[1] "ofn"        "-oTHNSC-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/HNSC-TP/15078978/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/15111022/HNSC-TP.mergedcluster.txt"

nPatients in clinical file=522, in cluster file=528, common to both=522
[1]  10 522
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
153 133 189  41 
  1   2   3   4 
153 133 189  41 
[1] "METHLYATION_CNMF"
[1] 3
 1  2  3  4  5  6  7 
87 79 95 90 77 75 19 
 1  2  3  4  5  6  7 
87 79 95 90 77 75 19 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4 
55 52 37 68 
 1  2  3  4 
55 52 37 68 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3 
78 85 49 
 1  2  3 
78 85 49 
[1] "MRNASEQ_CNMF"
[1] 3
  1   2   3 
144 210 160 
  1   2   3 
144 210 160 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
179 102 169  64 
  1   2   3   4 
179 102 169  64 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
219 151 148 
  1   2   3 
219 151 148 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
193 142 183 
  1   2   3 
193 142 183 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3   4   5 
 74 137  98 116  47 
  1   2   3   4   5 
 74 137  98 116  47 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
143 241  88 
  1   2   3 
143 241  88 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "HISTOLOGICAL_TYPE"                     
[16] "RADIATIONS_RADIATION_REGIMENINDICATION"
[17] "NUMBER_PACK_YEARS_SMOKED"              
[18] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[19] "NUMBER_OF_LYMPH_NODES"                 
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 522 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=60,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=188,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 4:'DAYS_TO_LAST_FOLLOWUP':	nDistinctValues=332,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=6,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=8,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=5,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=22,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=44,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=87,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=23,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=26,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 522 columns, 1 survival variables, and 13 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                        
 [2] "NEOPLASM_DISEASESTAGE"                 
 [3] "PATHOLOGY_T_STAGE"                     
 [4] "PATHOLOGY_N_STAGE"                     
 [5] "PATHOLOGY_M_STAGE"                     
 [6] "GENDER"                                
 [7] "HISTOLOGICAL_TYPE"                     
 [8] "RADIATIONS_RADIATION_REGIMENINDICATION"
 [9] "NUMBER_PACK_YEARS_SMOKED"              
[10] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[11] "NUMBER_OF_LYMPH_NODES"                 
[12] "RACE"                                  
[13] "ETHNICITY"                             
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=6, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=5, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T0  T1  T2  T3  T4 
  1  49 136 100 174 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   50   136   100   174 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  49 136 100 174 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   50   136   100   174 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
179  66 169   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
179  66 169   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
179  66 169   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
179  66 169   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, binary=FALSE, numeric=FALSE
RADIATIONS_RADIATION_REGIMENINDICATION, nv=2, binary=FALSE, numeric=FALSE
NUMBER_PACK_YEARS_SMOKED, nv=87, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=59, binary=FALSE, numeric=TRUE
NUMBER_OF_LYMPH_NODES, nv=23, binary=FALSE, numeric=TRUE
RACE, nv=4, binary=FALSE, numeric=FALSE
ETHNICITY, nv=2, binary=FALSE, numeric=FALSE

Clustering(1) Variable = CN_CNMF
D1V1, survival
          sevent
clus2        0   1
  subtype1  83  69
  subtype2  85  48
  subtype3 120  67
  subtype4  25  16
subtype1 subtype2 subtype3 subtype4 
     152      133      187       41 
subtype1 subtype2 subtype3 subtype4 
      69       48       67       16 
$subtype1
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-4076 TCGA-BA-5149 TCGA-BA-5558 TCGA-BA-6868 
        3.35         9.30        13.64        26.50        53.79        15.52 
TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BB-4224 TCGA-BB-7872 
       12.62         4.01        29.42        14.47         9.14        38.40 
TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4723 
       25.71        10.55        27.19         8.81         6.28        23.70 
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4742 
        4.67        12.89        26.86        12.99        20.55        13.05 
TCGA-CN-5367 TCGA-CN-6013 TCGA-CN-6995 TCGA-CN-A641 TCGA-CQ-5326 TCGA-CQ-5329 
       11.57        20.65         3.68        12.07         2.93        46.75 
TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       45.80        10.42        41.19        32.38        34.75        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 
        4.24        14.99        51.29        33.11        16.73        64.11 
TCGA-CQ-A4CG TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 TCGA-CR-6493 
       14.14        18.54        11.64        12.46        11.51         9.27 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7379 TCGA-CR-7380 
       39.16        47.34        35.84        24.95        34.06        19.92 
TCGA-CR-7390 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5444 TCGA-CV-5970 
       29.82        76.24        19.20        17.95        80.12        13.35 
TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6933 TCGA-CV-6934 
       86.83        48.59        43.23        54.74        90.12         2.14 
TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6956 
        9.70        20.52        12.03        42.38        65.82         7.13 
TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 TCGA-CV-7102 
        8.42        28.34         2.50       126.15        18.81         1.84 
TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 
       12.92        71.21        10.75        31.36        26.20        18.97 
TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7409 TCGA-CV-7416 TCGA-CV-7423 
       17.13        11.87         2.10        17.85        25.08       100.57 
TCGA-CV-7428 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U 
       54.94        16.64         6.38        22.19       180.16        35.47 
TCGA-CV-A45X TCGA-CV-A465 TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU 
        6.51         7.07         6.38        29.79        22.03         3.62 
TCGA-CV-A6K1 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-8569 
       22.52        34.36        25.41         9.60        23.05        25.32 
TCGA-D6-A4Z9 TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5631 
       17.72        14.30        12.10        12.79        58.45        18.02 
TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61W 
        9.83        37.18        16.11         3.02        19.23         0.46 
TCGA-H7-8502 TCGA-H7-A6C5 TCGA-HD-7229 TCGA-HD-8635 TCGA-HD-A633 TCGA-IQ-7630 
       15.06        21.11         0.07        22.85        13.84        15.95 
TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-MT-A51X TCGA-MT-A7BN 
       19.33        14.47         5.29        11.54         7.96        15.42 
TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T8 TCGA-QK-A64Z 
       56.75        18.97         2.04        29.00        13.15        21.07 
TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6VB TCGA-QK-A8Z8 TCGA-QK-A8Z9 TCGA-QK-A8ZA 
       11.74        16.70        14.79         5.62        11.57        12.10 
TCGA-QK-A8ZB TCGA-T2-A6WZ TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A7JC TCGA-UF-A7JD 
        9.73        15.91        13.25        43.59        17.95        24.16 
TCGA-UF-A7JK TCGA-WA-A7GZ 
       13.94        20.55 

$subtype2
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6870 
       15.19        37.28         9.07        17.10        21.17        14.83 
TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DL 
        3.55         7.76        28.11        30.18        27.95        20.48 
TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
       16.41         4.41        36.72        50.20        66.28        24.66 
TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4725 TCGA-CN-4727 TCGA-CN-4731 TCGA-CN-4735 
       71.05        20.52        38.04        40.44        32.65        41.10 
TCGA-CN-4739 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-6010 TCGA-CN-6011 
       43.73        35.54        11.54        11.84        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 TCGA-CN-6989 
       20.68         9.07        36.49        11.08        10.45        20.09 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49A 
       12.95        24.16        14.10        35.01        14.56        12.85 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-6221 
        7.40        17.29        11.44         6.18        48.20        32.88 
TCGA-CQ-6225 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-6477 
       13.25        23.24        31.23        84.23        11.77        16.90 
TCGA-CR-6478 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 
        6.02         7.69        47.18        40.93         3.45         3.09 
TCGA-CR-7374 TCGA-CR-7383 TCGA-CR-7398 TCGA-CR-7399 TCGA-CV-5430 TCGA-CV-5431 
        0.99        17.13         5.13         5.95       139.43        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6936 
      129.21       108.95       107.51         7.07         9.60         5.46 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7091 
       26.43        11.24        15.09        30.08         4.14       111.16 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7242 
       12.66         5.26        52.31        21.80        77.16        36.00 
TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7415 
       47.97        36.13        18.41        35.54         0.46        22.85 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7432 
       25.94         0.07        34.09        14.89        16.27        84.49 
TCGA-CV-7435 TCGA-CV-A45W TCGA-CV-A461 TCGA-CV-A6JE TCGA-CX-7082 TCGA-CX-7086 
      153.86        45.96        67.86        35.34        10.42        18.84 
TCGA-D6-8568 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 
       24.95        12.36        13.94        11.11        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7595 TCGA-F7-A623 TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-8224 
       18.90        10.65        20.25         0.16         1.22        14.66 
TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-KU-A66T TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SX 
        3.65        11.84        18.15        17.98        15.78        47.01 
TCGA-QK-A8Z7 TCGA-QK-AA3J TCGA-QK-AA3K TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B 
        6.51         9.76         8.32        54.67         2.83        43.36 
TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JH 
       41.16        42.02        44.65        62.27        49.22        21.86 
TCGA-UF-A7JS 
       22.36 

$subtype3
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-A4IH 
       23.74        42.35        57.93        23.84        20.48        20.45 
TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DJ TCGA-BB-4217 
        7.10         5.69         7.82         2.27        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7863 TCGA-BB-7866 
       94.62         4.60        18.35        22.42        33.70        44.98 
TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4738 
       12.92        12.69        26.27        37.84        21.11        14.33 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5364 
       27.58        41.69        34.36         8.58        12.39        16.21 
TCGA-CN-5369 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6016 TCGA-CN-6017 
       12.49         8.52        22.45        56.94        19.53        20.68 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6022 TCGA-CN-A49C TCGA-CN-A63V 
       19.07        14.20         6.74         9.24        21.21        15.91 
TCGA-CN-A63Y TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CQ-5324 TCGA-CQ-5325 
        5.75        10.09         7.33         7.69        39.68        21.50 
TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6229 TCGA-CQ-7063 
       54.58        45.99        11.21         4.24        38.76        70.13 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CH TCGA-CR-5248 
       43.04        41.88        28.83        29.36        12.46        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 
       37.87        26.27        50.01        39.52        34.52        36.99 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6492 TCGA-CR-7376 TCGA-CR-7377 
       11.90        10.22        11.34        15.75        31.96         9.17 
TCGA-CR-7382 TCGA-CR-7385 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7391 
       26.17        32.78        47.01        27.06        12.89        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 
       31.10        29.85        29.52        30.58         7.10        35.41 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6436 TCGA-CV-6938 
       29.95        48.39        91.53        23.05        62.43         4.73 
TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7089 
       21.90       126.08        19.79        53.95        10.98        64.83 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7250 
        7.99         9.01       130.88         4.73        47.47        95.34 
TCGA-CV-7252 TCGA-CV-7406 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7425 
        4.96        57.47       210.97        89.33         9.67        56.48 
TCGA-CV-7427 TCGA-CV-7433 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T 
      156.49        19.76        27.98        24.99       169.38       159.65 
TCGA-CV-A45V TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 
        1.05        88.87        48.20        60.43         0.76        56.61 
TCGA-CV-A468 TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K0 TCGA-CV-A6K2 TCGA-CX-7085 
       15.25         6.48        21.24        19.92        10.42        10.55 
TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EK 
       13.25         2.53        16.14        11.44        18.67        15.88 
TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7596 
       33.86        25.48        20.45        12.13        12.10        11.18 
TCGA-F7-8489 TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       21.63        12.62        17.85        12.43        13.38        15.16 
TCGA-H7-A6C4 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-A4C1 
       13.61         6.77        25.74        22.03        12.66         0.36 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I 
        4.27         6.90        34.75        12.76        14.50         0.07 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A6H7 TCGA-KU-A6H8 TCGA-MT-A67D TCGA-MT-A67F 
       11.84        13.35        12.43        10.75         1.84        12.62 
TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW 
        7.13        16.08        29.92        51.25        10.85        36.82 
TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6II TCGA-QK-A6IJ 
       19.00        75.55        12.99        17.65         9.34        12.72 
TCGA-QK-A6V9 TCGA-QK-A6VC TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 
       18.64        12.43        16.96         6.87         7.10        32.45 
TCGA-TN-A7HL TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UF-A7JV TCGA-UP-A6WW 
       13.68        16.11        20.75        32.65         2.96        17.03 
TCGA-WA-A7H4 
       14.56 

$subtype4
TCGA-BA-5559 TCGA-BA-A6DA TCGA-BA-A6DI TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-6996 
       57.44        11.54        11.05        33.11         8.32        17.42 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A640 TCGA-CN-A642 TCGA-CN-A6V3 
       11.74        17.59        29.72         4.41         2.70         9.80 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CR-6467 TCGA-CR-7373 
       44.48        11.61        32.81        25.81        58.42        29.23 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6433 TCGA-CV-6952 
       94.88        76.50        17.92        60.49        21.07         6.08 
TCGA-CV-7429 TCGA-CV-7434 TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-D6-A6EM TCGA-DQ-5625 
        3.52         7.17         5.98        23.47         7.63        35.54 
TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A622 TCGA-IQ-A61H TCGA-MT-A51W TCGA-MT-A67A 
       20.25        18.94        11.80        13.55        14.37        30.05 
TCGA-MT-A67G TCGA-P3-A6T7 TCGA-QK-A6IG TCGA-RS-A6TO TCGA-TN-A7HI 
        3.68        16.01         7.30        12.72        13.55 

subtype1 subtype2 subtype3 subtype4 
    0.07     0.07     0.07     2.70 
subtype1 subtype2 subtype3 subtype4 
  180.16   153.86   210.97    94.88 
subtype1 subtype2 subtype3 subtype4 
  17.425   20.090   19.000   16.010 
[1] "0.1 - 180.2 (17.4)" "0.1 - 153.9 (20.1)" "0.1 - 211.0 (19.0)"
[4] "2.7 - 94.9 (16.0)" 
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       7       20        22        85         5         1
  subtype2       6       16        19        69         4         0
  subtype3      12       34        29        79         1         0
  subtype4       2        7         7        19         2         0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          7        6       12        2
  STAGE II        20       16       34        7
  STAGE III       22       19       29        7
  STAGE IVA       85       69       79       19
  STAGE IVB        5        4        1        2
  STAGE IVC        1        0        0        0
[1] 6 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    12 39 32 59
  subtype2    10 29 30 48
  subtype3    25 54 26 53
  subtype4     3 11 11 12
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       12       10       25        3
  T2          39       29       54       11
  T3          32       30       26       11
  T4          59       48       53       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       N0 N1 N2 N3
  subtype1 50 19 59  2
  subtype2 44 13 47  3
  subtype3 73 25 45  1
  subtype4 11  9 14  2
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       50       44       73       11
  N1       19       13       25        9
  N2       59       47       45       14
  N3        2        3        1        2
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 52  1
  subtype2 38  0
  subtype3 73  0
  subtype4 20  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   52    1
  subtype2   38    0
  subtype3   73    0
  subtype4   20    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       52       38       73       20
  1        1        0        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  39 114
  subtype2  27 106
  subtype3  58 131
  subtype4  15  26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39  114
  subtype2   27  106
  subtype3   58  131
  subtype4   15   26
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       39       27       58       15
  MALE        114      106      131       26
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   153
  subtype2                                   129
  subtype3                                   182
  subtype4                                    41
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           0
  subtype3                                                           1
  subtype4                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   0
  subtype2                                                   4
  subtype3                                                   6
  subtype4                                                   0
D1V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            153      129
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        4
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            182       41
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                6        0
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V9, binary
          cls
clus         0   1
  subtype1  24 129
  subtype2  23 110
  subtype3  30 159
  subtype4   4  37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24  129
  subtype2   23  110
  subtype3   30  159
  subtype4    4   37
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        24       23       30        4
  YES      129      110      159       37
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V10, continuous
D1V11, continuous
D1V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     5                        16
  subtype2                                0     1                        16
  subtype3                                1     4                        10
  subtype4                                0     1                         3
          vv
clus       WHITE
  subtype1   124
  subtype2   113
  subtype3   168
  subtype4    36
D1V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0
  ASIAN                                   5        1        4        1
  BLACK OR AFRICAN AMERICAN              16       16       10        3
  WHITE                                 124      113      168       36
[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"
D1V14, binary
          cls
clus         0   1
  subtype1  10 133
  subtype2   5 114
  subtype3   9 168
  subtype4   1  39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  133
  subtype2    5  114
  subtype3    9  168
  subtype4    1   39
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           10        5        9        1
  NOT HISPANIC OR LATINO      133      114      168       39
[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 49 36
  subtype2 55 24
  subtype3 54 41
  subtype4 49 41
  subtype5 61 16
  subtype6 39 35
  subtype7  9 10
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      85       79       95       90       77       74       19 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      36       24       41       41       16       35       10 
$subtype1
TCGA-4P-AA8J TCGA-BA-5557 TCGA-BA-A4II TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DG 
        3.35        20.48        30.18         7.10         5.69         2.27 
TCGA-BA-A6DI TCGA-BB-4217 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4728 
       11.05         6.15        38.40        71.05        12.69        37.84 
TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5369 
       21.11        14.33         8.58        12.39        11.84        12.49 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6022 TCGA-CN-6996 TCGA-CN-A640 TCGA-CQ-5325 
       19.53        20.68         9.24        17.42         4.41        21.50 
TCGA-CQ-5326 TCGA-CQ-5331 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6227 TCGA-CQ-6229 
        2.93        45.99        15.75        66.28         4.24        38.76 
TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6478 TCGA-CR-6488 
       44.48        29.36        12.46        18.54         6.02        12.46 
TCGA-CR-6492 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7388 
       15.75        31.96         9.17        26.17        17.13        27.06 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CV-5971 
       30.02        31.10        29.85        29.52         7.10        23.05 
TCGA-CV-6943 TCGA-CV-6961 TCGA-CV-7089 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7410 
       19.79         2.50        64.83         4.73        47.47       210.97 
TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45T TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A468 
       19.76        30.48       159.65        88.87        56.61        15.25 
TCGA-CV-A6JO TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-8568 
        6.48        19.92        10.55        13.25         2.53        24.95 
TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-5630 TCGA-F7-8489 TCGA-F7-A620 TCGA-H7-A6C4 
       17.72         7.63        33.86        21.63        17.85        13.61 
TCGA-HD-8634 TCGA-IQ-7632 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-P3-A6T8 TCGA-QK-A652 
       12.66        14.50        10.75        14.37        13.15        11.74 
TCGA-QK-A6VC TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JV 
       12.43         8.32        43.59        62.27        16.11         2.96 
TCGA-WA-A7H4 
       14.56 

$subtype2
TCGA-BA-4074 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DL 
       15.19        17.10        21.17        29.42        14.47        20.48 
TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 
       50.20        66.28        27.19        40.44        26.86        32.65 
TCGA-CN-4737 TCGA-CN-4739 TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-6988 
       20.55        43.73        27.58        34.36        35.54        10.45 
TCGA-CN-A497 TCGA-CN-A49A TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63V TCGA-CN-A63W 
       35.01        12.85         7.40        17.29        15.91        11.44 
TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-7072 TCGA-CQ-A4C9 
       12.07         9.80        13.25        14.99        64.11        23.24 
TCGA-CR-5247 TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5441 
       11.77        47.18        24.95         5.13        29.95        94.88 
TCGA-CV-6933 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6960 TCGA-CV-7091 
       90.12        11.24        65.82         7.13        28.34       111.16 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7409 
       36.00        26.20        95.34        11.87        18.41        17.85 
TCGA-CV-7421 TCGA-CV-7428 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A45Z 
        0.07        54.94       153.86        22.19        45.96        48.20 
TCGA-CV-A461 TCGA-CV-A6JU TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-A6EO TCGA-D6-A74Q 
       67.86         3.62        18.84        23.05        14.30        11.11 
TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A61V TCGA-H7-A6C5 TCGA-HD-7917 TCGA-HD-8224 
       10.65        37.18        12.62        21.11         1.22        14.66 
TCGA-IQ-7631 TCGA-KU-A66S TCGA-P3-A5QF TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.76        13.35        10.85        14.79         6.51         5.62 
TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A7JD TCGA-UF-A7JF 
        9.76        54.67        43.36        41.16        24.16        49.22 
TCGA-UF-A7JH 
       21.86 

$subtype3
TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4224 TCGA-BB-4227 
        9.30        26.50        12.62         4.01         9.14         4.41 
TCGA-BB-A5HU TCGA-CN-4725 TCGA-CN-4736 TCGA-CN-4742 TCGA-CN-5365 TCGA-CN-5367 
       25.71        38.04        12.99        13.05        11.54        11.57 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6020 TCGA-CN-6998 TCGA-CQ-5329 TCGA-CQ-6218 
        8.52        22.45         6.74        11.74        46.75        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 
       32.38        34.75        56.58        51.29        33.11        41.88 
TCGA-CQ-A4CE TCGA-CR-6477 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7379 TCGA-CR-7401 
       25.81        16.90         9.27        39.16        34.06        35.41 
TCGA-CV-5436 TCGA-CV-5439 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5979 
       19.20        17.95        13.35        86.83        48.59        43.23 
TCGA-CV-6003 TCGA-CV-6950 TCGA-CV-6959 TCGA-CV-7090 TCGA-CV-7102 TCGA-CV-7104 
       54.74        15.09         8.42       126.15         1.84        12.92 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7255 
       71.21        10.75       130.88        31.36        18.97         2.10 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7438 TCGA-CV-A45R TCGA-CV-A45X 
       22.85        25.08       100.57         6.38       180.16         6.51 
TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JY TCGA-CV-A6K1 
        7.07        35.34        29.79        22.03        21.24        22.52 
TCGA-D6-6517 TCGA-D6-8569 TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
        9.60        25.32        12.10        12.79        58.45        35.54 
TCGA-DQ-7588 TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S 
       14.04         9.83        16.11        20.25        19.23        18.94 
TCGA-F7-A622 TCGA-H7-8502 TCGA-HD-7753 TCGA-IQ-7630 TCGA-IQ-A61J TCGA-IQ-A61K 
       11.80        15.06         0.16        15.95        14.47         5.29 
TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51X TCGA-P3-A5QA TCGA-P3-A6SX 
       11.54        11.84        18.15         7.96        56.75        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6II 
       19.00        18.97        29.00        21.07        16.70         9.34 
TCGA-RS-A6TO TCGA-TN-A7HJ TCGA-UF-A7JC TCGA-UF-A7JK TCGA-UF-A7JS 
       12.72        13.25        17.95        13.94        22.36 

$subtype4
TCGA-BA-4076 TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A6D8 
       13.64         9.07        15.52        14.83         7.76        27.95 
TCGA-BA-A6DA TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A5HY 
       11.54        16.41        36.72        24.66        20.52        10.55 
TCGA-CN-4723 TCGA-CN-4735 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 
       23.70        41.10        20.71        30.67        20.68        14.20 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6994 
        9.07        36.49        11.08        20.09        12.95        24.16 
TCGA-CN-6997 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-7370 
       14.10        10.42        32.88        14.14        31.23         3.45 
TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5432 
        3.09         0.99        12.89        29.82       139.43       129.21 
TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6937 
      108.95        76.24       107.51         7.07         9.70        20.52 
TCGA-CV-6940 TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7101 
       26.43        12.03        42.38        30.08         4.14         5.26 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 
       52.31        21.80        77.16        17.13        47.97        36.13 
TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7429 
       35.54         0.46        25.94        34.09        14.89         3.52 
TCGA-CV-7430 TCGA-CV-7437 TCGA-CV-7446 TCGA-CV-A45U TCGA-CV-A6JM TCGA-CX-7082 
       16.27        16.64        35.93        35.47         6.38        10.42 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6827 TCGA-D6-A4ZB TCGA-D6-A6EP TCGA-DQ-5629 
       34.36        25.41        18.67        12.36        13.94        30.94 
TCGA-DQ-7589 TCGA-F7-A50I TCGA-F7-A61W TCGA-F7-A623 TCGA-HD-8635 TCGA-HD-A6HZ 
       18.90         3.02         0.46        20.25        22.85         3.65 
TCGA-IQ-A61G TCGA-IQ-A61H TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T4 
       11.84        13.55        15.42        17.98        15.78         2.04 
TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-WA-A7GZ 
       12.10         9.73         2.83        42.02        44.65        20.55 

$subtype5
TCGA-BA-4077 TCGA-BA-5153 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH 
       37.28        57.93        57.44         3.55        28.11        20.45 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7866 TCGA-BB-A6UM 
       94.62         4.60        18.35        22.42        44.98        12.92 
TCGA-CN-4741 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
       41.69        56.94        20.65        14.56        17.59        29.72 
TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V6 TCGA-CN-A6V7 
       21.21         5.75        10.09         7.33         7.69         6.18 
TCGA-CQ-5323 TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       48.20        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 
       50.01        39.52        34.52        36.99        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7385 TCGA-CR-7399 TCGA-CR-7404 
       11.34         7.69        40.93        32.78         5.95        48.39 
TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6939 
       17.16        76.50        91.53        21.07         9.60        21.90 
TCGA-CV-7100 TCGA-CV-7406 TCGA-CV-A460 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 
        9.01        57.47        60.43        25.48        20.45        12.13 
TCGA-DQ-7594 TCGA-DQ-7596 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A634 
       12.10        11.18         6.77        25.74        22.03         4.27 
TCGA-HL-7533 TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
       34.75         0.07        12.43         3.68         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6V9 
       29.92        51.25        36.82        12.99        17.65        18.64 
TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UP-A6WW 
       16.96         7.10        13.55        13.68        17.03 

$subtype6
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-A6DF TCGA-BA-A6DJ 
       23.74        42.35        23.84        53.79         7.82        13.38 
TCGA-BB-7863 TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4722 TCGA-CN-4734 TCGA-CN-5363 
       33.70         8.81         6.28        26.27        24.92         8.32 
TCGA-CN-6018 TCGA-CN-6995 TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5330 
       19.07         3.68         2.70        39.68        54.58        45.80 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4CD 
       11.21         4.24        70.13        43.04        28.83        32.81 
TCGA-CR-6484 TCGA-CR-7373 TCGA-CR-7380 TCGA-CR-7386 TCGA-CR-7395 TCGA-CV-5444 
       11.64        29.23        19.92        47.01        30.58        80.12 
TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6952 
       17.92        60.49        62.43         4.73       126.08         6.08 
TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7252 TCGA-CV-7411 
       53.95        10.98        12.66         7.99         4.96        89.33 
TCGA-CV-7413 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45Q 
        9.67        56.48       156.49         7.17        27.98       169.38 
TCGA-CV-A45V TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-CV-A6K2 TCGA-D6-6825 
        1.05         0.76         5.98        23.47        10.42        16.14 
TCGA-D6-6826 TCGA-D6-A6EK TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-HD-7229 
       11.44        15.88        12.43        13.38        15.16         0.07 
TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-A61E TCGA-MT-A67A TCGA-MT-A67F 
        0.36        13.84         6.90        19.33        30.05        12.62 
TCGA-P3-A6T2 TCGA-P3-A6T7 TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-T2-A6WX TCGA-T2-A6X2 
       75.55        16.01         7.30        11.57         6.87        32.45 
TCGA-UF-A7JO TCGA-UF-A7JT 
       20.75        32.65 

$subtype7
TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-5355 TCGA-CN-5361 TCGA-CN-5364 TCGA-CQ-7067 
        4.67        12.89        33.11        55.27        16.21        16.73 
TCGA-CQ-A4C7 TCGA-CR-6491 TCGA-CR-7367 TCGA-CR-7369 TCGA-CV-6934 TCGA-CV-6936 
       11.61        11.51        47.34        35.84         2.14         5.46 
TCGA-CV-7095 TCGA-CV-7432 TCGA-CV-A45P TCGA-DQ-5631 TCGA-MT-A67D TCGA-QK-A6IJ 
       18.81        84.49        24.99        18.02         1.84        12.72 
TCGA-T2-A6WZ 
       15.91 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    2.27     0.07     0.16     0.46     0.07     0.07     1.84 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  210.97   153.86   180.16   139.43    94.62   169.38    84.49 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  16.110   21.170   18.940   17.555   20.450   17.030   16.210 
[1] "2.3 - 211.0 (16.1)" "0.1 - 153.9 (21.2)" "0.2 - 180.2 (18.9)"
[4] "0.5 - 139.4 (17.6)" "0.1 - 94.6 (20.4)"  "0.1 - 169.4 (17.0)"
[7] "1.8 - 84.5 (16.2)" 
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       9       15        12        45         0         0
  subtype2       3       14        12        40         3         1
  subtype3       6       14        18        46         2         0
  subtype4       2        8        12        52         3         0
  subtype5       2        9        11        25         1         0
  subtype6       3       15         9        40         3         0
  subtype7       2        3         3         9         0         0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I          9        3        6        2        2        3        2
  STAGE II        15       14       14        8        9       15        3
  STAGE III       12       12       18       12       11        9        3
  STAGE IVA       45       40       46       52       25       40        9
  STAGE IVB        0        3        2        3        1        3        0
  STAGE IVC        0        1        0        0        0        0        0
[1] 6 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1    15 27 14 26
  subtype2     8 17 16 33
  subtype3     8 27 24 28
  subtype4     4 19 18 37
  subtype5    10 22 11  8
  subtype6     3 19 13 35
  subtype7     2  5  4  7
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T0+T1       15        8        8        4       10        3        2
  T2          27       17       27       19       22       19        5
  T3          14       16       24       18       11       13        4
  T4          26       33       28       37        8       35        7
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 33 14 31  0
  subtype2 40 10 20  1
  subtype3 31 10 36  1
  subtype4 22  9 37  3
  subtype5 14  9 22  1
  subtype6 34 10 15  2
  subtype7  5  4  8  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       33       40       31       22       14       34        5
  N1       14       10       10        9        9       10        4
  N2       31       20       36       37       22       15        8
  N3        0        1        1        3        1        2        0
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 45  0
  subtype2 30  1
  subtype3 38  0
  subtype4 20  0
  subtype5 19  0
  subtype6 24  0
  subtype7  8  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    0
  subtype2   30    1
  subtype3   38    0
  subtype4   20    0
  subtype5   19    0
  subtype6   24    0
  subtype7    8    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       45       30       38       20       19       24        8
  1        0        1        0        0        0        0        0
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 29 58
  subtype2 13 66
  subtype3 30 65
  subtype4 18 72
  subtype5  9 68
  subtype6 38 37
  subtype7  4 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   58
  subtype2   13   66
  subtype3   30   65
  subtype4   18   72
  subtype5    9   68
  subtype6   38   37
  subtype7    4   15
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       29       13       30       18        9       38        4
  MALE         58       66       65       72       68       37       15
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    87
  subtype2                                    76
  subtype3                                    94
  subtype4                                    88
  subtype5                                    72
  subtype6                                    75
  subtype7                                    19
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           0
  subtype3                                                           1
  subtype4                                                           0
  subtype5                                                           0
  subtype6                                                           0
  subtype7                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   0
  subtype2                                                   3
  subtype3                                                   0
  subtype4                                                   2
  subtype5                                                   5
  subtype6                                                   0
  subtype7                                                   0
D2V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             87       76
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        3
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             94       88
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        2
                                                             clus
vv                                                            subtype5 subtype6
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             72       75
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                5        0
                                                             clus
vv                                                            subtype7
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             19
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V9, binary
          cls
clus        0  1
  subtype1 16 71
  subtype2 10 69
  subtype3 14 81
  subtype4 19 71
  subtype5 13 64
  subtype6  8 67
  subtype7  3 16
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   71
  subtype2   10   69
  subtype3   14   81
  subtype4   19   71
  subtype5   13   64
  subtype6    8   67
  subtype7    3   16
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        16       10       14       19       13        8        3
  YES       71       69       81       71       64       67       16
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V10, continuous
D2V11, continuous
D2V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                         6
  subtype2                                0     0                        12
  subtype3                                1     1                         4
  subtype4                                0     2                        13
  subtype5                                0     0                         3
  subtype6                                0     4                         5
  subtype7                                0     0                         2
          vv
clus       WHITE
  subtype1    71
  subtype2    62
  subtype3    85
  subtype4    74
  subtype5    74
  subtype6    65
  subtype7    16
D2V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0        0
  ASIAN                                   4        0        1        2        0
  BLACK OR AFRICAN AMERICAN               6       12        4       13        3
  WHITE                                  71       62       85       74       74
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        0        0
  ASIAN                                   4        0
  BLACK OR AFRICAN AMERICAN               5        2
  WHITE                                  65       16
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V14, binary
          cls
clus        0  1
  subtype1  3 78
  subtype2  2 66
  subtype3  8 82
  subtype4  4 79
  subtype5  4 68
  subtype6  3 69
  subtype7  1 18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   78
  subtype2    2   66
  subtype3    8   82
  subtype4    4   79
  subtype5    4   68
  subtype6    3   69
  subtype7    1   18
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        2        8        4        4        3
  NOT HISPANIC OR LATINO       78       66       82       79       68       69
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       18
[1] 2 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 21 34
  subtype2 28 24
  subtype3 16 21
  subtype4 27 41
subtype1 subtype2 subtype3 subtype4 
      55       52       37       68 
subtype1 subtype2 subtype3 subtype4 
      34       24       21       41 
$subtype1
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6870 
       15.19        26.50        23.74        23.84        20.48        14.83 
TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4727 TCGA-CN-4728 TCGA-CN-4729 
       23.70        38.04         4.67        40.44        37.84        12.89 
TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5359 TCGA-CN-5363 
       21.11        41.10        14.33        43.73        12.39         8.32 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-6018 TCGA-CN-6020 TCGA-CQ-5326 
       16.21        11.84        12.49        19.07         6.74         2.93 
TCGA-CQ-5329 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5443 
       46.75        15.75        66.28        17.16        17.95        91.53 
TCGA-CV-5971 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6955 TCGA-CV-6959 
       23.05       126.08        12.03        15.09        10.98         8.42 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 
       28.34         2.50         4.14        64.83       126.15         7.99 
TCGA-CV-7100 TCGA-CV-7247 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7406 
        9.01        18.97         4.96        11.87        47.97        57.47 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CX-7219 TCGA-D6-6515 TCGA-D6-6823 TCGA-DQ-7592 
        6.38        22.19        34.36        13.25        23.05         9.83 
TCGA-IQ-7630 
       15.95 

$subtype2
TCGA-BA-4078 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-5559 TCGA-BA-6869 
        9.07        42.35        57.93        17.10        57.44        21.17 
TCGA-BA-6871 TCGA-BB-4217 TCGA-CN-4730 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 
        3.55         6.15        26.86        41.69        33.11        34.36 
TCGA-CN-5361 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6013 TCGA-CN-6023 TCGA-CN-6024 
       55.27        56.94        20.71        20.65        36.49        11.08 
TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6997 TCGA-CQ-5324 
       10.45        20.09        12.95         3.68        14.10        39.68 
TCGA-CQ-5332 TCGA-CQ-6228 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5440 
       10.42        14.99       139.43       129.21       108.95       107.51 
TCGA-CV-5441 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 
       94.88        21.07         9.60        90.12         9.70        21.90 
TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7242 TCGA-CV-7248 
       42.38        65.82       111.16        12.66        36.00        17.13 
TCGA-CV-7261 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7429 
       36.13        22.85        25.94        34.09        14.89         3.52 
TCGA-CV-7433 TCGA-CV-7437 TCGA-D6-6827 TCGA-DQ-7591 
       19.76        16.64        18.67        20.45 

$subtype3
TCGA-BA-6872 TCGA-BA-6873 TCGA-CN-4722 TCGA-CN-5365 TCGA-CN-6011 TCGA-CN-6021 
       12.62         4.01        26.27        11.54        30.67         9.07 
TCGA-CQ-5323 TCGA-CQ-5331 TCGA-CQ-6220 TCGA-CQ-7068 TCGA-CV-5442 TCGA-CV-5966 
       48.20        45.99        32.38        43.04        76.50        17.92 
TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6937 
       60.49        43.23        54.74        62.43         5.46        20.52 
TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-7177 TCGA-CV-7178 
       26.43        11.24         6.08        53.95        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7413 TCGA-CV-7427 TCGA-CV-7428 
       10.75        26.20        95.34         9.67       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6825 
       16.27        84.49         7.17        18.84        25.41        16.14 
TCGA-IQ-7632 
       14.50 

$subtype4
TCGA-CN-4731 TCGA-CN-4734 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 
       32.65        24.92        12.99        20.55        27.58        13.05 
TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 
        8.58        35.54        11.57         8.52        22.45        20.68 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6994 TCGA-CN-6996 
       19.53        20.68        14.20         9.24        24.16        17.42 
TCGA-CN-6998 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6218 
       11.74        21.50        54.58        45.80         4.24        41.19 
TCGA-CQ-6221 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 
       32.88        56.58        13.25         4.24        38.76        33.11 
TCGA-CV-5436 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 TCGA-CV-5978 
       19.20        80.12        13.35        86.83        48.59         7.07 
TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-6951 TCGA-CV-6956 TCGA-CV-7095 
        2.14         4.73        19.79        30.08         7.13        18.81 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7183 TCGA-CV-7235 
        5.26         1.84        52.31        12.92       130.88        77.16 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 
        4.73        47.47        31.36         2.10        18.41        35.54 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 
      210.97        89.33         0.46        25.08         0.07       100.57 
TCGA-CV-7425 TCGA-CV-7435 TCGA-CV-7446 TCGA-CV-7568 TCGA-CX-7085 TCGA-D6-6517 
       56.48       153.86        35.93        30.48        10.55         9.60 
TCGA-D6-6824 TCGA-D6-6826 
        2.53        11.44 

subtype1 subtype2 subtype3 subtype4 
    2.50     3.52     4.01     0.07 
subtype1 subtype2 subtype3 subtype4 
  126.15   139.43   156.49   210.97 
subtype1 subtype2 subtype3 subtype4 
  17.160   21.535   26.200   20.615 
[1] "2.5 - 126.2 (17.2)" "3.5 - 139.4 (21.5)" "4.0 - 156.5 (26.2)"
[4] "0.1 - 211.0 (20.6)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       1       14         9        28         1
  subtype2       2        4         7        33         1
  subtype3       3        8         6        16         1
  subtype4       3       13         9        40         1
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          1        2        3        3
  STAGE II        14        4        8       13
  STAGE III        9        7        6        9
  STAGE IVA       28       33       16       40
  STAGE IVB        1        1        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"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     3 19 12 19
  subtype2     3  6 14 25
  subtype3     3 13  6 13
  subtype4     4 21 21 22
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        3        3        3        4
  T2          19        6       13       21
  T3          12       14        6       21
  T4          19       25       13       22
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 20  5 19  1
  subtype2 15  3 25  1
  subtype3 17  5  8  1
  subtype4 20  8 27  1
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       20       15       17       20
  N1        5        3        5        8
  N2       19       25        8       27
  N3        1        1        1        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus       0
  subtype1 9
  subtype2 6
  subtype3 1
  subtype4 6
[1] "NOT AVAILABLE: table only has an event [0]"
D3V7, binary
          cls
clus        0  1
  subtype1 13 42
  subtype2  7 45
  subtype3 15 22
  subtype4 27 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13   42
  subtype2    7   45
  subtype3   15   22
  subtype4   27   41
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       13        7       15       27
  MALE         42       45       22       41
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    55
  subtype2                                    52
  subtype3                                    37
  subtype4                                    68
[1] "NOT AVAILABLE: table dimension [4x1]"
D3V9, binary
          cls
clus        0  1
  subtype1 21 34
  subtype2 20 32
  subtype3  4 33
  subtype4 16 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21   34
  subtype2   20   32
  subtype3    4   33
  subtype4   16   52
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        21       20        4       16
  YES       34       32       33       52
[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, continuous
D3V11, continuous
D3V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     0                         8
  subtype2                                0     1                         7
  subtype3                                0     0                         1
  subtype4                                0     2                         3
          vv
clus       WHITE
  subtype1    44
  subtype2    43
  subtype3    36
  subtype4    60
D3V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0
  ASIAN                                   0        1        0        2
  BLACK OR AFRICAN AMERICAN               8        7        1        3
  WHITE                                  44       43       36       60
[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"
D3V14, binary
          cls
clus        0  1
  subtype1  5 47
  subtype2  2 46
  subtype3  2 35
  subtype4  4 62
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5   47
  subtype2    2   46
  subtype3    2   35
  subtype4    4   62
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            5        2        2        4
  NOT HISPANIC OR LATINO       47       46       35       62
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 35 43
  subtype2 31 54
  subtype3 26 23
subtype1 subtype2 subtype3 
      78       85       49 
subtype1 subtype2 subtype3 
      43       54       23 
$subtype1
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-6870 
       15.19        26.50        23.74        23.84        20.48        14.83 
TCGA-BA-6873 TCGA-BB-4217 TCGA-CN-4723 TCGA-CN-4727 TCGA-CN-4729 TCGA-CN-4733 
        4.01         6.15        23.70        40.44        12.89        21.11 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5363 
       41.10        43.73        33.11        12.39        55.27         8.32 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6018 
       16.21        11.84        12.49        30.67        20.65        19.07 
TCGA-CN-6020 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5331 TCGA-CQ-6219 TCGA-CQ-6220 
        6.74         2.93        46.75        45.99        15.75        32.38 
TCGA-CQ-7068 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5966 
       43.04        17.16       129.21        17.95        91.53        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6436 
       13.35        23.05        60.49        43.23        54.74        62.43 
TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6955 
        5.46        26.43       126.08        12.03        15.09        10.98 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 
        8.42         2.50         4.14        64.83       126.15         7.99 
TCGA-CV-7100 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7247 TCGA-CV-7248 
        9.01        71.21        10.75       130.88        18.97        17.13 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7422 
        4.96        11.87        47.97        36.13        57.47        34.09 
TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-7440 TCGA-CX-7219 
      156.49        16.27        84.49         6.38        22.19        34.36 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-6825 TCGA-DQ-7592 TCGA-IQ-7630 
       13.25        25.41        23.05        16.14         9.83        15.95 

$subtype2
TCGA-BA-4078 TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
        9.07        57.44         3.55        38.04         4.67        37.84 
TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 
       32.65        12.99        20.55        27.58        41.69         8.58 
TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6016 
       35.54        11.57         8.52        20.71        20.68        19.53 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6988 
       20.68        14.20         9.24        36.49        11.08        10.45 
TCGA-CN-6989 TCGA-CN-6992 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 
       20.09        12.95         3.68        17.42        14.10        11.74 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5334 TCGA-CQ-6221 
       21.50        54.58        45.80        10.42         4.24        32.88 
TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CV-5430 
       66.28        56.58        13.25         4.24        14.99       139.43 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5976 
      108.95        19.20       107.51        94.88        80.12        48.59 
TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6938 
        7.07        21.07         9.60         2.14         9.70         4.73 
TCGA-CV-6939 TCGA-CV-6943 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-7095 
       21.90        19.79        42.38        30.08        65.82        18.81 
TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7235 
       12.66         5.26         1.84        52.31        12.92        77.16 
TCGA-CV-7236 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7414 TCGA-CV-7415 
        4.73        18.41        35.54       210.97         0.46        22.85 
TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7429 
       25.08        25.94         0.07        14.89        56.48         3.52 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7446 TCGA-CV-7568 TCGA-D6-6827 
       19.76       153.86        16.64        35.93        30.48        18.67 
TCGA-DQ-7591 
       20.45 

$subtype3
TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6872 TCGA-CN-4722 
       42.35        57.93        17.10        21.17        12.62        26.27 
TCGA-CN-4730 TCGA-CN-4734 TCGA-CN-4738 TCGA-CN-4742 TCGA-CN-5356 TCGA-CN-5365 
       26.86        24.92        14.33        13.05        34.36        11.54 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6021 TCGA-CN-6994 TCGA-CQ-5323 TCGA-CQ-5324 
       22.45        56.94         9.07        24.16        48.20        39.68 
TCGA-CQ-6218 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6933 
       41.19        38.76        33.11        76.50        86.83        90.12 
TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6956 TCGA-CV-6960 
       20.52        11.24         6.08        53.95         7.13        28.34 
TCGA-CV-7091 TCGA-CV-7177 TCGA-CV-7238 TCGA-CV-7242 TCGA-CV-7243 TCGA-CV-7245 
      111.16        21.80        47.47        36.00        31.36        26.20 
TCGA-CV-7250 TCGA-CV-7255 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7423 TCGA-CV-7428 
       95.34         2.10        89.33         9.67       100.57        54.94 
TCGA-CV-7434 TCGA-CX-7085 TCGA-CX-7086 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 
        7.17        10.55        18.84         9.60         2.53        11.44 
TCGA-IQ-7632 
       14.50 

subtype1 subtype2 subtype3 
    2.50     0.07     2.10 
subtype1 subtype2 subtype3 
  156.49   210.97   111.16 
subtype1 subtype2 subtype3 
  20.565   19.790   26.200 
[1] "2.5 - 156.5 (20.6)" "0.1 - 211.0 (19.8)" "2.1 - 111.2 (26.2)"
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       3       18        12        41         1
  subtype2       2       11         7        57         2
  subtype3       4       10        12        19         1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          3        2        4
  STAGE II        18       11       10
  STAGE III       12        7       12
  STAGE IVA       41       57       19
  STAGE IVB        1        2        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"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     5 26 12 33
  subtype2     4 19 27 31
  subtype3     4 14 14 15
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1        5        4        4
  T2          26       19       14
  T3          12       27       14
  T4          33       31       15
[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 29  9 26  1
  subtype2 15  5 45  2
  subtype3 28  7  8  1
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       29       15       28
  N1        9        5        7
  N2       26       45        8
  N3        1        2        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus       0
  subtype1 9
  subtype2 8
  subtype3 5
[1] "NOT AVAILABLE: table only has an event [0]"
D4V7, binary
          cls
clus        0  1
  subtype1 22 56
  subtype2 21 64
  subtype3 19 30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   56
  subtype2   21   64
  subtype3   19   30
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       22       21       19
  MALE         56       64       30
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    78
  subtype2                                    85
  subtype3                                    49
[1] "NOT AVAILABLE: table dimension [3x1]"
D4V9, binary
          cls
clus        0  1
  subtype1 22 56
  subtype2 28 57
  subtype3 11 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   56
  subtype2   28   57
  subtype3   11   38
     clus
vv    subtype1 subtype2 subtype3
  NO        22       28       11
  YES       56       57       38
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V10, continuous
D4V11, continuous
D4V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     0                        10
  subtype2                                0     2                         6
  subtype3                                0     1                         3
          vv
clus       WHITE
  subtype1    65
  subtype2    74
  subtype3    44
D4V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0
  ASIAN                                   0        2        1
  BLACK OR AFRICAN AMERICAN              10        6        3
  WHITE                                  65       74       44
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V14, binary
          cls
clus        0  1
  subtype1  7 69
  subtype2  4 75
  subtype3  2 46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   69
  subtype2    4   75
  subtype3    2   46
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            7        4        2
  NOT HISPANIC OR LATINO       69       75       46
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2        0   1
  subtype1  79  63
  subtype2 139  71
  subtype3  93  66
subtype1 subtype2 subtype3 
     142      210      159 
subtype1 subtype2 subtype3 
      63       71       66 
$subtype1
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DB 
        3.35         9.30        26.50        57.44         4.01         7.10 
TCGA-BA-A6DG TCGA-BA-A8YP TCGA-BB-7872 TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 
        2.27        16.41        38.40        71.05        38.04        37.84 
TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5358 
       21.11        12.99        20.55        27.58        33.11         8.58 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6013 
        8.32        16.21        11.84        11.57         8.52        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 
       19.53        20.68        19.07        14.20         9.24        11.08 
TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-A642 TCGA-CQ-5325 TCGA-CQ-5329 
       20.09         3.68        17.42         2.70        21.50        46.75 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 
       45.80        11.21        15.75        66.28        56.58         4.24 
TCGA-CQ-6229 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CH 
       38.76        16.73        64.11        44.48        11.61        12.46 
TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 
       18.54        16.90        12.46        39.16        24.95        31.96 
TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
        9.17        26.17        17.13        47.01        30.02        31.10 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 
        7.10        35.41       108.95        76.24        19.20       107.51 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5979 
       80.12        17.92        13.35        23.05        48.59        43.23 
TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6940 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6956 
        9.60         2.14        26.43        15.09        30.08         7.13 
TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7103 
        8.42         2.50        18.81        12.66         1.84        52.31 
TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7263 
       12.92        71.21        47.47        31.36        18.97        18.41 
TCGA-CV-7406 TCGA-CV-7415 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7568 
       57.47        22.85         3.52       153.86         6.38        30.48 
TCGA-CV-A45R TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 
      180.16        56.61        15.25        22.03         3.62        19.92 
TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 
       10.42        10.55        13.25        16.14        24.95        25.32 
TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 
       17.72         7.63        58.45        35.54        33.86        18.02 
TCGA-DQ-7592 TCGA-F7-8298 TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-H7-A6C4 
        9.83        16.11        12.62         0.46        17.85        13.61 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61H 
        0.16        14.66        22.85         3.65        19.33        13.55 
TCGA-IQ-A61J TCGA-IQ-A61O TCGA-KU-A6H8 TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T2 
       14.47        11.84        10.75        56.75        47.01        75.55 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A8Z9 TCGA-UF-A71A TCGA-UF-A7JD 
       13.15        11.74         7.30        11.57         2.83        24.16 
TCGA-UF-A7JH TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-WA-A7H4 
       21.86        22.36        20.55        14.56 

$subtype2
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6868 
       15.19        37.28         9.07        57.93        17.10        15.52 
TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A4IG TCGA-BA-A4IH 
       21.17         3.55         7.76        29.42        28.11        20.45 
TCGA-BA-A6D8 TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
       27.95        11.05        20.48         6.15        94.62         4.60 
TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 
        4.41        18.35        22.42        36.72        50.20        44.98 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A5HY TCGA-BB-A6UM TCGA-CN-4723 
       66.28        24.66        20.52        10.55        12.92        23.70 
TCGA-CN-4727 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-4741 
       40.44        32.65        41.10        14.33        43.73        41.69 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5361 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
       34.36        35.54        55.27        56.94        20.71        20.68 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 
        9.07        36.49        10.45        12.95        24.16        14.10 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A49C 
       35.01        14.56        17.59        12.85        29.72        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 
        7.40        17.29        10.09         7.33         9.80         7.69 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6225 TCGA-CQ-6228 
        6.18        48.20        10.42        32.88        13.25        14.99 
TCGA-CQ-A4C9 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 
       23.24        29.36        32.81        14.14        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       34.52        36.99         6.02        11.90        10.22        11.34 
TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 
        7.69        47.18        40.93        35.84         3.45         3.09 
TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7393 TCGA-CR-7398 
        0.99        32.78        27.06        12.89        29.85         5.13 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.95        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5443 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6936 
       91.53         7.07        21.07        90.12         9.70         5.46 
TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6960 
       20.52        21.90        11.24       126.08        42.38        28.34 
TCGA-CV-6962 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7236 
        4.14         9.01         5.26        21.80        77.16         4.73 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 
       36.00        26.20        17.13        95.34        11.87        47.97 
TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 
       36.13        35.54        17.85         0.46        25.94         0.07 
TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-7446 
       34.09        14.89        16.27        16.64        22.19        35.93 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       35.47        45.96        88.87        48.20        60.43        67.86 
TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A6EO 
        5.98        23.47         2.53        11.44        18.67        14.30 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 
       13.94        11.11        30.94        18.90        25.48        20.45 
TCGA-DQ-7593 TCGA-DQ-7594 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       12.13        12.10        10.65        11.18        37.18        21.63 
TCGA-F7-A50I TCGA-F7-A624 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A634 
        3.02        12.43         6.77        25.74        22.03         4.27 
TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-KU-A66S TCGA-KU-A6H7 
       34.75        12.76        11.84         0.07        13.35        12.43 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE 
       15.42         7.13        16.08        29.92        15.78        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T6 TCGA-QK-A64Z TCGA-QK-A6IF 
       10.85        36.82        19.00        12.99        21.07        17.65 
TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       18.64        14.79        12.43         6.51         5.62        12.10 
TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-TN-A7HI 
        9.76         8.32        16.96         6.87         7.10        13.55 
TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E 
       13.68        43.59        54.67        43.36        41.16        42.02 
TCGA-UF-A7J9 TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JV TCGA-UP-A6WW 
       44.65        62.27        49.22        20.75         2.96        17.03 

$subtype3
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 
       13.64        23.74        42.35        23.84        20.48        53.79 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE 
       14.83        12.62        30.18        11.54         5.69        14.47 
TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-A5HU TCGA-BB-A5HZ TCGA-BB-A6UO 
       13.38         9.14        33.70        25.71        27.19         8.81 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
        6.28        12.69        26.27         4.67        12.89        26.86 
TCGA-CN-4734 TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5373 
       24.92        13.05        12.39        11.54        12.49        22.45 
TCGA-CN-6011 TCGA-CN-6020 TCGA-CN-6998 TCGA-CN-A63V TCGA-CN-A63W TCGA-CN-A641 
       30.67         6.74        11.74        15.91        11.44        12.07 
TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 
       39.68         2.93        54.58        45.99         4.24        41.19 
TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-7063 TCGA-CQ-7065 TCGA-CQ-7068 TCGA-CQ-7069 
       32.38        34.75        70.13        33.11        43.04        41.88 
TCGA-CQ-7071 TCGA-CQ-A4CE TCGA-CR-6471 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 
       28.83        25.81        39.52        11.64        11.51        15.75 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7390 
        9.27        47.34        29.23        34.06        19.92        29.82 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5973 
       29.52        30.58        17.95        94.88        76.50        86.83 
TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-6945 
       60.49        54.74        62.43         4.73        19.79        12.03 
TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-7089 TCGA-CV-7090 
        6.08        53.95        65.82        10.98        64.83       126.15 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7252 TCGA-CV-7255 
      111.16         7.99        10.75       130.88         4.96         2.10 
TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7425 
      210.97        89.33         9.67        25.08       100.57        56.48 
TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
      156.49        54.94        84.49        19.76         7.17        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A463 
       24.99       169.38       159.65         1.05         6.51         0.76 
TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY 
        7.07        35.34         6.38        29.79         6.48        21.24 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 
       22.52        10.42        18.84        34.36        25.41         9.60 
TCGA-D6-6823 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-7588 
       23.05        12.36        15.88        12.10        12.79        14.04 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A622 TCGA-F7-A623 TCGA-H7-7774 
       20.25        19.23        18.94        11.80        20.25        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-8634 TCGA-HD-A4C1 
       15.16        15.06         0.07         1.22        12.66         0.36 
TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-KU-A66T TCGA-MT-A51W 
       13.84         6.90        15.95        14.50        18.15        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A7D7 TCGA-P3-A6T3 
        7.96        30.05         1.84        12.62        17.98        18.97 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ 
        2.04        29.00        16.01        16.70         9.34        12.72 
TCGA-QK-A8ZB TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-UF-A7JC 
        9.73        12.72        15.91        32.45        13.25        17.95 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT 
       16.11        13.94        32.65 

subtype1 subtype2 subtype3 
    0.16     0.07     0.07 
subtype1 subtype2 subtype3 
  180.16   139.43   210.97 
subtype1 subtype2 subtype3 
  18.215   19.725   17.950 
[1] "0.2 - 180.2 (18.2)" "0.1 - 139.4 (19.7)" "0.1 - 211.0 (17.9)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      15       24        20        71         4         0
  subtype2       4       25        30        97         5         1
  subtype3       8       26        26        85         3         0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         15        4        8
  STAGE II        24       25       26
  STAGE III       20       30       26
  STAGE IVA       71       97       85
  STAGE IVB        4        5        3
  STAGE IVC        0        1        0
[1] 6 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    19 49 27 41
  subtype2    18 45 39 64
  subtype3    12 38 32 68
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       19       18       12
  T2          49       45       38
  T3          27       39       32
  T4          41       64       68
[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 47 19 59  3
  subtype2 62 23 61  4
  subtype3 66 23 46  1
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       47       62       66
  N1       19       23       23
  N2       59       61       46
  N3        3        4        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 53  0
  subtype2 64  1
  subtype3 62  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53    0
  subtype2   64    1
  subtype3   62    0
   clus
vv  subtype1 subtype2 subtype3
  0       53       64       62
  1        0        1        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus         0   1
  subtype1  37 107
  subtype2  41 169
  subtype3  57 103
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37  107
  subtype2   41  169
  subtype3   57  103
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       37       41       57
  MALE        107      169      103
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   143
  subtype2                                   200
  subtype3                                   160
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           1
  subtype2                                                           0
  subtype3                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   0
  subtype2                                                  10
  subtype3                                                   0
D5V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            143      200
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0       10
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            160
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V9, binary
          cls
clus         0   1
  subtype1  29 115
  subtype2  31 179
  subtype3  23 137
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29  115
  subtype2   31  179
  subtype3   23  137
     clus
vv    subtype1 subtype2 subtype3
  NO        29       31       23
  YES      115      179      137
[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, continuous
D5V11, continuous
D5V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     4                        11
  subtype2                                1     1                        23
  subtype3                                0     6                        11
          vv
clus       WHITE
  subtype1   121
  subtype2   179
  subtype3   139
D5V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   4        1        6
  BLACK OR AFRICAN AMERICAN              11       23       11
  WHITE                                 121      179      139
[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"
D5V14, binary
          cls
clus         0   1
  subtype1  10 126
  subtype2   9 179
  subtype3   5 148
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  126
  subtype2    9  179
  subtype3    5  148
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           10        9        5
  NOT HISPANIC OR LATINO      126      179      148
[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  95  82
  subtype2  61  41
  subtype3 102  66
  subtype4  53  11
subtype1 subtype2 subtype3 subtype4 
     177      102      168       64 
subtype1 subtype2 subtype3 subtype4 
      82       41       66       11 
$subtype1
TCGA-4P-AA8J TCGA-BA-4075 TCGA-BA-5149 TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-A6DB 
        3.35         9.30        26.50        57.44         4.01         7.10 
TCGA-BA-A6DG TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z 
        2.27        16.41         9.14        38.40        71.05         6.28 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 
       12.69        38.04         4.67        37.84        21.11        12.99 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 
       20.55        27.58        13.05        33.11         8.58        35.54 
TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        8.32        16.21        11.84        11.57         8.52        22.45 
TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 TCGA-CN-6019 
       56.94        20.65        19.53        20.68        19.07        14.20 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 
        9.24        11.08        20.09         3.68        17.42        11.74 
TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        2.70         7.69        21.50        54.58        46.75        45.80 
TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 
       11.21        15.75        32.38        66.28        56.58         4.24 
TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       38.76        33.11        16.73        64.11        44.48        11.61 
TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 
       12.46        18.54        16.90        12.46         9.27        39.16 
TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 
       24.95        31.96         9.17        34.06        26.17        17.13 
TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 
       47.01        30.02        31.10        29.85        29.52         7.10 
TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 
       35.41       108.95        76.24        19.20       107.51        80.12 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 
       17.92        13.35        23.05        48.59        60.49        43.23 
TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6940 TCGA-CV-6943 TCGA-CV-6950 
       54.74         9.60         2.14        26.43        19.79        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7095 
       30.08         6.08         7.13         8.42         2.50        18.81 
TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7238 
       12.66         1.84        52.31        12.92        71.21        47.47 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7422 
       31.36        18.97         2.10        18.41        57.47        34.09 
TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45P 
      100.57         3.52       153.86         6.38        30.48        24.99 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 
      169.38       180.16       159.65        56.61         7.07        15.25 
TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7085 
       29.79        22.03         3.62        19.92        10.42        10.55 
TCGA-D6-6515 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM 
       13.25        16.14        24.95        25.32        17.72         7.63 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7594 
       58.45        35.54        33.86        18.02         9.83        12.10 
TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-H7-A6C4 
       20.25        19.23         0.46        17.85        11.80        13.61 
TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 TCGA-HD-8635 TCGA-HD-A6HZ 
        0.16        14.66        22.03        12.66        22.85         3.65 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-MT-A51X TCGA-P3-A5QA 
       19.33        13.55        14.47        10.75         7.96        56.75 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IG 
       47.01        75.55        18.97        13.15        11.74         7.30 
TCGA-QK-A6II TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
        9.34         2.83        44.65        17.95        24.16        21.86 
TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        20.55        14.56 

$subtype2
TCGA-BA-4074 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-7269 TCGA-BA-A4IF TCGA-BA-A6D8 
       15.19        17.10        21.17         7.76        29.42        27.95 
TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
       14.47        20.48        36.72        50.20        66.28        24.66 
TCGA-BB-8601 TCGA-BB-A5HZ TCGA-CN-4727 TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4738 
       20.52        27.19        40.44        26.86        32.65        14.33 
TCGA-CN-5356 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 
       34.36        20.71        20.68         9.07        36.49        10.45 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W 
       12.95        14.10        35.01         7.40        17.29        11.44 
TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-A4C9 
       12.07        39.68        10.42        13.25        14.99        23.24 
TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-7364 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 
       31.23        11.77        47.18         3.45         3.09         0.99 
TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7402 TCGA-CV-5432 TCGA-CV-5441 
       27.06        29.82         5.13        29.95       129.21        94.88 
TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6948 
        7.07        90.12         9.70        21.90        11.24        42.38 
TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7242 
       65.82        28.34         4.14         5.26        21.80        36.00 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       26.20        17.13        95.34        11.87        47.97        36.13 
TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7424 
       35.54        17.85         0.46        25.94         0.07        14.89 
TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45W 
       54.94        16.27        16.64        22.19        35.93        45.96 
TCGA-CV-A45Z TCGA-CV-A461 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-A6EO TCGA-D6-A74Q 
       48.20        67.86        23.05         2.53        14.30        11.11 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A61V TCGA-IQ-7631 
       30.94        18.90        10.65        37.18        12.62        12.76 
TCGA-KU-A66S TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-TN-A7HI 
       13.35        14.79         6.51         5.62        12.10        13.55 
TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JF TCGA-UF-A7JO 
       54.67        43.36        41.16        42.02        49.22        20.75 

$subtype3
TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5557 
       13.64        37.28        23.74        42.35        23.84        20.48 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A4II TCGA-BA-A6DA 
       53.79        15.52        14.83        12.62        30.18        11.54 
TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-A5HU 
        5.69        11.05        13.38         4.41        33.70        25.71 
TCGA-BB-A5HY TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4734 
       10.55         8.81        26.27        23.70        12.89        24.92 
TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-6011 TCGA-CN-6020 
       12.39        55.27        11.54        12.49        30.67         6.74 
TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A TCGA-CN-A49B TCGA-CN-A63V 
       24.16        14.56        17.59        12.85        29.72        15.91 
TCGA-CN-A6V3 TCGA-CQ-5326 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6221 
        9.80         2.93        45.99         4.24        41.19        32.88 
TCGA-CQ-6223 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CB 
       34.75        70.13        43.04        41.88        28.83        29.36 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-6471 TCGA-CR-6478 TCGA-CR-6484 
       32.81        25.81        14.14        39.52         6.02        11.64 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7380 TCGA-CR-7389 
       11.51        15.75        47.34        29.23        19.92        12.89 
TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6436 TCGA-CV-6936 
       30.58        17.95        76.50        86.83        62.43         5.46 
TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6953 TCGA-CV-6955 
       20.52         4.73       126.08        12.03        53.95        10.98 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 
       64.83       126.15       111.16         7.99         9.01        10.75 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7252 TCGA-CV-7410 TCGA-CV-7411 
      130.88        77.16         4.73         4.96       210.97        89.33 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7432 
        9.67        22.85        25.08        56.48       156.49        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X 
       19.76         7.17        27.98        35.47         1.05         6.51 
TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO 
       88.87         0.76         5.98        35.34         6.38         6.48 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7086 TCGA-CX-7219 
       21.24        23.47        22.52        10.42        18.84        34.36 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EP 
       25.41         9.60        11.44        12.36        15.88        13.94 
TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-7588 TCGA-F7-8298 TCGA-F7-8489 TCGA-F7-A50I 
       12.10        12.79        14.04        16.11        21.63         3.02 
TCGA-F7-A61S TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 
       18.94        20.25        12.43        13.38        15.16        15.06 
TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 
        0.07         1.22         0.36        13.84         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61O TCGA-KU-A66T 
       34.75        15.95        14.50        11.84        11.84        18.15 
TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A7D7 
       14.37        30.05         1.84        12.62        15.42        17.98 
TCGA-P3-A5Q6 TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z 
       15.78        19.00         2.04        29.00        16.01        21.07 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K 
       16.70        12.72        12.43        11.57         9.73         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HJ 
       12.72        16.96         6.87        15.91        32.45        13.25 
TCGA-UF-A718 TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT TCGA-UF-A7JV 
       43.59        62.27        16.11        13.94        32.65         2.96 

$subtype4
TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BB-4217 
        9.07        57.93         3.55        28.11        20.45         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7866 TCGA-BB-A6UM 
       94.62         4.60        18.35        22.42        44.98        12.92 
TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-A49C TCGA-CN-A6UY TCGA-CN-A6V1 
       41.10        43.73        41.69        21.21        10.09         7.33 
TCGA-CN-A6V7 TCGA-CQ-5323 TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 
        6.18        48.20        84.23        54.67        37.87        26.27 
TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 
       58.42        50.01        34.52        36.99        11.90        10.22 
TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7385 TCGA-CR-7399 
       11.34         7.69        40.93        35.84        32.78         5.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5443 TCGA-CV-6433 TCGA-CV-A460 
       48.39       139.43        17.16        91.53        21.07        60.43 
TCGA-D6-6827 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-H7-A76A 
       18.67        25.48        20.45        12.13        11.18         6.77 
TCGA-HD-7754 TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       25.74         0.07        12.43         7.13        16.08        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6V9 
       51.25        10.85        36.82        12.99        17.65        18.64 
TCGA-QK-AA3J TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UP-A6WW 
        9.76         7.10        13.68        17.03 

subtype1 subtype2 subtype3 subtype4 
    0.16     0.07     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 
  180.16   129.21   210.97   139.43 
subtype1 subtype2 subtype3 subtype4 
   18.97    20.73    15.91    20.45 
[1] "0.2 - 180.2 (19.0)" "0.1 - 129.2 (20.7)" "0.1 - 211.0 (15.9)"
[4] "0.1 - 139.4 (20.4)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      17       26        31        88         4         0
  subtype2       0       15        17        54         3         1
  subtype3       6       29        22        90         4         0
  subtype4       4        5         6        21         1         0
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         17        0        6        4
  STAGE II        26       15       29        5
  STAGE III       31       17       22        6
  STAGE IVA       88       54       90       21
  STAGE IVB        4        3        4        1
  STAGE IVC        0        1        0        0
[1] 6 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    25 54 42 47
  subtype2     5 22 23 41
  subtype3     9 42 25 77
  subtype4    10 14  8  8
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       25        5        9       10
  T2          54       22       42       14
  T3          42       23       25        8
  T4          47       41       77        8
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 58 25 71  3
  subtype2 37 12 31  3
  subtype3 70 23 45  1
  subtype4 10  5 19  1
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       58       37       70       10
  N1       25       12       23        5
  N2       71       31       45       19
  N3        3        3        1        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 68  0
  subtype2 27  1
  subtype3 67  0
  subtype4 17  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68    0
  subtype2   27    1
  subtype3   67    0
  subtype4   17    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       68       27       67       17
  1        0        1        0        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus         0   1
  subtype1  53 126
  subtype2  22  80
  subtype3  56 113
  subtype4   4  60
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53  126
  subtype2   22   80
  subtype3   56  113
  subtype4    4   60
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       53       22       56        4
  MALE        126       80      113       60
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   178
  subtype2                                    98
  subtype3                                   168
  subtype4                                    59
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           0
  subtype3                                                           1
  subtype4                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   1
  subtype2                                                   4
  subtype3                                                   0
  subtype4                                                   5
D6V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            178       98
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1        4
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            168       59
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        5
[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"
D6V9, binary
          cls
clus         0   1
  subtype1  35 144
  subtype2  14  88
  subtype3  18 151
  subtype4  16  48
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35  144
  subtype2   14   88
  subtype3   18  151
  subtype4   16   48
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        35       14       18       16
  YES      144       88      151       48
[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"
D6V10, continuous
D6V11, continuous
D6V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                        11
  subtype2                                0     1                        14
  subtype3                                1     2                        15
  subtype4                                0     0                         5
          vv
clus       WHITE
  subtype1   152
  subtype2    83
  subtype3   145
  subtype4    59
D6V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0
  ASIAN                                   8        1        2        0
  BLACK OR AFRICAN AMERICAN              11       14       15        5
  WHITE                                 152       83      145       59
[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"
D6V14, binary
          cls
clus         0   1
  subtype1  10 159
  subtype2   2  88
  subtype3   8 149
  subtype4   4  57
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  159
  subtype2    2   88
  subtype3    8  149
  subtype4    4   57
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           10        2        8        4
  NOT HISPANIC OR LATINO      159       88      149       57
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2        0   1
  subtype1 137  82
  subtype2  98  52
  subtype3  79  67
subtype1 subtype2 subtype3 
     219      150      146 
subtype1 subtype2 subtype3 
      82       52       67 
$subtype1
TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5555 TCGA-BA-6870 
        3.35        13.64        37.28         9.07        17.10        14.83 
TCGA-BA-6871 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DL 
        3.55        20.45        27.95         5.69        11.05        20.48 
TCGA-BA-A8YP TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4227 TCGA-BB-4228 TCGA-BB-7861 
       16.41        94.62         4.60         4.41        18.35        22.42 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A6UO 
       36.72        50.20        66.28        24.66        20.52         8.81 
TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 
       26.27        23.70        32.65        41.10        14.33        43.73 
TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 
       41.69        34.36        12.39        35.54        56.94        20.71 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 
       20.68        20.65        19.07        36.49        10.45        12.95 
TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A49A TCGA-CN-A49C TCGA-CN-A63V 
       24.16        14.10        35.01        12.85        21.21        15.91 
TCGA-CN-A63Y TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-5324 
        5.75        10.09         7.33         9.80        48.20        39.68 
TCGA-CQ-5326 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 
        2.93        10.42        41.19        34.75        13.25        14.99 
TCGA-CQ-7068 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CI 
       43.04        41.88        64.11        23.24        32.81        31.23 
TCGA-CR-5243 TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       84.23        11.77        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 
       50.01        39.52        34.52        11.90        10.22        11.34 
TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        7.69        47.18        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7398 
        3.09         0.99        32.78        27.06        12.89         5.13 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5432 
        5.95        29.95        48.39       139.43        17.16       129.21 
TCGA-CV-5435 TCGA-CV-5443 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6933 TCGA-CV-6935 
       76.24        91.53         7.07        21.07        90.12         9.70 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6953 
        5.46        20.52        21.90        11.24        42.38        53.95 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 
       28.34         4.14       111.16         7.99         9.01         5.26 
TCGA-CV-7177 TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
       21.80         4.73        36.00        26.20        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7409 
        4.96        11.87        47.97        36.13        57.47        17.85 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7424 
        0.46        22.85        25.08        25.94         0.07        14.89 
TCGA-CV-7425 TCGA-CV-7430 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7446 
       56.48        16.27         7.17       153.86        16.64        35.93 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A461 
       35.47        45.96        88.87        48.20        60.43        67.86 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 
        5.98        35.34         6.38        23.47        22.52        10.42 
TCGA-CX-7082 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB TCGA-D6-A6EP 
       10.42         9.60        11.44        18.67        12.36        13.94 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-DQ-7596 
       12.79        11.11        30.94        20.45        10.65        11.18 
TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-H7-7774 TCGA-H7-A6C5 TCGA-H7-A76A 
       37.18        16.11         3.02        13.38        21.11         6.77 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A633 TCGA-HD-A634 TCGA-IQ-7631 TCGA-IQ-A61O 
       25.74         1.22        13.84         4.27        12.76        11.84 
TCGA-KU-A66S TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A7D7 
       13.35        12.43         3.68        15.42         7.13        17.98 
TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 
       29.92        15.78        51.25        10.85        36.82        19.00 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IF 
        2.04        29.00        12.99        16.01        21.07        17.65 
TCGA-QK-A6IH TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       16.70        18.64        14.79         6.51         5.62        12.10 
TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-QK-AA3K TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X0 
        9.73         9.76         8.32        16.96        15.91         7.10 
TCGA-T2-A6X2 TCGA-TN-A7HI TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 
       32.45        13.55        13.25        13.68        43.59        54.67 
TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        2.83        43.36        41.16        42.02        44.65        62.27 
TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UP-A6WW 
       49.22        20.75        17.03 

$subtype2
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 
       15.19        26.50        23.74        42.35        57.93        23.84 
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6872 TCGA-BA-A4IF 
       20.48        53.79        15.52        21.17        12.62        29.42 
TCGA-BA-A4IG TCGA-BA-A4II TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DJ 
       28.11        30.18        11.54        14.47         7.82        13.38 
TCGA-BB-4217 TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-7872 TCGA-BB-A5HU 
        6.15         9.14        33.70        44.98        38.40        25.71 
TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4726 TCGA-CN-4727 
       10.55        27.19         6.28        12.69         4.67        40.44 
TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-5361 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-5373 
       12.89        26.86        55.27        11.54        12.49        22.45 
TCGA-CN-6011 TCGA-CN-6021 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 
       30.67         9.07         3.68        11.74        14.56        17.59 
TCGA-CN-A49B TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A642 
       29.72         7.40        17.29        11.44        12.07         2.70 
TCGA-CN-A6V7 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6221 TCGA-CQ-7063 TCGA-CQ-7064 
        6.18        45.99         4.24        32.88        70.13        51.29 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CB TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH 
       28.83        44.48        29.36        25.81        14.14        12.46 
TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 
       36.99         6.02        11.64        11.51        15.75         9.27 
TCGA-CR-7373 TCGA-CR-7390 TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5441 
       29.23        29.82        29.52        30.58        17.95        94.88 
TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6954 
       76.50        86.83        60.49        62.43         4.73        65.82 
TCGA-CV-6955 TCGA-CV-7089 TCGA-CV-7235 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       10.98        64.83        77.16       210.97        89.33         9.67 
TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7440 TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45T 
      156.49        84.49        22.19        27.98        24.99       159.65 
TCGA-CV-A45X TCGA-CV-A463 TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY 
        6.51         0.76         7.07        29.79         6.48        21.24 
TCGA-CX-7086 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6823 TCGA-D6-A4Z9 TCGA-D6-A6EK 
       18.84        34.36        25.41        23.05        17.72        15.88 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5631 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-DQ-7593 
       14.30        12.10        18.02        14.04        18.90        12.13 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V TCGA-F7-A620 
       21.63        20.25        19.23        18.94        12.62        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 
       11.80        20.25        12.43        15.16        15.06         0.07 
TCGA-HD-7753 TCGA-HD-8634 TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 
        0.16        12.66         0.36         6.90        34.75        15.95 
TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L 
       14.50        19.33        11.84         0.07         5.29        11.54 
TCGA-KU-A66T TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MZ-A6I9 
       18.15        14.37        30.05         1.84        12.62        16.08 
TCGA-P3-A5QA TCGA-P3-A6T3 TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC 
       56.75        18.97         7.30         9.34        12.72        12.43 
TCGA-RS-A6TO TCGA-T2-A6WX TCGA-UF-A7JJ TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       12.72         6.87        16.11        22.36        32.65         2.96 

$subtype3
TCGA-BA-5559 TCGA-BA-6873 TCGA-BA-7269 TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BB-8596 
       57.44         4.01         7.76         7.10         2.27        71.05 
TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 
       38.04        37.84        21.11        12.99        20.55        27.58 
TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 
       13.05        33.11         8.58         8.32        16.21        11.84 
TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6020 
       11.57         8.52        19.53        20.68        14.20         6.74 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A640 TCGA-CN-A6V6 
        9.24        11.08        20.09        17.42         4.41         7.69 
TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 
       21.50        54.58        46.75        45.80        11.21        15.75 
TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7065 
       32.38        66.28        56.58         4.24        38.76        33.11 
TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 
       16.73        11.61        18.54        16.90        12.46        39.16 
TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       24.95        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7397 
       17.13        47.01        30.02        31.10        29.85         7.10 
TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 
       35.41       108.95        19.20       107.51        80.12        17.92 
TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
       13.35        23.05        48.59        43.23        54.74         9.60 
TCGA-CV-6934 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
        2.14        26.43       126.08        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 
       30.08         6.08         7.13         8.42         2.50       126.15 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 
       18.81        12.66         1.84        52.31        12.92        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7255 
       10.75       130.88        47.47        31.36        18.97         2.10 
TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7428 TCGA-CV-7429 
       18.41        35.54        34.09       100.57        54.94         3.52 
TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45V 
       19.76         6.38        30.48       169.38       180.16         1.05 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7085 
       56.61        15.25        22.03         3.62        19.92        10.55 
TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EM 
       13.25         2.53        16.14        24.95        25.32         7.63 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7592 TCGA-DQ-7594 
       58.45        35.54        33.86        25.48         9.83        12.10 
TCGA-F7-A61W TCGA-H7-A6C4 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A6HZ 
        0.46        13.61        14.66        22.03        22.85         3.65 
TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-MT-A51X TCGA-P3-A6SX TCGA-P3-A6T2 
       13.55        14.47        10.75         7.96        47.01        75.55 
TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A8Z9 TCGA-UF-A7JC TCGA-UF-A7JD TCGA-UF-A7JH 
       13.15        11.74        11.57        17.95        24.16        21.86 
TCGA-UF-A7JK TCGA-WA-A7H4 
       13.94        14.56 

subtype1 subtype2 subtype3 
    0.07     0.07     0.46 
subtype1 subtype2 subtype3 
  153.86   210.97   180.16 
subtype1 subtype2 subtype3 
  18.670   17.655   18.890 
[1] "0.1 - 153.9 (18.7)" "0.1 - 211.0 (17.7)" "0.5 - 180.2 (18.9)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       6       28        27       113         7         1
  subtype2      10       23        25        70         2         0
  subtype3      11       26        23        74         3         0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          6       10       11
  STAGE II        28       23       26
  STAGE III       27       25       23
  STAGE IVA      113       70       74
  STAGE IVB        7        2        3
  STAGE IVC        1        0        0
[1] 6 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    15 45 43 81
  subtype2    16 39 29 50
  subtype3    18 50 27 43
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       15       16       18
  T2          45       39       50
  T3          43       29       27
  T4          81       50       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       N0 N1 N2 N3
  subtype1 78 20 69  5
  subtype2 56 23 40  2
  subtype3 42 23 59  1
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       78       56       42
  N1       20       23       23
  N2       69       40       59
  N3        5        2        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 69  1
  subtype2 67  0
  subtype3 47  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69    1
  subtype2   67    0
  subtype3   47    0
   clus
vv  subtype1 subtype2 subtype3
  0       69       67       47
  1        1        0        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus         0   1
  subtype1  47 172
  subtype2  48 103
  subtype3  46 102
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   47  172
  subtype2   48  103
  subtype3   46  102
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       47       48       46
  MALE        172      103      102
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   209
  subtype2                                   151
  subtype3                                   147
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           1
  subtype2                                                           0
  subtype3                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   9
  subtype2                                                   0
  subtype3                                                   1
D7V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            209      151
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                9        0
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            147
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V9, binary
          cls
clus         0   1
  subtype1  32 187
  subtype2  19 132
  subtype3  31 117
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32  187
  subtype2   19  132
  subtype3   31  117
     clus
vv    subtype1 subtype2 subtype3
  NO        32       19       31
  YES      187      132      117
[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"
D7V10, continuous
D7V11, continuous
D7V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        25
  subtype2                                0     7                        11
  subtype3                                1     3                         8
          vv
clus       WHITE
  subtype1   188
  subtype2   128
  subtype3   128
D7V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   1        7        3
  BLACK OR AFRICAN AMERICAN              25       11        8
  WHITE                                 188      128      128
[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"
D7V14, binary
          cls
clus         0   1
  subtype1   8 190
  subtype2   7 135
  subtype3  10 131
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  190
  subtype2    7  135
  subtype3   10  131
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        7       10
  NOT HISPANIC OR LATINO      190      135      131
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 103  88
  subtype2  87  55
  subtype3 124  58
subtype1 subtype2 subtype3 
     191      142      182 
subtype1 subtype2 subtype3 
      88       55       58 
$subtype1
TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-5559 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
        3.35        26.50        57.44        12.62         4.01        29.42 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A8YP TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A47Z 
        7.10         2.27        16.41        38.40        71.05         6.28 
TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 TCGA-CN-4737 
       12.69        38.04        37.84        21.11        12.99        20.55 
TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5360 TCGA-CN-5363 
       27.58        13.05        33.11         8.58        35.54         8.32 
TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6013 
       16.21        11.84        11.57         8.52        22.45        20.65 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6989 
       19.53        20.68        14.20         9.24        11.08        20.09 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A63V TCGA-CN-A640 
        3.68        17.42        11.74        12.85        15.91         4.41 
TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 
        2.70         7.69        21.50        54.58        46.75        45.80 
TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6224 
       11.21         4.24        15.75        32.38        66.28        56.58 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7067 TCGA-CQ-7072 
        4.24        38.76        51.29        33.11        16.73        64.11 
TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 
       44.48        11.61        25.81        12.46        18.54        16.90 
TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       12.46        39.16        24.95        31.96         9.17        34.06 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       26.17        17.13        47.01        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       29.52         7.10        35.41       129.21       108.95        76.24 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 
       19.20       107.51        80.12        17.92        13.35        23.05 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6934 
       48.59        60.49        43.23        54.74         9.60         2.14 
TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 
        9.70        26.43        19.79        12.03        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 
        6.08         7.13         8.42         2.50        18.81        12.66 
TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7238 
        1.84        52.31        12.92        71.21        10.75        47.47 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 
       31.36        18.97        11.87         2.10        18.41        57.47 
TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7433 
       35.54         0.46        34.09       100.57         3.52        19.76 
TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
        6.38        30.48        24.99       169.38       180.16       159.65 
TCGA-CV-A45V TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU 
        1.05        56.61         7.07        15.25        22.03         3.62 
TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6825 TCGA-D6-8568 
       19.92        10.42        10.55        13.25        16.14        24.95 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 
       25.32        17.72         7.63        58.45        35.54        33.86 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 
       18.02         9.83        12.10        12.62         0.46        17.85 
TCGA-F7-A622 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8634 
       11.80        13.61         0.16        14.66        22.03        12.66 
TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
       22.85         3.65        15.95        19.33        13.55        14.47 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-P3-A5QA 
        5.29        11.54        10.75         7.96        30.05        56.75 
TCGA-P3-A6SX TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T8 TCGA-QK-A652 TCGA-QK-A6IG 
       47.01        75.55        18.97        13.15        11.74         7.30 
TCGA-QK-A6II TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JC 
        9.34        11.57         9.76         2.83        44.65        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 
       24.16        21.86        22.36        32.65        14.56 

$subtype2
TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6870 
       13.64        42.35        17.10        23.84        53.79        14.83 
TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DL TCGA-BB-4227 
        7.76        27.95        14.47         7.82        20.48         4.41 
TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-CN-4722 
       33.70        66.28        25.71        10.55        27.19        26.27 
TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-5356 
       23.70        12.89        26.86        14.33        43.73        34.36 
TCGA-CN-5361 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6018 
       55.27        11.54        12.49        20.71        30.67        19.07 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-A63T TCGA-CN-A63U 
        6.74        10.45        12.95        24.16         7.40        17.29 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V3 TCGA-CQ-5332 TCGA-CQ-6221 TCGA-CQ-6223 
       11.44        12.07         9.80        10.42        32.88        34.75 
TCGA-CQ-6225 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CR-6478 
       13.25        41.88        28.83        23.24        32.81         6.02 
TCGA-CR-6482 TCGA-CR-6484 TCGA-CR-7364 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7388 
       11.34        11.64        47.18         3.45         0.99        27.06 
TCGA-CR-7390 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5439 
       29.82         5.13         5.95        29.95        17.16        17.95 
TCGA-CV-5441 TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6948 
       94.88         7.07        90.12        20.52        11.24        42.38 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7236 
       53.95        65.82       111.16         5.26        77.16         4.73 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7261 
       36.00        26.20        17.13        95.34         4.96        36.13 
TCGA-CV-7409 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 
       17.85        89.33         9.67        22.85        25.08        25.94 
TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7425 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-7446 
        0.07        14.89        56.48       153.86        22.19        35.93 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JM 
       35.47        45.96         6.51        67.86        35.34         6.38 
TCGA-CV-A6JY TCGA-CV-A6K2 TCGA-CX-7086 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB 
       21.24        10.42        18.84        11.44        18.67        12.36 
TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 TCGA-DQ-7595 TCGA-F7-8298 
       12.79        11.11        30.94        14.04        10.65        16.11 
TCGA-F7-A624 TCGA-H7-A6C5 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-IQ-7631 TCGA-IQ-7632 
       12.43        21.11         0.36        13.84        12.76        14.50 
TCGA-IQ-A61O TCGA-KU-A66S TCGA-KU-A66T TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A7D7 
       11.84        13.35        18.15         1.84        15.42        17.98 
TCGA-P3-A6T0 TCGA-P3-A6T5 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB 
       19.00        29.00        21.07        16.70        12.72        14.79 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO 
       12.43         6.51         5.62         9.73         8.32        12.72 
TCGA-T2-A6X2 TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
       32.45        13.25        43.59        54.67        43.36        41.16 
TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       62.27        16.11        13.94        20.75 

$subtype3
TCGA-BA-4074 TCGA-BA-4077 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-5557 
       15.19        37.28         9.07        23.74        57.93        20.48 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A4II 
       15.52        21.17         3.55        28.11        20.45        30.18 
TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4223 
       11.54         5.69        11.05        13.38         6.15        94.62 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
        9.14         4.60        18.35        22.42        36.72        50.20 
TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A6UO TCGA-CN-4726 TCGA-CN-4727 
       44.98        24.66        20.52         8.81         4.67        40.44 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6012 
       32.65        41.10        41.69        12.39        56.94        20.68 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
        9.07        36.49        14.10        35.01        14.56        17.59 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V7 
       29.72        21.21         5.75        10.09         7.33         6.18 
TCGA-CQ-5323 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5331 TCGA-CQ-6218 TCGA-CQ-6228 
       48.20        39.68         2.93        45.99        41.19        14.99 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 
       70.13        43.04        29.36        14.14        31.23        84.23 
TCGA-CR-5247 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       11.77        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6487 
       39.52        34.52        36.99        11.90        10.22         7.69 
TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 
       11.51        15.75         9.27        47.34        40.93        35.84 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7380 TCGA-CR-7385 TCGA-CR-7389 TCGA-CR-7395 
        3.09        29.23        19.92        32.78        12.89        30.58 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5973 TCGA-CV-6433 
       48.39       139.43        76.50        91.53        86.83        21.07 
TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6955 
       62.43         5.46         4.73        21.90       126.08        10.98 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 
       28.34         4.14        64.83       126.15         7.99         9.01 
TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7254 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 
       21.80       130.88        47.97       210.97       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45Y 
       16.27        84.49         7.17        16.64        27.98        88.87 
TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO 
       48.20        60.43         0.76         5.98        29.79         6.48 
TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 
       23.47        22.52        34.36        25.41         9.60        23.05 
TCGA-D6-6824 TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-7589 
        2.53        15.88        14.30        13.94        12.10        18.90 
TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 
       25.48        20.45        12.13        11.18        37.18        21.63 
TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-7774 
       20.25         3.02        19.23        18.94        20.25        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 
       15.16        15.06         6.77         0.07        25.74         1.22 
TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-KU-A6H7 
        4.27         6.90        34.75        11.84         0.07        12.43 
TCGA-MT-A51W TCGA-MT-A67F TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 
       14.37        12.62         3.68         7.13        16.08        29.92 
TCGA-P3-A5Q6 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-P3-A6T6 
       15.78        51.25        10.85        36.82         2.04        12.99 
TCGA-P3-A6T7 TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A8ZA TCGA-RS-A6TP TCGA-T2-A6WX 
       16.01        17.65        18.64        12.10        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71E TCGA-UF-A7JF 
       15.91         7.10        13.55        13.68        42.02        49.22 
TCGA-UF-A7JV TCGA-UP-A6WW 
        2.96        17.03 

subtype1 subtype2 subtype3 
    0.16     0.07     0.07 
subtype1 subtype2 subtype3 
  180.16   153.86   210.97 
subtype1 subtype2 subtype3 
  17.950   17.900   19.575 
[1] "0.2 - 180.2 (17.9)" "0.1 - 153.9 (17.9)" "0.1 - 211.0 (19.6)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      19       32        30        94         5         0
  subtype2       3       18        19        79         5         1
  subtype3       5       27        26        84         2         0
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         19        3        5
  STAGE II        32       18       27
  STAGE III       30       19       26
  STAGE IVA       94       79       84
  STAGE IVB        5        5        2
  STAGE IVC        0        1        0
[1] 6 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    27 58 41 55
  subtype2     5 29 27 65
  subtype3    17 47 31 54
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       27        5       17
  T2          58       29       47
  T3          41       27       31
  T4          55       65       54
[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 67 25 73  3
  subtype2 61 14 39  4
  subtype3 48 27 56  1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       67       61       48
  N1       25       14       27
  N2       73       39       56
  N3        3        4        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 74  0
  subtype2 50  1
  subtype3 59  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74    0
  subtype2   50    1
  subtype3   59    0
   clus
vv  subtype1 subtype2 subtype3
  0       74       50       59
  1        0        1        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  58 135
  subtype2  47  95
  subtype3  36 147
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58  135
  subtype2   47   95
  subtype3   36  147
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       58       47       36
  MALE        135       95      147
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   191
  subtype2                                   139
  subtype3                                   177
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           1
  subtype3                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   2
  subtype2                                                   2
  subtype3                                                   6
D8V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            191      139
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2        2
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            177
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                6
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V9, binary
          cls
clus         0   1
  subtype1  35 158
  subtype2  14 128
  subtype3  33 150
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35  158
  subtype2   14  128
  subtype3   33  150
     clus
vv    subtype1 subtype2 subtype3
  NO        35       14       33
  YES      158      128      150
[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"
D8V10, continuous
D8V11, continuous
D8V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     8                        12
  subtype2                                0     2                        18
  subtype3                                1     1                        14
          vv
clus       WHITE
  subtype1   164
  subtype2   118
  subtype3   162
D8V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   8        2        1
  BLACK OR AFRICAN AMERICAN              12       18       14
  WHITE                                 164      118      162
[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"
D8V14, binary
          cls
clus         0   1
  subtype1  12 169
  subtype2   4 126
  subtype3   9 161
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  169
  subtype2    4  126
  subtype3    9  161
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           12        4        9
  NOT HISPANIC OR LATINO      169      126      161
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 39 34
  subtype2 88 49
  subtype3 72 26
  subtype4 62 52
  subtype5 28 19
subtype1 subtype2 subtype3 subtype4 subtype5 
      73      137       98      114       47 
subtype1 subtype2 subtype3 subtype4 subtype5 
      34       49       26       52       19 
$subtype1
TCGA-4P-AA8J TCGA-BB-7871 TCGA-BB-8596 TCGA-CN-6016 TCGA-CN-6018 TCGA-CN-6019 
        3.35        24.66        71.05        19.53        19.07        14.20 
TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-A49A TCGA-CN-A63V TCGA-CQ-5330 TCGA-CQ-5333 
        9.24        11.08        12.85        15.91        45.80        11.21 
TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-7067 TCGA-CQ-7072 TCGA-CR-7397 
       15.75        66.28        56.58        16.73        64.11         7.10 
TCGA-CV-5434 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5971 
      108.95        19.20       107.51        80.12        17.92        23.05 
TCGA-CV-5978 TCGA-CV-6441 TCGA-CV-6934 TCGA-CV-6937 TCGA-CV-6945 TCGA-CV-6951 
        7.07         9.60         2.14        20.52        12.03        30.08 
TCGA-CV-6961 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 
        2.50         1.84        52.31         4.73        47.47        31.36 
TCGA-CV-7247 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7413 
       18.97        18.41        57.47        35.54       210.97         9.67 
TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7568 TCGA-CV-A45V TCGA-CV-A464 
       22.85         0.07        34.09        30.48         1.05        56.61 
TCGA-CV-A6JU TCGA-D6-6824 TCGA-D6-8568 TCGA-D6-A6EP TCGA-DQ-5630 TCGA-DQ-7594 
        3.62         2.53        24.95        13.94        33.86        12.10 
TCGA-F7-8298 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-IQ-7631 TCGA-IQ-A61H 
       16.11        14.66        22.03        22.85        12.76        13.55 
TCGA-KU-A6H8 TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K 
       10.75        47.01        13.15        11.57         9.73         8.32 
TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JJ TCGA-UF-A7JK 
        2.83        44.65        24.16        21.86        16.11        13.94 
TCGA-WA-A7H4 
       14.56 

$subtype2
TCGA-BA-5149 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-A4IF TCGA-BA-A4II TCGA-BA-A6DA 
       26.50        42.35        23.84        29.42        30.18        11.54 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DG TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL 
       14.47         7.82         2.27        11.05        13.38        20.48 
TCGA-BB-7872 TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z 
       38.40        25.71        10.55        27.19         8.81         6.28 
TCGA-C9-A480 TCGA-CN-4742 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A63T 
       12.69        13.05        14.56        17.59        29.72         7.40 
TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 TCGA-CN-A641 TCGA-CN-A642 TCGA-CQ-5326 
       11.44         5.75         4.41        12.07         2.70         2.93 
TCGA-CQ-5331 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C7 
       45.99        51.29        33.11        28.83        44.48        11.61 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-6477 
       29.36        32.81        25.81        14.14        12.46        16.90 
TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-6493 TCGA-CV-5441 TCGA-CV-5976 TCGA-CV-5977 
       12.46        15.75         9.27        94.88        48.59        60.49 
TCGA-CV-7411 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-A45O 
       89.33        25.08       100.57        56.48       156.49        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45X TCGA-CV-A463 TCGA-CV-A465 
       24.99       169.38       180.16         6.51         0.76         7.07 
TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT 
        5.98        35.34         6.38        29.79         6.48        22.03 
TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-D6-A4Z9 
       21.24        23.47        19.92        22.52        10.42        17.72 
TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EM TCGA-D6-A6EQ TCGA-DQ-5631 TCGA-DQ-7588 
       12.36        15.88         7.63        12.10        18.02        14.04 
TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
        9.83        20.25         3.02        19.23        18.94        12.62 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
        0.46        17.85        11.80        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6HZ 
       15.16        13.61         0.16         0.36        13.84         3.65 
TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        6.90        34.75        15.95        14.50        19.33        11.84 
TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-KU-A66T TCGA-MT-A51W 
       14.47         5.29        11.54        11.84        18.15        14.37 
TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5Q6 TCGA-P3-A5QA 
        7.96        30.05         1.84        12.62        15.78        56.75 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z 
       75.55        18.97         2.04        29.00        16.01        21.07 
TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC 
       11.74         7.30        16.70         9.34        12.72        12.43 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-TN-A7HJ 
       12.72        16.96         6.87        15.91        32.45        13.25 
TCGA-UF-A7JC TCGA-UF-A7JO TCGA-UF-A7JS TCGA-UF-A7JT TCGA-UF-A7JV 
       17.95        20.75        22.36        32.65         2.96 

$subtype3
TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4IH TCGA-BA-A6D8 
       17.10        21.17         3.55        28.11        20.45        27.95 
TCGA-BA-A8YP TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8601 
       16.41        36.72        50.20        44.98        66.28        20.52 
TCGA-CN-4739 TCGA-CN-6012 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6988 TCGA-CN-6992 
       43.73        20.68         9.07        36.49        10.45        12.95 
TCGA-CN-A497 TCGA-CN-A49C TCGA-CN-A63U TCGA-CN-A6UY TCGA-CN-A6V3 TCGA-CQ-5332 
       35.01        21.21        17.29        10.09         9.80        10.42 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       13.25        14.99        23.24        31.23        84.23        11.77 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6480 
       37.87        26.27        58.42        34.52        36.99        11.90 
TCGA-CR-7364 TCGA-CR-7374 TCGA-CR-7388 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 
       47.18         0.99        27.06         5.13         5.95        29.95 
TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5435 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6948 
      139.43       129.21        76.24        76.50        86.83        42.38 
TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7409 TCGA-CV-7414 
       28.34         4.14        36.00        95.34        17.85         0.46 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7446 TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A461 
       25.94        14.89        35.93        35.47        45.96        67.86 
TCGA-CX-7082 TCGA-CX-7086 TCGA-D6-6827 TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q 
       10.42        18.84        18.67        14.30        12.79        11.11 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7595 TCGA-H7-A6C5 
       30.94        18.90        25.48        20.45        10.65        21.11 
TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A634 TCGA-KU-A66S TCGA-MT-A7BN TCGA-MZ-A5BI 
       25.74         1.22         4.27        13.35        15.42         7.13 
TCGA-MZ-A7D7 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T6 TCGA-QK-A6VB 
       17.98        51.25        10.85        19.00        12.99        14.79 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-T2-A6X0 TCGA-TN-A7HI 
        6.51         5.62        12.10         9.76         7.10        13.55 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D TCGA-UF-A71E TCGA-UF-A7JA 
       43.59        54.67        43.36        41.16        42.02        62.27 
TCGA-UF-A7JF TCGA-UP-A6WW 
       49.22        17.03 

$subtype4
TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       20.48        53.79        15.52        12.62         4.01         7.76 
TCGA-BB-4227 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6013 TCGA-CN-6020 
        4.41         8.52        20.71        30.67        20.65         6.74 
TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6997 TCGA-CN-6998 TCGA-CQ-5323 
       24.16         3.68        17.42        14.10        11.74        48.20 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5334 TCGA-CQ-6218 TCGA-CQ-6220 
       39.68        54.58        46.75         4.24        41.19        32.38 
TCGA-CQ-6223 TCGA-CQ-6229 TCGA-CQ-7063 TCGA-CQ-7069 TCGA-CR-6471 TCGA-CR-6474 
       34.75        38.76        70.13        41.88        39.52        18.54 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7368 
       11.64         7.69        11.51        39.16        47.34        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7372 TCGA-CR-7373 TCGA-CR-7376 
       35.84         3.45         3.09        24.95        29.23        31.96 
TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
        9.17        34.06        19.92        26.17        17.13        47.01 
TCGA-CR-7389 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       12.89        29.82        30.02        31.10        29.85        29.52 
TCGA-CR-7395 TCGA-CR-7401 TCGA-CR-7404 TCGA-CV-5970 TCGA-CV-5979 TCGA-CV-6003 
       30.58        35.41        48.39        13.35        43.23        54.74 
TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6942 
       62.43         9.70         5.46        26.43        11.24       126.08 
TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6956 
       19.79        15.09         6.08        53.95        65.82         7.13 
TCGA-CV-6959 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7095 TCGA-CV-7097 
        8.42        64.83       126.15       111.16        18.81        12.66 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
        7.99         9.01         5.26        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7245 TCGA-CV-7252 TCGA-CV-7253 
       10.75       130.88        77.16        26.20         4.96        11.87 
TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7428 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7432 
        2.10        36.13        54.94         3.52        16.27        84.49 
TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7437 TCGA-CV-7438 TCGA-CV-7440 
       19.76         7.17       153.86        16.64         6.38        22.19 
TCGA-CX-7219 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 
       34.36        25.41         9.60        23.05        16.14        11.44 
TCGA-D6-8569 TCGA-DQ-5624 TCGA-DQ-5625 TCGA-F7-7848 TCGA-H7-8502 TCGA-HD-7229 
       25.32        58.45        35.54        37.18        15.06         0.07 

$subtype5
TCGA-BA-5559 TCGA-BA-6870 TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BB-4217 TCGA-BB-7861 
       57.44        14.83         7.10         5.69         6.15        22.42 
TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-5358 TCGA-CN-6017 TCGA-CN-A6V1 TCGA-CN-A6V6 
       21.11        14.33         8.58        20.68         7.33         7.69 
TCGA-CQ-5325 TCGA-CQ-6221 TCGA-CQ-7068 TCGA-CR-5248 TCGA-CR-6470 TCGA-CR-6478 
       21.50        32.88        43.04        54.67        50.01         6.02 
TCGA-CR-6481 TCGA-CR-7385 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-6433 
       10.22        32.78        17.16        17.95        91.53        21.07 
TCGA-CV-6939 TCGA-CV-6955 TCGA-CV-7248 TCGA-CV-A45T TCGA-CV-A45Y TCGA-CV-A45Z 
       21.90        10.98        17.13       159.65        88.87        48.20 
TCGA-CV-A460 TCGA-CV-A468 TCGA-CX-7085 TCGA-D6-6515 TCGA-DQ-7593 TCGA-DQ-7596 
       60.43        15.25        10.55        13.25        12.13        11.18 
TCGA-F7-8489 TCGA-H7-A76A TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A6I9 
       21.63         6.77         0.07        12.43         3.68        16.08 
TCGA-P3-A5Q5 TCGA-P3-A6SW TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-TN-A7HL 
       29.92        36.82        17.65        18.64        13.68 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.07     0.16     0.46     0.07     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  210.97   180.16   139.43   153.86   159.65 
subtype1 subtype2 subtype3 subtype4 subtype5 
   16.73    15.16    20.60    22.62    17.16 
[1] "0.1 - 211.0 (16.7)" "0.2 - 180.2 (15.2)" "0.5 - 139.4 (20.6)"
[4] "0.1 - 153.9 (22.6)" "0.1 - 159.7 (17.2)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       2       14         9        44         3         0
  subtype2       7       21        25        64         2         0
  subtype3       2        7        15        47         3         1
  subtype4      11       20        18        58         1         0
  subtype5       3       11         3        17         1         0
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          2        7        2       11        3
  STAGE II        14       21        7       20       11
  STAGE III        9       25       15       18        3
  STAGE IVA       44       64       47       58       17
  STAGE IVB        3        2        3        1        1
  STAGE IVC        0        0        1        0        0
[1] 6 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     4 22 13 33
  subtype2    12 37 28 45
  subtype3     6 18 22 29
  subtype4    13 31 21 43
  subtype5    11 13  6  7
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        4       12        6       13       11
  T2          22       37       18       31       13
  T3          13       28       22       21        6
  T4          33       45       29       43        7
[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 29 10 28  1
  subtype2 50 22 40  1
  subtype3 27 12 30  3
  subtype4 41 17 36  0
  subtype5 14  2 17  1
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       29       50       27       41       14
  N1       10       22       12       17        2
  N2       28       40       30       36       17
  N3        1        1        3        0        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"
D9V6, binary
          cls
clus        0  1
  subtype1 21  0
  subtype2 75  0
  subtype3 29  1
  subtype4 30  0
  subtype5 15  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    0
  subtype2   75    0
  subtype3   29    1
  subtype4   30    0
  subtype5   15    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       21       75       29       30       15
  1        0        0        1        0        0
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V7, binary
          cls
clus        0  1
  subtype1 20 54
  subtype2 50 87
  subtype3 17 81
  subtype4 32 84
  subtype5 11 36
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   20   54
  subtype2   50   87
  subtype3   17   81
  subtype4   32   84
  subtype5   11   36
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       20       50       17       32       11
  MALE         54       87       81       84       36
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                    73
  subtype2                                   136
  subtype3                                    91
  subtype4                                   116
  subtype5                                    45
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           1
  subtype3                                                           0
  subtype4                                                           0
  subtype5                                                           0
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   1
  subtype2                                                   0
  subtype3                                                   7
  subtype4                                                   0
  subtype5                                                   2
D9V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             73      136
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1        0
                                                             clus
vv                                                            subtype3 subtype4
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             91      116
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                7        0
                                                             clus
vv                                                            subtype5
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             45
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2
[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"
D9V9, binary
          cls
clus         0   1
  subtype1   8  66
  subtype2   8 129
  subtype3  13  85
  subtype4  25  91
  subtype5   9  38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8   66
  subtype2    8  129
  subtype3   13   85
  subtype4   25   91
  subtype5    9   38
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO         8        8       13       25        9
  YES       66      129       85       91       38
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V10, continuous
D9V11, continuous
D9V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         9
  subtype2                                1     8                         5
  subtype3                                0     1                        13
  subtype4                                0     2                         8
  subtype5                                1     0                         6
          vv
clus       WHITE
  subtype1    60
  subtype2   120
  subtype3    81
  subtype4   101
  subtype5    39
D9V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        0        0        1
  ASIAN                                   0        8        1        2        0
  BLACK OR AFRICAN AMERICAN               9        5       13        8        6
  WHITE                                  60      120       81      101       39
[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"
D9V14, binary
          cls
clus         0   1
  subtype1   3  63
  subtype2   7 121
  subtype3   4  82
  subtype4   7 105
  subtype5   3  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   63
  subtype2    7  121
  subtype3    4   82
  subtype4    7  105
  subtype5    3   41
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        7        4        7        3
  NOT HISPANIC OR LATINO       63      121       82      105       41
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  78  64
  subtype2 163  77
  subtype3  48  39
subtype1 subtype2 subtype3 
     142      240       87 
subtype1 subtype2 subtype3 
      64       77       39 
$subtype1
TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A6DB TCGA-BA-A8YP 
        3.35        26.50        12.62         4.01         7.10        16.41 
TCGA-BB-7872 TCGA-BB-8596 TCGA-CN-4733 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5370 
       38.40        71.05        21.11        13.05         8.58         8.52 
TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6022 TCGA-CN-6024 TCGA-CN-6988 
       19.53        20.68        14.20         9.24        11.08        10.45 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A63V TCGA-CN-A640 TCGA-CQ-5325 
        3.68        17.42        11.74        15.91         4.41        21.50 
TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6220 
       54.58        46.75        45.80         4.24        15.75        32.38 
TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7067 
       66.28        56.58        13.25        38.76        51.29        16.73 
TCGA-CQ-7072 TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 
       64.11        11.77        18.54        16.90        12.46        39.16 
TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 TCGA-CR-7382 
       24.95        31.96         9.17        34.06        19.92        26.17 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 
       17.13        47.01        29.82        30.02        31.10        29.85 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5432 TCGA-CV-5434 
       29.52        30.58         7.10        35.41       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5970 
       76.24        19.20       107.51        80.12        17.92        13.35 
TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 
       23.05        48.59        60.49        43.23        54.74         9.60 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6940 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 
        2.14         9.70        26.43        19.79        15.09        30.08 
TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7095 
        6.08         7.13         8.42         2.50       126.15        18.81 
TCGA-CV-7097 TCGA-CV-7100 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 
       12.66         9.01         1.84        52.31        12.92        71.21 
TCGA-CV-7180 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 
       10.75        77.16         4.73        47.47        31.36        18.97 
TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7414 TCGA-CV-7422 
        2.10        18.41        57.47        35.54         0.46        34.09 
TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45V TCGA-CV-A464 
       19.76       153.86         6.38        30.48         1.05        56.61 
TCGA-CV-A468 TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7082 TCGA-CX-7085 TCGA-D6-6515 
       15.25         3.62        19.92        10.42        10.55        13.25 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5624 
       23.05        16.14        24.95        25.32         7.63        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7594 TCGA-F7-8298 TCGA-H7-8501 
       35.54        33.86        18.02        12.10        16.11        15.16 
TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-8635 TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-KU-A6H8 
       14.66        22.03        22.85         3.65        13.55        10.75 
TCGA-P3-A6SX TCGA-P3-A6T8 TCGA-QK-A6VB TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-UF-A71A 
       47.01        13.15        14.79        11.57         9.76         2.83 
TCGA-UF-A7J9 TCGA-UF-A7JD TCGA-UF-A7JH TCGA-WA-A7H4 
       44.65        24.16        21.86        14.56 

$subtype2
TCGA-BA-5152 TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5557 TCGA-BA-5558 TCGA-BA-5559 
       42.35        17.10        23.84        20.48        53.79        57.44 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-6871 TCGA-BA-7269 TCGA-BA-A4IG 
       15.52        21.17        14.83         3.55         7.76        28.11 
TCGA-BA-A4IH TCGA-BA-A4II TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DE TCGA-BA-A6DF 
       20.45        30.18        27.95        11.54        14.47         7.82 
TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4217 TCGA-BB-4227 TCGA-BB-7861 
       11.05        13.38        20.48         6.15         4.41        22.42 
TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 
       36.72        50.20        44.98        66.28        24.66        20.52 
TCGA-BB-A5HZ TCGA-C9-A47Z TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-6010 TCGA-CN-6011 
       27.19         6.28        14.33        43.73        20.71        30.67 
TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6021 TCGA-CN-6023 
       20.68        20.65        19.07         6.74         9.07        36.49 
TCGA-CN-6992 TCGA-CN-6994 TCGA-CN-6997 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       12.95        24.16        14.10        35.01        14.56        17.59 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y 
       29.72        21.21         7.40        17.29        11.44         5.75 
TCGA-CN-A641 TCGA-CN-A6UY TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CN-A6V6 TCGA-CQ-5323 
       12.07        10.09         7.33         9.80         7.69        48.20 
TCGA-CQ-5324 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6228 
       39.68        45.99        10.42        41.19        34.75        14.99 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CG TCGA-CQ-A4CI 
       70.13        43.04        28.83        23.24        14.14        31.23 
TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 
       84.23        54.67        37.87        26.27        58.42        50.01 
TCGA-CR-6471 TCGA-CR-6472 TCGA-CR-6473 TCGA-CR-6478 TCGA-CR-6480 TCGA-CR-6481 
       39.52        34.52        36.99         6.02        11.90        10.22 
TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-6493 TCGA-CR-7364 
       11.64         7.69        11.51        15.75         9.27        47.18 
TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7373 
       47.34        40.93        35.84         3.45         3.09        29.23 
TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7398 TCGA-CR-7399 
        0.99        32.78        27.06        12.89         5.13         5.95 
TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5441 
       29.95        48.39       139.43        17.16        17.95        94.88 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6433 TCGA-CV-6436 
       76.50        91.53        86.83         7.07        21.07        62.43 
TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6948 
        5.46        20.52        21.90        11.24       126.08        42.38 
TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 
       53.95        65.82        10.98        28.34         4.14        64.83 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7183 TCGA-CV-7242 
      111.16         7.99         5.26        21.80       130.88        36.00 
TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 
       26.20        17.13        95.34         4.96        11.87        36.13 
TCGA-CV-7409 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 
       17.85        25.94        14.89       156.49        54.94        16.27 
TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O 
       84.49         7.17        16.64        22.19        35.93        27.98 
TCGA-CV-A45U TCGA-CV-A45W TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
       35.47        45.96         6.51        88.87        48.20        60.43 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A6JM TCGA-CV-A6JY TCGA-CX-7086 TCGA-CX-7219 
       67.86         0.76         6.38        21.24        18.84        34.36 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB 
       25.41         9.60         2.53        11.44        18.67        12.36 
TCGA-D6-A6EK TCGA-D6-A6EO TCGA-D6-A6ES TCGA-D6-A74Q TCGA-DQ-5629 TCGA-DQ-7588 
       15.88        14.30        12.79        11.11        30.94        14.04 
TCGA-DQ-7589 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7593 TCGA-DQ-7595 TCGA-DQ-7596 
       18.90        25.48        20.45        12.13        10.65        11.18 
TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-7774 
       37.18        21.63         3.02        18.94        20.25        13.38 
TCGA-H7-A6C5 TCGA-H7-A76A TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7917 TCGA-HD-A633 
       21.11         6.77         0.07        25.74         1.22        13.84 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61I 
        4.27        34.75        12.76        14.50        11.84         0.07 
TCGA-KU-A66S TCGA-KU-A66T TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67D TCGA-MT-A67F 
       13.35        18.15        12.43        14.37         1.84        12.62 
TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 
        3.68        15.42         7.13        16.08        17.98        29.92 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T0 TCGA-P3-A6T4 TCGA-P3-A6T5 
       51.25        10.85        36.82        19.00         2.04        29.00 
TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6IJ TCGA-QK-A6V9 TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       12.99        17.65        12.72        18.64         6.51         5.62 
TCGA-QK-A8ZA TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-T2-A6X2 TCGA-TN-A7HI 
       12.10        16.96         6.87         7.10        32.45        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71D 
       13.25        13.68        43.59        54.67        43.36        41.16 
TCGA-UF-A71E TCGA-UF-A7JA TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UF-A7JV TCGA-UP-A6WW 
       42.02        62.27        49.22        20.75         2.96        17.03 

$subtype3
TCGA-BA-A4IF TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BB-A5HU TCGA-BB-A5HY TCGA-BB-A6UO 
       29.42         5.69         2.27        25.71        10.55         8.81 
TCGA-C9-A480 TCGA-CN-A49A TCGA-CN-A642 TCGA-CQ-5326 TCGA-CQ-5333 TCGA-CQ-6221 
       12.69        12.85         2.70         2.93        11.21        32.88 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4C6 TCGA-CQ-A4C7 TCGA-CQ-A4CB TCGA-CQ-A4CD 
       33.11        41.88        44.48        11.61        29.36        32.81 
TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CV-6945 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 
       25.81        12.46        12.03       210.97        89.33         9.67 
TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7429 
       22.85        25.08         0.07       100.57        56.48         3.52 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A465 TCGA-CV-A6JD 
       24.99       169.38       180.16       159.65         7.07         5.98 
TCGA-CV-A6JE TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JT TCGA-CV-A6JZ TCGA-CV-A6K1 
       35.34        29.79         6.48        22.03        23.47        22.52 
TCGA-CV-A6K2 TCGA-D6-A4Z9 TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-7592 TCGA-F7-A50G 
       10.42        17.72        13.94        12.10         9.83        20.25 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-F7-A624 
       19.23        12.62         0.46        17.85        11.80        12.43 
TCGA-H7-8502 TCGA-H7-A6C4 TCGA-HD-7753 TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-IQ-7630 
       15.06        13.61         0.16         0.36         6.90        15.95 
TCGA-IQ-A61E TCGA-IQ-A61J TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-MT-A51X 
       19.33        14.47         5.29        11.54        11.84         7.96 
TCGA-MT-A67A TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T7 
       30.05        15.78        56.75        75.55        18.97        16.01 
TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A6II TCGA-QK-A6VC 
       21.07        11.74         7.30        16.70         9.34        12.43 
TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WZ TCGA-UF-A7JC TCGA-UF-A7JJ 
        9.73         8.32        12.72        15.91        17.95        16.11 
TCGA-UF-A7JK TCGA-UF-A7JS TCGA-UF-A7JT 
       13.94        22.36        32.65 

subtype1 subtype2 subtype3 
    0.46     0.07     0.07 
subtype1 subtype2 subtype3 
  153.86   156.49   210.97 
subtype1 subtype2 subtype3 
   18.89    18.92    15.06 
[1] "0.5 - 153.9 (18.9)" "0.1 - 156.5 (18.9)" "0.1 - 211.0 (15.1)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      14       23        22        73         3         0
  subtype2       7       34        33       116         4         1
  subtype3       4       16        15        41         3         0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         14        7        4
  STAGE II        23       34       16
  STAGE III       22       33       15
  STAGE IVA       73      116       41
  STAGE IVB        3        4        3
  STAGE IVC        0        1        0
[1] 6 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 42 31 44
  subtype2    20 55 40 83
  subtype3     8 24 19 30
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       18       20        8
  T2          42       55       24
  T3          31       40       19
  T4          44       83       30
[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 21 54  1
  subtype2 81 31 67  4
  subtype3 31 11 30  1
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       49       81       31
  N1       21       31       11
  N2       54       67       30
  N3        1        4        1
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 44  0
  subtype2 76  1
  subtype3 50  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    0
  subtype2   76    1
  subtype3   50    0
   clus
vv  subtype1 subtype2 subtype3
  0       44       76       50
  1        0        1        0
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  44  99
  subtype2  62 179
  subtype3  24  64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44   99
  subtype2   62  179
  subtype3   24   64
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       44       62       24
  MALE         99      179       64
[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       HEAD AND NECK SQUAMOUS CELL CARCINOMA
  subtype1                                   141
  subtype2                                   233
  subtype3                                    87
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT
  subtype1                                                           0
  subtype2                                                           0
  subtype3                                                           1
          vv
clus       HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                   2
  subtype2                                                   8
  subtype3                                                   0
D10V8, multiclass
                                                             clus
vv                                                            subtype1 subtype2
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                            141      233
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        0        0
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2        8
                                                             clus
vv                                                            subtype3
  HEAD AND NECK SQUAMOUS CELL CARCINOMA                             87
  HEAD AND NECK SQUAMOUS CELL CARCINOMA  SPINDLE CELL VARIANT        1
  HEAD AND NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V9, binary
          cls
clus         0   1
  subtype1  26 117
  subtype2  35 206
  subtype3   2  86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26  117
  subtype2   35  206
  subtype3    2   86
     clus
vv    subtype1 subtype2 subtype3
  NO        26       35        2
  YES      117      206       86
[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"
D10V10, continuous
D10V11, continuous
D10V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     2                         9
  subtype2                                1     4                        26
  subtype3                                1     5                         6
          vv
clus       WHITE
  subtype1   127
  subtype2   204
  subtype3    70
D10V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1
  ASIAN                                   2        4        5
  BLACK OR AFRICAN AMERICAN               9       26        6
  WHITE                                 127      204       70
[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"
D10V14, binary
          cls
clus         0   1
  subtype1   8 129
  subtype2  11 209
  subtype3   5  74
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  129
  subtype2   11  209
  subtype3    5   74
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8       11        5
  NOT HISPANIC OR LATINO      129      209       74
[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"
