIB        10        7        5        4
  STAGE IIIC        22       17        9        2
  STAGE IV           3        3        5        2
[1] 14  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    23 21 28 25
  subtype2    19 20 11 14
  subtype3     5 18 12 12
  subtype4     5  2  6  5
D10V6, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       23       19        5        5
  T2          21       20       18        2
  T3          28       11       12        6
  T4          25       14       12        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 63 20 14 16
  subtype2 37 18 10 14
  subtype3 29 10  6  6
  subtype4 13  3  4  2
D10V7, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       63       37       29       13
  N1       20       18       10        3
  N2       14       10        6        4
  N3       16       14        6        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        M0  M1 M1A M1B M1C
  subtype1 108   1   1   1   1
  subtype2  77   0   0   1   2
  subtype3  48   2   1   0   2
  subtype4  21   1   0   1   0
D10V8, multiclass
     clus
vv    subtype1 subtype2 subtype3 subtype4
  M0       108       77       48       21
  M1         1        0        2        1
  M1A        1        0        1        0
  M1B        1        1        0        1
  M1C        1        2        2        0
[1] 5 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus        0  1
  subtype1 48 32
  subtype2 23 19
  subtype3 25 16
  subtype4  8  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   48   32
  subtype2   23   19
  subtype3   25   16
  subtype4    8    7
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        48       23       25        8
  YES       32       19       16        7
[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"
D10V10, binary
          cls
clus         0   1
  subtype1  13 106
  subtype2  16  70
  subtype3   3  52
  subtype4   4  21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13  106
  subtype2   16   70
  subtype3    3   52
  subtype4    4   21
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        13       16        3        4
  YES      106       70       52       21
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
D10V12, binary
          cls
clus        0  1
  subtype1 47 72
  subtype2 28 58
  subtype3 20 35
  subtype4 10 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47   72
  subtype2   28   58
  subtype3   20   35
  subtype4   10   15
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       47       28       20       10
  MALE         72       58       35       15
[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       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1     2                         1   115
  subtype2     2                         0    83
  subtype3     0                         0    55
  subtype4     1                         0    24
D10V13, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4
  ASIAN                            2        2        0        1
  BLACK OR AFRICAN AMERICAN        1        0        0        0
  WHITE                          115       83       55       24
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V14, binary
          cls
clus         0   1
  subtype1   2 115
  subtype2   2  81
  subtype3   0  54
  subtype4   0  25
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2  115
  subtype2    2   81
  subtype3    0   54
  subtype4    0   25
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        2        0        0
  NOT HISPANIC OR LATINO      115       81       54       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"
