[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/22506490/HNSC-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/HNSC-TP/22541004/HNSC-TP.mergedcluster.txt"

nPatients in clinical file=528, in cluster file=528, common to both=528
[1]  10 528
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
203 128 145  46 
  1   2   3   4 
203 128 145  46 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5   6   7 
 87  87 104  91  78  75   6 
  1   2   3   4   5   6   7 
 87  87 104  91  78  75   6 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
51 30 33 29 69 
 1  2  3  4  5 
51 30 33 29 69 
[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   4 
136 114 172  98 
  1   2   3   4 
136 114 172  98 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
179 104 172  65 
  1   2   3   4 
179 104 172  65 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5 
 81 140 132  91  79 
  1   2   3   4   5 
 81 140 132  91  79 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
193 144 186 
  1   2   3 
193 144 186 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
144 189 144 
  1   2   3 
144 189 144 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3 
174 104 199 
  1   2   3 
174 104 199 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "DAYS_TO_LAST_KNOWN_ALIVE"            
[13] "RADIATION_THERAPY"                   
[14] "HISTOLOGICAL_TYPE"                   
[15] "NUMBER_PACK_YEARS_SMOKED"            
[16] "YEAR_OF_TOBACCO_SMOKING_ONSET"       
[17] "NUMBER_OF_LYMPH_NODES"               
[18] "RACE"                                
[19] "ETHNICITY"                           

Input Data has 19 rows and 528 columns.

[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=206,	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=287,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	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:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'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 12:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=21,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 13:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'HISTOLOGICAL_TYPE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=87,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=59,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 17:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=19,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 18:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 19:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[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 528 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"                "PATHOLOGIC_STAGE"             
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "RADIATION_THERAPY"             "HISTOLOGICAL_TYPE"            
 [9] "NUMBER_PACK_YEARS_SMOKED"      "YEAR_OF_TOBACCO_SMOKING_ONSET"
[11] "NUMBER_OF_LYMPH_NODES"         "RACE"                         
[13] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=60, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, 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  49 140 101 175 
[1] "table(vv)"
vv
T0+T1    T2    T3    T4 
   50   140   101   175 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T0  T1  T2  T3  T4 
  1  49 140 101 175 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


T0+T1    T2    T3    T4 
   50   140   101   175 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
180  68 172   8 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
180  68 172   8 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
180  68 172   8 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
180  68 172   8 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=3, 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=19, 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 107  95
  subtype2  78  50
  subtype3  90  54
  subtype4  26  20
subtype1 subtype2 subtype3 subtype4 
     202      128      144       46 
subtype1 subtype2 subtype3 subtype4 
      95       50       54       20 
$subtype1
TCGA-BA-4075 TCGA-BB-A5HU TCGA-CN-6997 TCGA-CQ-7067 TCGA-CR-6478 TCGA-CX-7219 
        9.30        25.71        32.48        16.73         6.02        34.36 
TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-4076 TCGA-BA-5149 
       14.04        21.11        22.85         3.35        13.64        26.50 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-7269 
       65.59        15.52        14.83        12.62         4.01        41.85 
TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7872 TCGA-BB-A5HY 
       29.42        14.47        16.41         9.14        38.40        10.55 
TCGA-BB-A5HZ TCGA-BB-A6UO TCGA-C9-A47Z TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4729 
       27.19         8.81         6.28         4.67        56.68        12.89 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4738 TCGA-CN-4742 
       32.81        57.11        12.99        20.55        14.33        13.05 
TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5365 TCGA-CN-5367 TCGA-CN-5373 
       42.02         8.32        16.21        11.54        11.57        52.08 
TCGA-CN-6013 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-A49A TCGA-CN-A49B TCGA-CQ-5326 
       23.90        32.22         3.68        17.29        29.72         2.93 
TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6224 
       70.45        62.37        10.42        41.19        46.95        56.58 
TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-7072 
        4.24        14.99        64.87        53.52        41.88        77.56 
TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6484 TCGA-CR-6488 TCGA-CR-6491 
       29.36        11.77        18.54        11.64        12.46        22.78 
TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7369 TCGA-CR-7372 TCGA-CR-7380 
        9.27        39.16        47.34        35.84        24.95        19.92 
TCGA-CR-7383 TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5435 TCGA-CV-5436 
       17.13        12.89        49.58       139.43        76.24        19.20 
TCGA-CV-5439 TCGA-CV-5440 TCGA-CV-5441 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 
       17.95       107.51        94.88        80.12        13.35        86.83 
TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6441 TCGA-CV-6933 
       48.59        60.49        43.23        54.74         9.60        90.12 
TCGA-CV-6934 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6945 
        2.14         9.70         5.46        20.52        26.43        12.03 
TCGA-CV-6948 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 
       42.38         7.13         8.42        28.34         2.50       172.67 
TCGA-CV-7095 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7235 TCGA-CV-7236 
       18.81         1.84        12.92        71.21        77.16         4.73 
TCGA-CV-7243 TCGA-CV-7245 TCGA-CV-7247 TCGA-CV-7248 TCGA-CV-7253 TCGA-CV-7254 
       31.36        26.20        18.97        17.13        11.87        47.97 
TCGA-CV-7255 TCGA-CV-7409 TCGA-CV-7413 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 
        2.10        17.85         9.67         0.46        22.85        25.08 
TCGA-CV-7423 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 
      100.57        14.89        54.94        84.49         7.17        16.64 
TCGA-CV-7438 TCGA-CV-7440 TCGA-CV-A45R TCGA-CV-A45U TCGA-CV-A45X TCGA-CV-A465 
        6.38        22.19       180.16        35.47         6.51         7.07 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6JZ 
       35.34         6.38        29.79        28.01         3.62        23.47 
TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-8569 
       25.41         9.60        23.05        16.14        11.44        25.32 
TCGA-D6-A4Z9 TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-5625 
       17.72        24.95        12.10        12.79        58.45        37.25 
TCGA-DQ-5631 TCGA-DQ-7592 TCGA-F7-7848 TCGA-F7-8298 TCGA-F7-A50I TCGA-F7-A50J 
       18.02        37.58        37.18        32.71         3.02        31.13 
TCGA-F7-A61V TCGA-F7-A61W TCGA-F7-A623 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7753 
       24.95         0.46        20.25        15.06        33.76        28.47 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-A633 TCGA-IQ-7630 TCGA-IQ-A61G TCGA-IQ-A61J 
       21.93        27.48        13.84        15.95        11.84        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SG TCGA-IQ-A6SH TCGA-MT-A51X TCGA-MT-A7BN 
        5.29        13.68        19.04        15.48         7.96        15.42 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 
       71.74        47.01        18.97         2.04        29.00        16.01 
TCGA-P3-A6T8 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB 
       13.15        21.07        21.21        21.47        12.72        21.07 
TCGA-QK-A8Z9 TCGA-QK-A8ZA TCGA-QK-A8ZB TCGA-QK-AA3J TCGA-T2-A6WZ TCGA-T3-A92M 
       14.76        12.20        17.82        15.32        15.91        13.71 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JC TCGA-UF-A7JD 
       13.25        64.80        54.67        49.51        17.95        24.30 
TCGA-UF-A7JF TCGA-UF-A7JK TCGA-WA-A7GZ TCGA-KU-A66T 
       55.43        13.94        20.55        18.15 

$subtype2
TCGA-BA-4077 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 TCGA-CN-6021 
       37.28         3.55        28.11        30.18        51.29         9.07 
TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CQ-5323 TCGA-CQ-6221 TCGA-CX-7082 
       52.08        11.08        35.05        48.20        32.88         0.36 
TCGA-DQ-5629 TCGA-DQ-7589 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5555 
       30.94        46.32        48.03        15.19         9.07        17.10 
TCGA-BA-6869 TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A6DL 
       21.17        20.45        27.95         7.10         2.27        20.48 
TCGA-BB-4223 TCGA-BB-4227 TCGA-BB-7862 TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7871 
      105.90         4.41        36.72        50.20        66.28        24.66 
TCGA-BB-8596 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4725 TCGA-CN-4730 TCGA-CN-4739 
       71.05        20.52        55.86        38.04        26.86        45.83 
TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5366 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6011 
       46.32        71.31        11.84        56.94        50.07        30.67 
TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A49C 
       48.00        34.13        10.45        35.01        25.41        21.21 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A6V7 TCGA-CQ-6225 
        7.40        31.69        12.39        12.07        19.53        13.25 
TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-6477 TCGA-CR-6487 
       23.24        31.23        84.23        54.67        16.90         7.69 
TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7379 
       47.18        40.93         3.45         3.09         0.99        34.06 
TCGA-CR-7385 TCGA-CR-7397 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5431 
       32.78        24.79         5.13         5.95        48.39        17.16 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5978 TCGA-CV-6941 TCGA-CV-6950 TCGA-CV-6951 
      129.21       108.95         7.07        11.24        15.09        30.08 
TCGA-CV-6954 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7101 TCGA-CV-7103 TCGA-CV-7177 
       65.82       111.16        12.66         5.26        52.31        21.80 
TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7261 TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 
       10.75        36.00        49.71        18.41        57.47        35.54 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7429 TCGA-CV-7430 TCGA-CV-7435 
       25.94         0.07        34.09         3.52        16.27       153.86 
TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A461 TCGA-CX-7086 TCGA-D6-8568 TCGA-D6-A4ZB 
       45.96        48.20        67.86        18.84        24.95        12.36 
TCGA-D6-A6EP TCGA-D6-A74Q TCGA-DQ-7594 TCGA-DQ-7595 TCGA-HD-7917 TCGA-HD-8224 
       13.94        23.34        40.04        39.12        27.48        14.66 
TCGA-HD-A6HZ TCGA-IQ-A61O TCGA-MT-A67D TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 
        3.65        13.84         1.84         6.25         7.13        16.08 
TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6SW TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 
       17.98        15.78        36.82        19.73        12.89         5.62 
TCGA-QK-AA3K TCGA-T2-A6X0 TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 TCGA-UF-A7JA 
        8.32         7.10         2.83        49.45        44.65        74.47 
TCGA-UF-A7JH TCGA-UF-A7JS 
       29.46        22.36 

$subtype3
TCGA-CN-6022 TCGA-CN-A6V1 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6472 TCGA-DQ-7593 
        9.24        19.82        70.13        43.04        34.52        40.24 
TCGA-UF-A7JV TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5556 TCGA-BA-A6DD 
        2.96        23.74        42.35        57.93        23.84         5.69 
TCGA-BA-A6DF TCGA-BA-A6DJ TCGA-BB-4217 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 
        7.82        13.38         6.15         4.80        18.38        22.42 
TCGA-BB-7863 TCGA-BB-7866 TCGA-BB-A6UM TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4733 
       33.70        44.98        12.92        12.69        48.76        52.14 
TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 TCGA-CN-5369 TCGA-CN-6016 TCGA-CN-6017 
       27.58        73.61         8.58        12.49        47.44        28.04 
TCGA-CN-6020 TCGA-CN-A63V TCGA-CN-A63Y TCGA-CN-A642 TCGA-CN-A6UY TCGA-CN-A6V6 
        6.74        22.32        16.57         2.70        23.44        20.88 
TCGA-CQ-5324 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-5333 TCGA-CQ-5334 
       52.37        21.50        54.58        45.99        11.21         4.24 
TCGA-CQ-7071 TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6470 
       43.10        14.14        12.46        37.87        26.27        50.01 
TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6492 
       39.52        36.99        11.90        10.22        11.34        15.75 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 TCGA-CR-7386 TCGA-CR-7388 TCGA-CR-7391 
       31.96         9.17        26.17        47.01        27.06        30.02 
TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7401 TCGA-CV-5443 
       46.85        32.65        44.25        30.58        35.41        91.53 
TCGA-CV-5971 TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6943 TCGA-CV-6953 
       23.05        62.43         4.73        21.90        19.79        53.95 
TCGA-CV-6955 TCGA-CV-7089 TCGA-CV-7100 TCGA-CV-7183 TCGA-CV-7238 TCGA-CV-7250 
       10.98        64.83         9.01       130.88        89.65        95.34 
TCGA-CV-7252 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7433 
        4.96       210.97        89.33        56.48       156.49        19.76 
TCGA-CV-A45O TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45Y 
       27.98        21.01       169.38       159.65         1.05        88.87 
TCGA-CV-A460 TCGA-CV-A463 TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JO TCGA-CV-A6JY 
       60.43         0.76        56.61        15.25         6.48        21.24 
TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7085 TCGA-CX-A4AQ TCGA-D6-6515 
       19.92        22.52        10.42        10.55        51.12        13.25 
TCGA-D6-6824 TCGA-D6-6827 TCGA-D6-A6EK TCGA-DQ-5630 TCGA-DQ-7590 TCGA-DQ-7591 
        2.53        18.67        28.77        33.86        46.45        20.45 
TCGA-DQ-7596 TCGA-F7-8489 TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-A76A 
       41.59        21.63        12.43        13.38        15.16        20.94 
TCGA-HD-7754 TCGA-HD-8314 TCGA-HD-A4C1 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 
       25.74        22.03         0.36         4.27         6.90        34.75 
TCGA-IQ-7631 TCGA-IQ-7632 TCGA-IQ-A61I TCGA-KU-A6H8 TCGA-MT-A67A TCGA-MT-A67F 
       38.53        14.50         0.07        10.75        30.05        12.62 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6T0 TCGA-P3-A6T6 TCGA-QK-A6IF 
       29.92        51.25        10.85        19.00        12.99        23.15 
TCGA-QK-A6II TCGA-QK-A6V9 TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-TN-A7HL 
        9.34        27.39        16.96         6.87        32.45        20.35 
TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JT TCGA-UP-A6WW TCGA-WA-A7H4 TCGA-KU-A66S 
       18.05        20.75        32.65        17.03        14.56        13.35 

$subtype4
TCGA-BA-5557 TCGA-BA-5559 TCGA-CN-A6V3 TCGA-CQ-A4C7 TCGA-HD-8634 TCGA-BA-A6DA 
       20.48        68.48        24.39        11.61        12.66        11.54 
TCGA-BA-A6DI TCGA-CN-5359 TCGA-CN-5370 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-6996 
       11.05        12.39         8.52        19.07        38.89        17.42 
TCGA-CN-6998 TCGA-CN-A499 TCGA-CN-A640 TCGA-CQ-6220 TCGA-CQ-6229 TCGA-CQ-A4C6 
       11.74        23.57         4.41        32.38        38.76        44.48 
TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CR-6467 TCGA-CR-7373 TCGA-CR-7402 TCGA-CV-5442 
       33.60        29.49        58.42        29.23        29.95        76.50 
TCGA-CV-5966 TCGA-CV-6433 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6962 TCGA-CV-7099 
       17.92        21.07       140.78         6.08         4.14         7.99 
TCGA-CV-A6JD TCGA-D6-A6EM TCGA-D6-A6EN TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A620 
        5.98         7.63        22.59        20.25        18.94        17.85 
TCGA-F7-A622 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-KU-A6H7 TCGA-MT-A51W TCGA-P3-A6T2 
       11.80        37.71        37.41        19.27        14.37        75.55 
TCGA-QK-A6IG TCGA-RS-A6TO TCGA-T3-A92N TCGA-TN-A7HI 
        7.30        12.72         3.12        13.55 

subtype1 subtype2 subtype3 subtype4 
    0.46     0.07     0.07     3.12 
subtype1 subtype2 subtype3 subtype4 
  180.16   153.86   210.97   140.78 
subtype1 subtype2 subtype3 subtype4 
  19.120   24.870   22.175   19.005 
[1] "0.5 - 180.2 (19.1)" "0.1 - 153.9 (24.9)" "0.1 - 211.0 (22.2)"
[4] "3.1 - 140.8 (19.0)"
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      12       27        28       106         9         0
  subtype2       4       16        16        65         2         1
  subtype3       9       25        25        62         1         0
  subtype4       2        8        13        19         0         0
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         12        4        9        2
  STAGE II        27       16       25        8
  STAGE III       28       16       25       13
  STAGE IVA      106       65       62       19
  STAGE IVB        9        2        1        0
  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    19 53 39 74
  subtype2    10 28 29 42
  subtype3    18 40 19 47
  subtype4     3 16 13 10
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       19       10       18        3
  T2          53       28       40       16
  T3          39       29       19       13
  T4          74       42       47       10
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 65 25 79  5
  subtype2 40 14 42  2
  subtype3 61 18 33  1
  subtype4 13 11 14  0
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       65       40       61       13
  N1       25       14       18       11
  N2       79       42       33       14
  N3        5        2        1        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 68  0
  subtype2 41  1
  subtype3 59  0
  subtype4 22  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68    0
  subtype2   41    1
  subtype3   59    0
  subtype4   22    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       68       41       59       22
  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"
D1V7, binary
          cls
clus         0   1
  subtype1  49 154
  subtype2  27 101
  subtype3  45 100
  subtype4  19  27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49  154
  subtype2   27  101
  subtype3   45  100
  subtype4   19   27
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       49       27       45       19
  MALE        154      101      100       27
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1  63 114
  subtype2  32  78
  subtype3  49  82
  subtype4  18  27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   63  114
  subtype2   32   78
  subtype3   49   82
  subtype4   18   27
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        63       32       49       18
  YES      114       78       82       27
[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 & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                 202
  subtype2                                 122
  subtype3                                 141
  subtype4                                  46
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                 1
  subtype2                                                 5
  subtype3                                                 4
  subtype4                                                 0
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         0
  subtype4                                                         0
D1V9, multiclass
                                                           clus
vv                                                          subtype1 subtype2
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            202      122
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1        5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        1
                                                           clus
vv                                                          subtype3 subtype4
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            141       46
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                4        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        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"
D1V10, continuous
D1V11, continuous
D1V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                        24
  subtype2                                0     0                        14
  subtype3                                1     4                         8
  subtype4                                0     1                         2
          vv
clus       WHITE
  subtype1   164
  subtype2   112
  subtype3   129
  subtype4    41
D1V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1        0
  ASIAN                                   6        0        4        1
  BLACK OR AFRICAN AMERICAN              24       14        8        2
  WHITE                                 164      112      129       41
[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  14 176
  subtype2   3 113
  subtype3   5 130
  subtype4   4  40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14  176
  subtype2    3  113
  subtype3    5  130
  subtype4    4   40
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           14        3        5        4
  NOT HISPANIC OR LATINO      176      113      130       40
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(2) Variable = METHLYATION_CNMF
D2V1, survival
          sevent
clus2       0  1
  subtype1 48 37
  subtype2 52 35
  subtype3 55 49
  subtype4 44 47
  subtype5 59 19
  subtype6 44 31
  subtype7  1  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      85       87      104       91       78       75        6 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      37       35       49       47       19       31        5 
$subtype1
TCGA-BA-5557 TCGA-BA-A4II TCGA-CN-6022 TCGA-CR-6478 TCGA-HD-8634 TCGA-UF-A7JV 
       20.48        30.18         9.24         6.02        12.66         2.96 
TCGA-4P-AA8J TCGA-BA-A6DB TCGA-BA-A6DD TCGA-BA-A6DG TCGA-BB-4217 TCGA-BB-7872 
        3.35         7.10         5.69         2.27         6.15        38.40 
TCGA-BB-8596 TCGA-C9-A480 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4738 TCGA-CN-5358 
       71.05        12.69        56.68        52.14        14.33         8.58 
TCGA-CN-5359 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       12.39        11.84        12.49        47.44        28.04        19.07 
TCGA-CN-6996 TCGA-CN-A63V TCGA-CN-A640 TCGA-CQ-5325 TCGA-CQ-5326 TCGA-CQ-5331 
       17.42        22.32         4.41        21.50         2.93        45.99 
TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-A4CB TCGA-CQ-A4CH 
       15.75        66.28         4.24        38.76        29.36        12.46 
TCGA-CR-6474 TCGA-CR-6488 TCGA-CR-6492 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
       18.54        12.46        15.75        31.96         9.17        26.17 
TCGA-CR-7383 TCGA-CR-7388 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       17.13        27.06        30.02        46.85        32.65        44.25 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5971 TCGA-CV-6943 TCGA-CV-6961 TCGA-CV-7089 
       24.79        35.41        23.05        19.79         2.50        64.83 
TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7410 TCGA-CV-7433 TCGA-CV-7568 TCGA-CV-A45T 
        4.73        89.65       210.97        19.76        30.48       159.65 
TCGA-CV-A45Y TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JO TCGA-CV-A6K0 TCGA-CX-7085 
       88.87        56.61        15.25         6.48        19.92        10.55 
TCGA-D6-6515 TCGA-D6-6824 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-5630 TCGA-F7-8489 
       13.25         2.53        17.72         7.63        33.86        21.63 
TCGA-F7-A620 TCGA-HD-7831 TCGA-IQ-7632 TCGA-KU-A6H8 TCGA-MT-A51W TCGA-P3-A6T8 
       17.85        21.93        14.50        10.75        14.37        13.15 
TCGA-QK-A652 TCGA-QK-A6VC TCGA-QK-AA3K TCGA-UF-A718 TCGA-UF-A7JA TCGA-UF-A7JJ 
       21.21        19.73         8.32        64.80        74.47        18.05 
TCGA-WA-A7H4 
       14.56 

$subtype2
TCGA-CN-4727 TCGA-CN-A6V3 TCGA-H7-A6C5 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-5555 
       51.29        24.39        21.11        48.03        15.19        17.10 
TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A6DE TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-7864 
       21.17        29.42        14.47        11.05        20.48        50.20 
TCGA-BB-7870 TCGA-BB-A5HZ TCGA-CN-4730 TCGA-CN-4731 TCGA-CN-4737 TCGA-CN-4739 
       66.28        27.19        26.86        32.81        20.55        45.83 
TCGA-CN-4740 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A49A 
       27.58        46.32        71.31        10.45        35.01        17.29 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-6225 TCGA-CQ-6228 
        7.40        31.69        12.39        12.07        13.25        14.99 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-7364 TCGA-CR-7372 TCGA-CR-7398 
       77.56        23.24        11.77        47.18        24.95         5.13 
TCGA-CR-7402 TCGA-CV-5441 TCGA-CV-6933 TCGA-CV-6941 TCGA-CV-6954 TCGA-CV-6956 
       29.95        94.88        90.12        11.24        65.82         7.13 
TCGA-CV-6960 TCGA-CV-7091 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 
       28.34       111.16        10.75        36.00        26.20        95.34 
TCGA-CV-7253 TCGA-CV-7263 TCGA-CV-7409 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7428 
       11.87        18.41        17.85         0.07        34.09        54.94 
TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JM 
      153.86        22.19        45.96        48.20        67.86         6.38 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-8568 TCGA-D6-A6EO 
        3.62        21.24        18.84        23.05        24.95        24.95 
TCGA-D6-A74Q TCGA-DQ-5631 TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A61V TCGA-HD-7917 
       23.34        18.02        39.12        37.18        24.95        27.48 
TCGA-HD-8224 TCGA-IQ-7631 TCGA-MT-A51X TCGA-P3-A5QF TCGA-QK-A6IJ TCGA-QK-A6VB 
       14.66        38.53         7.96        10.85        12.72        21.07 
TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-AA3J TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A7JD 
       12.89         5.62        15.32        54.67        49.51        24.30 
TCGA-UF-A7JF TCGA-UF-A7JH TCGA-KU-A66S 
       55.43        29.46        13.35 

$subtype3
TCGA-BA-4075 TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CQ-A4C7 TCGA-BA-5149 TCGA-BA-5151 
        9.30        70.13        43.04        11.61        26.50        23.74 
TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-A6DA TCGA-BA-A6DF TCGA-BA-A6DJ 
       42.35        23.84        65.59        11.54         7.82        13.38 
TCGA-BB-7863 TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4734 
       33.70         8.81        48.76         4.67        12.89        55.56 
TCGA-CN-4736 TCGA-CN-5355 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-6020 TCGA-CN-6995 
       12.99        42.02         8.32        11.54         6.74         3.68 
TCGA-CN-A642 TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 
        2.70        52.37        54.58        62.37        11.21         4.24 
TCGA-CQ-7064 TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4CD TCGA-CR-6484 TCGA-CR-6491 
       64.87        43.10        44.48        33.60        11.64        22.78 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7373 TCGA-CR-7380 TCGA-CR-7386 TCGA-CR-7395 
       39.16        47.34        29.23        19.92        47.01        30.58 
TCGA-CV-5444 TCGA-CV-5966 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-6436 TCGA-CV-6934 
       80.12        17.92        48.59        60.49        62.43         2.14 
TCGA-CV-6936 TCGA-CV-6938 TCGA-CV-6942 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
        5.46         4.73       140.78         6.08        53.95        10.98 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7252 TCGA-CV-7411 TCGA-CV-7413 
       18.81        12.66         7.99         4.96        89.33         9.67 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-A45O TCGA-CV-A45P 
       56.48       156.49        84.49         7.17        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45V TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JT TCGA-CV-A6JZ 
      169.38         1.05         0.76         5.98        28.01        23.47 
TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-D6-6825 TCGA-D6-6826 TCGA-D6-A6EK TCGA-D6-A6EN 
       22.52        10.42        16.14        11.44        28.77        22.59 
TCGA-DQ-5625 TCGA-F7-A50G TCGA-F7-A61S TCGA-F7-A624 TCGA-H7-7774 TCGA-H7-8501 
       37.25        20.25        18.94        12.43        13.38        15.16 
TCGA-HD-7229 TCGA-HD-7832 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 TCGA-IQ-A61E 
       33.76        27.48         0.36        13.84         6.90        37.71 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A6T2 TCGA-P3-A6T7 TCGA-QK-A64Z 
       30.05         1.84        12.62        75.55        16.01        21.07 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A8Z9 TCGA-T2-A6WX TCGA-T2-A6X2 TCGA-UF-A7JO 
        7.30         9.34        14.76         6.87        32.45        20.75 
TCGA-UF-A7JS TCGA-UF-A7JT 
       22.36        32.65 

$subtype4
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-6221 
        9.07        52.08        11.08        35.05        32.48        32.88 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-HD-8635 TCGA-BA-4076 
        0.36        34.36        30.94        46.32        22.85        13.64 
TCGA-BA-4078 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A8YP 
        9.07        15.52        14.83        41.85        27.95        16.41 
TCGA-BB-7862 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A5HY TCGA-CN-4723 TCGA-CN-4735 
       36.72        24.66        20.52        10.55        55.86        57.11 
TCGA-CN-5361 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6989 
       69.70        50.07        30.67        48.00        34.13        32.22 
TCGA-CN-6994 TCGA-CQ-5332 TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-7370 TCGA-CR-7371 
       38.89        10.42        14.14        31.23         3.45         3.09 
TCGA-CR-7374 TCGA-CR-7389 TCGA-CR-7390 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 
        0.99        12.89        49.58       139.43       129.21       108.95 
TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5978 TCGA-CV-6935 TCGA-CV-6937 TCGA-CV-6940 
       76.24       107.51         7.07         9.70        20.52        26.43 
TCGA-CV-6945 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7101 TCGA-CV-7103 
       12.03        42.38        30.08         4.14         5.26        52.31 
TCGA-CV-7177 TCGA-CV-7235 TCGA-CV-7248 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 
       21.80        77.16        17.13        47.97        49.71        35.54 
TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7430 
        0.46        22.85        25.94        14.89         3.52        16.27 
TCGA-CV-7437 TCGA-CV-7446 TCGA-CV-A45U TCGA-D6-6516 TCGA-D6-6827 TCGA-D6-A4ZB 
       16.64        35.93        35.47        25.41        18.67        12.36 
TCGA-D6-A6EP TCGA-F7-A50I TCGA-F7-A623 TCGA-HD-A6HZ TCGA-IQ-A61G TCGA-IQ-A61H 
       13.94         3.02        20.25         3.65        11.84        37.41 
TCGA-IQ-A6SG TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T4 TCGA-QK-A8ZA 
       19.04        15.42        17.98        15.78         2.04        12.20 
TCGA-QK-A8ZB TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A71A TCGA-UF-A71E TCGA-UF-A7J9 
       17.82        13.71         3.12         2.83        49.45        44.65 
TCGA-WA-A7GZ 
       20.55 

$subtype5
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-A6V1 TCGA-CQ-5323 
       37.28        68.48         3.55        28.11        19.82        48.20 
TCGA-CR-6472 TCGA-DQ-7593 TCGA-BA-5153 TCGA-BA-A4IH TCGA-BB-4223 TCGA-BB-4225 
       34.52        40.24        57.93        20.45       105.90         4.80 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7866 TCGA-BB-A6UM TCGA-CN-4741 TCGA-CN-5374 
       18.38        22.42        44.98        12.92        73.61        56.94 
TCGA-CN-6013 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63Y 
       23.90        25.41        23.57        29.72        21.21        16.57 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 
       23.44        20.88        19.53        84.23        54.67        37.87 
TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 TCGA-CR-6480 
       26.27        58.42        50.01        39.52        36.99        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7385 TCGA-CR-7399 
       10.22        11.34         7.69        40.93        32.78         5.95 
TCGA-CR-7404 TCGA-CV-5431 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-6433 TCGA-CV-6441 
       48.39        17.16        76.50        91.53        21.07         9.60 
TCGA-CV-6939 TCGA-CV-7100 TCGA-CV-7406 TCGA-CV-A460 TCGA-CX-A4AQ TCGA-DQ-7590 
       21.90         9.01        57.47        60.43        51.12        46.45 
TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7596 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-8314 
       20.45        40.04        41.59        20.94        25.74        22.03 
TCGA-HD-A634 TCGA-HL-7533 TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MZ-A5BI 
        4.27        34.75         0.07        19.27         6.25         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A6SW TCGA-P3-A6T6 TCGA-QK-A6IF 
       16.08        29.92        51.25        36.82        12.99        23.15 
TCGA-QK-A6V9 TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UP-A6WW 
       27.39        16.96         7.10        13.55        20.35        17.03 

$subtype6
TCGA-BB-A5HU TCGA-DQ-7588 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4224 TCGA-BB-4227 
       25.71        14.04        12.62         4.01         9.14         4.41 
TCGA-C9-A47Z TCGA-CN-4725 TCGA-CN-4742 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-5373 
        6.28        38.04        13.05        11.57         8.52        52.08 
TCGA-CN-6998 TCGA-CQ-5329 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 TCGA-CQ-6224 
       11.74        70.45        41.19        32.38        46.95        56.58 
TCGA-CQ-7065 TCGA-CQ-7069 TCGA-CQ-A4CE TCGA-CR-6477 TCGA-CR-6493 TCGA-CR-7379 
       53.52        41.88        29.49        16.90         9.27        34.06 
TCGA-CV-5439 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5979 TCGA-CV-6003 TCGA-CV-6950 
       17.95        13.35        86.83        43.23        54.74        15.09 
TCGA-CV-6959 TCGA-CV-7090 TCGA-CV-7102 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7183 
        8.42       172.67         1.84        12.92        71.21       130.88 
TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7255 TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7438 
       31.36        18.97         2.10        25.08       100.57         6.38 
TCGA-CV-A45R TCGA-CV-A45X TCGA-CV-A465 TCGA-CV-A6JE TCGA-CV-A6JN TCGA-D6-6517 
      180.16         6.51         7.07        35.34        29.79         9.60 
TCGA-D6-8569 TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5624 TCGA-DQ-7592 TCGA-F7-8298 
       25.32        12.10        12.79        58.45        37.58        32.71 
TCGA-F7-A50J TCGA-F7-A61W TCGA-H7-8502 TCGA-HD-7753 TCGA-IQ-7630 TCGA-IQ-A61J 
       31.13         0.46        15.06        28.47        15.95        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-P3-A5QA TCGA-P3-A6SX 
        5.29        13.68        13.84        15.48        71.74        47.01 
TCGA-P3-A6T0 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-QK-A6IH TCGA-RS-A6TO TCGA-TN-A7HJ 
       19.00        18.97        29.00        21.47        12.72        13.25 
TCGA-UF-A7JC TCGA-UF-A7JK TCGA-KU-A66T 
       17.95        13.94        18.15 

$subtype7
TCGA-CQ-7067 TCGA-CN-5364 TCGA-CR-7369 TCGA-CV-5436 TCGA-F7-A622 TCGA-T2-A6WZ 
       16.73        16.21        35.84        19.20        11.80        15.91 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    2.27     0.07     0.36     0.36     0.07     0.46    11.80 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  210.97   153.86   169.38   139.43   105.90   180.16    35.84 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  18.540   24.390   20.880   20.550   23.735   18.970   16.470 
[1] "2.3 - 211.0 (18.5)" "0.1 - 153.9 (24.4)" "0.4 - 169.4 (20.9)"
[4] "0.4 - 139.4 (20.6)" "0.1 - 105.9 (23.7)" "0.5 - 180.2 (19.0)"
[7] "11.8 - 35.8 (16.5)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      10       12        13        47         0         0
  subtype2       3       16        13        42         3         1
  subtype3       4       20        17        52         4         0
  subtype4       2        8        13        52         3         0
  subtype5       2        9        11        25         1         0
  subtype6       5       12        14        36         1         0
  subtype7       1        0         1         3         0         0
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I         10        3        4        2        2        5        1
  STAGE II        12       16       20        8        9       12        0
  STAGE III       13       13       17       13       11       14        1
  STAGE IVA       47       42       52       52       25       36        3
  STAGE IVB        0        3        4        3        1        1        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    16 25 14 28
  subtype2     9 20 16 34
  subtype3     5 27 21 45
  subtype4     4 19 19 38
  subtype5    10 23 11  8
  subtype6     5 26 17 20
  subtype7     1  0  3  2
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T0+T1       16        9        5        4       10        5        1
  T2          25       20       27       19       23       26        0
  T3          14       16       21       19       11       17        3
  T4          28       34       45       38        8       20        2
[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 32  0
  subtype2 41 12 21  1
  subtype3 44 16 23  3
  subtype4 23  8 39  3
  subtype5 14  9 23  1
  subtype6 24  9 30  0
  subtype7  1  0  4  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0       33       41       44       23       14       24        1
  N1       14       12       16        8        9        9        0
  N2       32       21       23       39       23       30        4
  N3        0        1        3        3        1        0        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 44  0
  subtype2 35  1
  subtype3 40  0
  subtype4 20  0
  subtype5 21  0
  subtype6 28  0
  subtype7  3  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   44    0
  subtype2   35    1
  subtype3   40    0
  subtype4   20    0
  subtype5   21    0
  subtype6   28    0
  subtype7    3    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0       44       35       40       20       21       28        3
  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 30 57
  subtype2 14 73
  subtype3 44 60
  subtype4 17 74
  subtype5  9 69
  subtype6 27 48
  subtype7  1  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   57
  subtype2   14   73
  subtype3   44   60
  subtype4   17   74
  subtype5    9   69
  subtype6   27   48
  subtype7    1    5
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE       30       14       44       17        9       27        1
  MALE         57       73       60       74       69       48        5
[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"
D2V8, binary
          cls
clus        0  1
  subtype1 35 45
  subtype2 27 52
  subtype3 37 58
  subtype4 20 49
  subtype5 16 55
  subtype6 24 42
  subtype7  4  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   35   45
  subtype2   27   52
  subtype3   37   58
  subtype4   20   49
  subtype5   16   55
  subtype6   24   42
  subtype7    4    2
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  NO        35       27       37       20       16       24        4
  YES       45       52       58       49       55       42        2
[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 & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                  87
  subtype2                                  84
  subtype3                                 104
  subtype4                                  89
  subtype5                                  73
  subtype6                                  74
  subtype7                                   6
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                 0
  subtype2                                                 3
  subtype3                                                 0
  subtype4                                                 2
  subtype5                                                 5
  subtype6                                                 0
  subtype7                                                 0
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         0
  subtype4                                                         0
  subtype5                                                         0
  subtype6                                                         1
  subtype7                                                         0
D2V9, multiclass
                                                           clus
vv                                                          subtype1 subtype2
  HEAD & NECK SQUAMOUS CELL CARCINOMA                             87       84
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        3
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        0
                                                           clus
vv                                                          subtype3 subtype4
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            104       89
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        0
                                                           clus
vv                                                          subtype5 subtype6
  HEAD & NECK SQUAMOUS CELL CARCINOMA                             73       74
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                5        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        1
                                                           clus
vv                                                          subtype7
  HEAD & NECK SQUAMOUS CELL CARCINOMA                              6
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        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"
D2V10, continuous
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      53       57       53       63       42       28        2 
  [1] "subtype3" "subtype5" "subtype5" "subtype1" "subtype2" "subtype4"
  [7] "subtype4" "subtype4" "subtype4" "subtype4" "subtype2" "subtype5"
 [13] "subtype4" "subtype3" "subtype3" "subtype4" "subtype4" "subtype4"
 [19] "subtype6" "subtype4" "subtype5" "subtype1" "subtype2" "subtype1"
 [25] "subtype4" "subtype2" "subtype2" "subtype4" "subtype4" "subtype3"
 [31] "subtype3" "subtype2" "subtype3" "subtype4" "subtype2" "subtype4"
 [37] "subtype6" "subtype6" "subtype4" "subtype2" "subtype5" "subtype4"
 [43] "subtype3" "subtype1" "subtype2" "subtype1" "subtype2" "subtype3"
 [49] "subtype2" "subtype4" "subtype1" "subtype5" "subtype6" "subtype5"
 [55] "subtype4" "subtype2" "subtype2" "subtype4" "subtype1" "subtype4"
 [61] "subtype5" "subtype3" "subtype3" "subtype1" "subtype3" "subtype2"
 [67] "subtype2" "subtype4" "subtype3" "subtype1" "subtype2" "subtype2"
 [73] "subtype5" "subtype6" "subtype3" "subtype1" "subtype1" "subtype2"
 [79] "subtype4" "subtype3" "subtype3" "subtype1" "subtype6" "subtype6"
 [85] "subtype5" "subtype4" "subtype4" "subtype4" "subtype1" "subtype1"
 [91] "subtype4" "subtype2" "subtype4" "subtype4" "subtype6" "subtype5"
 [97] "subtype5" "subtype5" "subtype2" "subtype2" "subtype1" "subtype2"
[103] "subtype3" "subtype5" "subtype5" "subtype3" "subtype1" "subtype1"
[109] "subtype3" "subtype1" "subtype4" "subtype3" "subtype6" "subtype1"
[115] "subtype1" "subtype6" "subtype6" "subtype1" "subtype2" "subtype2"
[121] "subtype3" "subtype2" "subtype1" "subtype1" "subtype4" "subtype4"
[127] "subtype2" "subtype5" "subtype5" "subtype5" "subtype5" "subtype5"
[133] "subtype1" "subtype5" "subtype5" "subtype3" "subtype1" "subtype6"
[139] "subtype2" "subtype3" "subtype5" "subtype4" "subtype4" "subtype3"
[145] "subtype4" "subtype1" "subtype1" "subtype6" "subtype1" "subtype5"
[151] "subtype3" "subtype1" "subtype4" "subtype4" "subtype1" "subtype1"
[157] "subtype3" "subtype2" "subtype5" "subtype1" "subtype2" "subtype3"
[163] "subtype5" "subtype2" "subtype3" "subtype4" "subtype2" "subtype4"
[169] "subtype3" "subtype1" "subtype3" "subtype3" "subtype4" "subtype2"
[175] "subtype2" "subtype4" "subtype2" "subtype4" "subtype4" "subtype2"
[181] "subtype5" "subtype1" "subtype4" "subtype2" "subtype4" "subtype3"
[187] "subtype2" "subtype4" "subtype3" "subtype1" "subtype3" "subtype2"
[193] "subtype4" "subtype1" "subtype1" "subtype2" "subtype5" "subtype1"
[199] "subtype1" "subtype3" "subtype6" "subtype1" "subtype2" "subtype3"
[205] "subtype3" "subtype3" "subtype1" "subtype2" "subtype5" "subtype4"
[211] "subtype6" "subtype2" "subtype1" "subtype3" "subtype4" "subtype2"
[217] "subtype6" "subtype1" "subtype4" "subtype3" "subtype4" "subtype3"
[223] "subtype1" "subtype2" "subtype5" "subtype5" "subtype6" "subtype2"
[229] "subtype2" "subtype6" "subtype1" "subtype3" "subtype4" "subtype6"
[235] "subtype3" "subtype2" "subtype6" "subtype1" "subtype4" "subtype3"
[241] "subtype6" "subtype6" "subtype5" "subtype3" "subtype5" "subtype3"
[247] "subtype5" "subtype2" "subtype1" "subtype3" "subtype4" "subtype4"
[253] "subtype6" "subtype6" "subtype5" "subtype1" "subtype1" "subtype2"
[259] "subtype3" "subtype5" "subtype4" "subtype5" "subtype4" "subtype5"
[265] "subtype6" "subtype6" "subtype4" "subtype6" "subtype3" "subtype1"
[271] "subtype3" "subtype3" "subtype2" "subtype2" "subtype2" "subtype3"
[277] "subtype4" "subtype5" "subtype5" "subtype3" "subtype4" "subtype4"
[283] "subtype5" "subtype5" "subtype1" "subtype2" "subtype4" "subtype6"
[289] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype4"
[295] "subtype1" "subtype2"
D2V11, continuous
[1] "Remove cluster labels:" "subtype7"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      52       51       50       59       40       28        2 
  [1] "subtype3" "subtype5" "subtype5" "subtype2" "subtype4" "subtype4"
  [7] "subtype4" "subtype4" "subtype4" "subtype2" "subtype5" "subtype4"
 [13] "subtype3" "subtype3" "subtype1" "subtype4" "subtype4" "subtype6"
 [19] "subtype4" "subtype5" "subtype1" "subtype2" "subtype1" "subtype4"
 [25] "subtype2" "subtype2" "subtype4" "subtype4" "subtype3" "subtype3"
 [31] "subtype3" "subtype4" "subtype2" "subtype4" "subtype6" "subtype6"
 [37] "subtype4" "subtype3" "subtype1" "subtype4" "subtype5" "subtype5"
 [43] "subtype4" "subtype1" "subtype4" "subtype5" "subtype3" "subtype1"
 [49] "subtype2" "subtype3" "subtype1" "subtype2" "subtype5" "subtype6"
 [55] "subtype1" "subtype1" "subtype2" "subtype4" "subtype3" "subtype3"
 [61] "subtype1" "subtype6" "subtype6" "subtype4" "subtype4" "subtype4"
 [67] "subtype1" "subtype1" "subtype4" "subtype4" "subtype6" "subtype5"
 [73] "subtype5" "subtype5" "subtype2" "subtype2" "subtype1" "subtype2"
 [79] "subtype5" "subtype5" "subtype3" "subtype1" "subtype3" "subtype1"
 [85] "subtype3" "subtype6" "subtype1" "subtype1" "subtype6" "subtype6"
 [91] "subtype1" "subtype2" "subtype2" "subtype3" "subtype2" "subtype1"
 [97] "subtype1" "subtype4" "subtype2" "subtype5" "subtype5" "subtype5"
[103] "subtype5" "subtype5" "subtype1" "subtype6" "subtype5" "subtype5"
[109] "subtype3" "subtype1" "subtype6" "subtype2" "subtype3" "subtype3"
[115] "subtype5" "subtype4" "subtype4" "subtype3" "subtype4" "subtype1"
[121] "subtype1" "subtype1" "subtype5" "subtype3" "subtype1" "subtype4"
[127] "subtype4" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[133] "subtype5" "subtype1" "subtype2" "subtype4" "subtype5" "subtype4"
[139] "subtype4" "subtype4" "subtype5" "subtype3" "subtype6" "subtype3"
[145] "subtype5" "subtype3" "subtype5" "subtype3" "subtype4" "subtype3"
[151] "subtype4" "subtype2" "subtype1" "subtype4" "subtype3" "subtype2"
[157] "subtype2" "subtype1" "subtype2" "subtype3" "subtype3" "subtype3"
[163] "subtype5" "subtype4" "subtype6" "subtype2" "subtype6" "subtype4"
[169] "subtype2" "subtype2" "subtype4" "subtype2" "subtype4" "subtype4"
[175] "subtype5" "subtype1" "subtype4" "subtype2" "subtype4" "subtype3"
[181] "subtype2" "subtype4" "subtype3" "subtype1" "subtype3" "subtype2"
[187] "subtype2" "subtype4" "subtype1" "subtype3" "subtype1" "subtype2"
[193] "subtype5" "subtype2" "subtype1" "subtype1" "subtype3" "subtype6"
[199] "subtype6" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
[205] "subtype3" "subtype2" "subtype4" "subtype6" "subtype2" "subtype1"
[211] "subtype3" "subtype4" "subtype2" "subtype6" "subtype1" "subtype4"
[217] "subtype3" "subtype4" "subtype2" "subtype3" "subtype1" "subtype2"
[223] "subtype5" "subtype5" "subtype6" "subtype2" "subtype2" "subtype6"
[229] "subtype1" "subtype3" "subtype4" "subtype6" "subtype3" "subtype2"
[235] "subtype6" "subtype1" "subtype4" "subtype3" "subtype6" "subtype5"
[241] "subtype5" "subtype3" "subtype5" "subtype2" "subtype1" "subtype3"
[247] "subtype4" "subtype6" "subtype5" "subtype1" "subtype1" "subtype2"
[253] "subtype3" "subtype5" "subtype4" "subtype6" "subtype6" "subtype4"
[259] "subtype1" "subtype3" "subtype3" "subtype2" "subtype2" "subtype4"
[265] "subtype5" "subtype4" "subtype5" "subtype5" "subtype1" "subtype2"
[271] "subtype4" "subtype6" "subtype2" "subtype2" "subtype2" "subtype1"
[277] "subtype3" "subtype4" "subtype1" "subtype2"
D2V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                         5
  subtype2                                0     0                        13
  subtype3                                0     4                         9
  subtype4                                0     1                        15
  subtype5                                0     0                         3
  subtype6                                1     3                         3
  subtype7                                0     0                         0
          vv
clus       WHITE
  subtype1    73
  subtype2    70
  subtype3    90
  subtype4    74
  subtype5    75
  subtype6    65
  subtype7     5
D2V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   3        0        4        1        0
  BLACK OR AFRICAN AMERICAN               5       13        9       15        3
  WHITE                                  73       70       90       74       75
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        1        0
  ASIAN                                   3        0
  BLACK OR AFRICAN AMERICAN               3        0
  WHITE                                  65        5
[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 74
  subtype3  4 96
  subtype4  5 79
  subtype5  4 69
  subtype6  7 64
  subtype7  1  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   78
  subtype2    2   74
  subtype3    4   96
  subtype4    5   79
  subtype5    4   69
  subtype6    7   64
  subtype7    1    5
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            3        2        4        5        4        7
  NOT HISPANIC OR LATINO       78       74       96       79       69       64
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO        5
[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 18 33
  subtype2  9 21
  subtype3 17 16
  subtype4 15 14
  subtype5 25 44
subtype1 subtype2 subtype3 subtype4 subtype5 
      51       30       33       29       69 
subtype1 subtype2 subtype3 subtype4 subtype5 
      33       21       16       14       44 
$subtype1
TCGA-BA-5557 TCGA-CN-4727 TCGA-CX-7219 TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-5151 
       20.48        51.29        34.36        15.19        26.50        23.74 
TCGA-BA-5556 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4735 TCGA-CN-4738 
       23.84        38.04         4.67        56.68        57.11        14.33 
TCGA-CN-4739 TCGA-CN-5358 TCGA-CN-5359 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 
       45.83         8.58        12.39         8.32        16.21        11.84 
TCGA-CN-5369 TCGA-CN-6018 TCGA-CN-6020 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-6222 
       12.49        19.07         6.74         2.93        70.45        66.28 
TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5971 TCGA-CV-6942 TCGA-CV-6950 
       17.16        17.95        91.53        23.05       140.78        15.09 
TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7090 
       10.98         8.42        28.34         2.50         4.14       172.67 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7247 TCGA-CV-7252 
        7.99         9.01        10.75       130.88        18.97         4.96 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 TCGA-CV-7438 TCGA-CV-7440 
       11.87        47.97        49.71        57.47         6.38        22.19 
TCGA-D6-6515 TCGA-D6-6823 TCGA-DQ-7592 
       13.25        23.05        37.58 

$subtype2
TCGA-BA-5559 TCGA-CN-6021 TCGA-CN-6023 TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-6870 
       68.48         9.07        52.08         9.07        57.93        14.83 
TCGA-BB-4217 TCGA-CN-4723 TCGA-CN-4733 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6017 
        6.15        55.86        52.14        56.94        23.90        28.04 
TCGA-CN-6989 TCGA-CN-6995 TCGA-CQ-5327 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CV-5430 
       32.22         3.68        54.58        15.75        32.38       139.43 
TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6939 TCGA-CV-6945 TCGA-CV-6954 TCGA-CV-7089 
       21.07         9.60        21.90        12.03        65.82        64.83 
TCGA-CV-7248 TCGA-CV-7422 TCGA-CV-7429 TCGA-CV-7433 TCGA-DQ-7591 TCGA-IQ-7630 
       17.13        34.09         3.52        19.76        20.45        15.95 

$subtype3
TCGA-BA-6871 TCGA-CN-6992 TCGA-CN-6997 TCGA-CQ-5323 TCGA-BA-5152 TCGA-BA-5555 
        3.55        35.05        32.48        48.20        42.35        17.10 
TCGA-BA-6869 TCGA-CN-4730 TCGA-CN-4741 TCGA-CN-5355 TCGA-CN-5356 TCGA-CN-5361 
       21.17        26.86        73.61        42.02        46.32        69.70 
TCGA-CN-6010 TCGA-CN-6988 TCGA-CQ-5324 TCGA-CQ-5332 TCGA-CV-5432 TCGA-CV-5434 
       50.07        10.45        52.37        10.42       129.21       108.95 
TCGA-CV-5441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6956 
       94.88        90.12         9.70        42.38        30.08         7.13 
TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7242 TCGA-CV-7250 TCGA-CV-7418 TCGA-CV-7424 
      111.16        12.66        36.00        95.34        25.94        14.89 
TCGA-CV-7437 TCGA-CV-7446 TCGA-CX-7086 
       16.64        35.93        18.84 

$subtype4
TCGA-CQ-7068 TCGA-BA-6872 TCGA-BA-6873 TCGA-CN-4722 TCGA-CN-4729 TCGA-CN-6011 
       43.04        12.62         4.01        48.76        12.89        30.67 
TCGA-CQ-5331 TCGA-CV-5442 TCGA-CV-5966 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
       45.99        76.50        17.92        60.49        43.23        54.74 
TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6953 
       62.43         5.46        20.52        26.43        11.24        53.95 
TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7245 TCGA-CV-7413 TCGA-CV-7427 TCGA-CV-7428 
       21.80        71.21        26.20         9.67       156.49        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-D6-6516 TCGA-D6-6825 TCGA-IQ-7632 
       16.27        84.49        25.41        16.14        14.50 

$subtype5
TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-6221 TCGA-CN-4731 TCGA-CN-4734 TCGA-CN-4736 
        9.24        11.08        32.88        32.81        55.56        12.99 
TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5360 TCGA-CN-5365 TCGA-CN-5367 
       20.55        27.58        13.05        71.31        11.54        11.57 
TCGA-CN-5370 TCGA-CN-5373 TCGA-CN-6012 TCGA-CN-6016 TCGA-CN-6019 TCGA-CN-6994 
        8.52        52.08        48.00        47.44        34.13        38.89 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-5334 TCGA-CQ-6218 
       17.42        11.74        21.50        62.37         4.24        41.19 
TCGA-CQ-6224 TCGA-CQ-6225 TCGA-CQ-6227 TCGA-CQ-6228 TCGA-CQ-6229 TCGA-CQ-7065 
       56.58        13.25         4.24        14.99        38.76        53.52 
TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5973 TCGA-CV-5976 
       19.20       107.51        80.12        13.35        86.83        48.59 
TCGA-CV-5978 TCGA-CV-6934 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-7095 
        7.07         2.14         4.73        19.79         6.08        18.81 
TCGA-CV-7101 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7235 TCGA-CV-7236 
        5.26         1.84        52.31        12.92        77.16         4.73 
TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7255 TCGA-CV-7263 TCGA-CV-7407 TCGA-CV-7410 
       89.65        31.36         2.10        18.41        35.54       210.97 
TCGA-CV-7411 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7423 
       89.33         0.46        22.85        25.08         0.07       100.57 
TCGA-CV-7425 TCGA-CV-7434 TCGA-CV-7435 TCGA-CV-7568 TCGA-CX-7085 TCGA-D6-6517 
       56.48         7.17       153.86        30.48        10.55         9.60 
TCGA-D6-6824 TCGA-D6-6826 TCGA-D6-6827 
        2.53        11.44        18.67 

subtype1 subtype2 subtype3 subtype4 subtype5 
    2.50     3.52     3.55     4.01     0.07 
subtype1 subtype2 subtype3 subtype4 subtype5 
  172.67   139.43   129.21   156.49   210.97 
subtype1 subtype2 subtype3 subtype4 subtype5 
   18.97    22.90    35.93    26.43    19.79 
[1] "2.5 - 172.7 (19.0)" "3.5 - 139.4 (22.9)" "3.5 - 129.2 (35.9)"
[4] "4.0 - 156.5 (26.4)" "0.1 - 211.0 (19.8)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB
  subtype1       1       16         7        25         1
  subtype2       0        2         3        19         0
  subtype3       2        3         8        18         1
  subtype4       2        7         5        13         0
  subtype5       4       11         8        42         2
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          1        0        2        2        4
  STAGE II        16        2        3        7       11
  STAGE III        7        3        8        5        8
  STAGE IVA       25       19       18       13       42
  STAGE IVB        1        0        1        0        2
[1] 5 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T0+T1 T2 T3 T4
  subtype1     2 20 11 17
  subtype2     1  4  7 13
  subtype3     2  4 13 13
  subtype4     2 12  3 11
  subtype5     6 19 19 25
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        2        1        2        2        6
  T2          20        4        4       12       19
  T3          11        7       13        3       19
  T4          17       13       13       11       25
[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 21  3 16  1
  subtype2  6  2 15  0
  subtype3 12  4 13  1
  subtype4 14  4  7  0
  subtype5 19  8 28  2
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       21        6       12       14       19
  N1        3        2        4        4        8
  N2       16       15       13        7       28
  N3        1        0        1        0        2
[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"
D3V6, binary
          cls
clus       0
  subtype1 8
  subtype2 4
  subtype3 3
  subtype4 1
  subtype5 7
[1] "NOT AVAILABLE: table only has an event [0]"
D3V7, binary
          cls
clus        0  1
  subtype1 11 40
  subtype2  7 23
  subtype3  2 31
  subtype4 13 16
  subtype5 29 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   11   40
  subtype2    7   23
  subtype3    2   31
  subtype4   13   16
  subtype5   29   40
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       11        7        2       13       29
  MALE         40       23       31       16       40
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus        0  1
  subtype1 18 24
  subtype2  7 18
  subtype3  9 13
  subtype4 13 10
  subtype5 26 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   24
  subtype2    7   18
  subtype3    9   13
  subtype4   13   10
  subtype5   26   22
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        18        7        9       13       26
  YES       24       18       13       10       22
[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 & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                  51
  subtype2                                  30
  subtype3                                  33
  subtype4                                  29
  subtype5                                  69
[1] "NOT AVAILABLE: table dimension [5x1]"
D3V10, continuous
D3V11, continuous
D3V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     0                         7
  subtype2                                0     1                         4
  subtype3                                0     1                         5
  subtype4                                0     0                         0
  subtype5                                0     1                         3
          vv
clus       WHITE
  subtype1    42
  subtype2    25
  subtype3    26
  subtype4    29
  subtype5    63
D3V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        0        0
  ASIAN                                   0        1        1        0        1
  BLACK OR AFRICAN AMERICAN               7        4        5        0        3
  WHITE                                  42       25       26       29       63
[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"
D3V14, binary
          cls
clus        0  1
  subtype1  4 44
  subtype2  3 25
  subtype3  1 30
  subtype4  2 27
  subtype5  3 64
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   44
  subtype2    3   25
  subtype3    1   30
  subtype4    2   27
  subtype5    3   64
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            4        3        1        2        3
  NOT HISPANIC OR LATINO       44       25       30       27       64
[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(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 32 46
  subtype2 26 59
  subtype3 26 23
subtype1 subtype2 subtype3 
      78       85       49 
subtype1 subtype2 subtype3 
      46       59       23 
$subtype1
TCGA-BA-5557 TCGA-CN-4727 TCGA-CQ-7068 TCGA-CX-7219 TCGA-BA-4074 TCGA-BA-5149 
       20.48        51.29        43.04        34.36        15.19        26.50 
TCGA-BA-5151 TCGA-BA-5556 TCGA-BA-6870 TCGA-BA-6873 TCGA-BB-4217 TCGA-CN-4723 
       23.74        23.84        14.83         4.01         6.15        55.86 
TCGA-CN-4729 TCGA-CN-4733 TCGA-CN-4735 TCGA-CN-4739 TCGA-CN-5355 TCGA-CN-5359 
       12.89        52.14        57.11        45.83        42.02        12.39 
TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-6011 
       69.70         8.32        16.21        11.84        12.49        30.67 
TCGA-CN-6013 TCGA-CN-6018 TCGA-CN-6020 TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5331 
       23.90        19.07         6.74         2.93        70.45        45.99 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CV-5431 TCGA-CV-5432 TCGA-CV-5439 TCGA-CV-5443 
       15.75        32.38        17.16       129.21        17.95        91.53 
TCGA-CV-5966 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5977 TCGA-CV-5979 TCGA-CV-6003 
       17.92        13.35        23.05        60.49        43.23        54.74 
TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6940 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6950 
       62.43         5.46        26.43       140.78        12.03        15.09 
TCGA-CV-6955 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       10.98         8.42         2.50         4.14        64.83       172.67 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7247 
        7.99         9.01        71.21        10.75       130.88        18.97 
TCGA-CV-7248 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7406 
       17.13         4.96        11.87        47.97        49.71        57.47 
TCGA-CV-7422 TCGA-CV-7427 TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7438 TCGA-CV-7440 
       34.09       156.49        16.27        84.49         6.38        22.19 
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        37.58        15.95 

$subtype2
TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-6022 TCGA-CN-6023 TCGA-CN-6024 TCGA-CN-6992 
       68.48         3.55         9.24        52.08        11.08        35.05 
TCGA-CN-6997 TCGA-CQ-6221 TCGA-BA-4078 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 
       32.48        32.88         9.07        38.04         4.67        56.68 
TCGA-CN-4731 TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4741 TCGA-CN-5358 
       32.81        12.99        20.55        27.58        73.61         8.58 
TCGA-CN-5360 TCGA-CN-5367 TCGA-CN-5370 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6016 
       71.31        11.57         8.52        50.07        48.00        47.44 
TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 
       28.04        34.13        10.45        32.22         3.68        17.42 
TCGA-CN-6998 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5330 TCGA-CQ-5332 TCGA-CQ-5334 
       11.74        21.50        54.58        62.37        10.42         4.24 
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-CN-6021 TCGA-CQ-5323 TCGA-BA-5152 TCGA-BA-5153 TCGA-BA-5555 TCGA-BA-6869 
        9.07        48.20        42.35        57.93        17.10        21.17 
TCGA-BA-6872 TCGA-CN-4722 TCGA-CN-4730 TCGA-CN-4734 TCGA-CN-4738 TCGA-CN-4742 
       12.62        48.76        26.86        55.56        14.33        13.05 
TCGA-CN-5356 TCGA-CN-5365 TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6994 TCGA-CQ-5324 
       46.32        11.54        52.08        56.94        38.89        52.37 
TCGA-CQ-6218 TCGA-CQ-6229 TCGA-CQ-7065 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-6933 
       41.19        38.76        53.52        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        89.65        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 
  172.67   210.97   111.16 
subtype1 subtype2 subtype3 
   22.62    21.50    31.36 
[1] "2.5 - 172.7 (22.6)" "0.1 - 211.0 (21.5)" "2.1 - 111.2 (31.4)"
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 10
  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"
D4V8, binary
          cls
clus        0  1
  subtype1 30 33
  subtype2 25 35
  subtype3 18 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   30   33
  subtype2   25   35
  subtype3   18   19
     clus
vv    subtype1 subtype2 subtype3
  NO        30       25       18
  YES       33       35       19
[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 & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                  78
  subtype2                                  85
  subtype3                                  49
[1] "NOT AVAILABLE: table dimension [3x1]"
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    66
  subtype2    74
  subtype3    45
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                                  66       74       45
[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  70  66
  subtype2  64  49
  subtype3 113  59
  subtype4  51  46
subtype1 subtype2 subtype3 subtype4 
     136      113      172       97 
subtype1 subtype2 subtype3 subtype4 
      66       49       59       46 
$subtype1
TCGA-BA-4075 TCGA-BA-6871 TCGA-BB-A5HU TCGA-CN-4727 TCGA-CN-6022 TCGA-CQ-6221 
        9.30         3.55        25.71        51.29         9.24        32.88 
TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-7588 TCGA-UF-A7JV TCGA-4P-AA8J 
       43.04         6.02        34.36        14.04         2.96         3.35 
TCGA-BA-4074 TCGA-BA-5149 TCGA-BA-6868 TCGA-BA-6872 TCGA-BA-7269 TCGA-BA-A6D8 
       15.19        26.50        15.52        12.62        41.85        27.95 
TCGA-BA-A8YP TCGA-BB-4227 TCGA-BB-7871 TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A6UO 
       16.41         4.41        24.66        38.40        10.55         8.81 
TCGA-CN-4723 TCGA-CN-4735 TCGA-CN-5361 TCGA-CN-5363 TCGA-CN-5365 TCGA-CN-5367 
       55.86        57.11        69.70         8.32        11.54        11.57 
TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6994 TCGA-CN-A49A TCGA-CN-A63V TCGA-CN-A642 
       30.67        19.07        38.89        17.29        22.32         2.70 
TCGA-CQ-5326 TCGA-CQ-5334 TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CQ-A4CD 
        2.93         4.24        41.88        77.56        29.36        33.60 
TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-6477 TCGA-CR-7373 TCGA-CR-7379 
       14.14        31.23        11.77        16.90        29.23        34.06 
TCGA-CR-7380 TCGA-CV-5431 TCGA-CV-5436 TCGA-CV-5966 TCGA-CV-5978 TCGA-CV-5979 
       19.92        17.16        19.20        17.92         7.07        43.23 
TCGA-CV-6003 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6942 TCGA-CV-6945 TCGA-CV-6954 
       54.74         5.46        20.52       140.78        12.03        65.82 
TCGA-CV-6960 TCGA-CV-6961 TCGA-CV-7090 TCGA-CV-7091 TCGA-CV-7100 TCGA-CV-7102 
       28.34         2.50       172.67       111.16         9.01         1.84 
TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7245 TCGA-CV-7252 TCGA-CV-7407 TCGA-CV-7410 
       77.16         4.73        26.20         4.96        35.54       210.97 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7429 TCGA-CV-7432 TCGA-CV-7433 
        9.67        22.85        25.08         3.52        84.49        19.76 
TCGA-CV-7434 TCGA-CV-7440 TCGA-CV-A45U TCGA-CV-A45Y TCGA-CV-A6JD TCGA-CV-A6JE 
        7.17        22.19        35.47        88.87         5.98        35.34 
TCGA-CV-A6JM TCGA-CV-A6JZ TCGA-CV-A6K2 TCGA-CX-A4AQ TCGA-D6-6517 TCGA-D6-6826 
        6.38        23.47        10.42        51.12         9.60        11.44 
TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-5631 TCGA-F7-8298 TCGA-F7-8489 
       22.59        13.94        12.10        18.02        32.71        21.63 
TCGA-F7-A61W TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7753 
        0.46        20.25        12.43        15.16        15.06        28.47 
TCGA-HD-7831 TCGA-HD-7832 TCGA-HD-A633 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7631 
       21.93        27.48        13.84        34.75        15.95        38.53 
TCGA-IQ-A61E TCGA-IQ-A61G TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-MT-A7BN TCGA-P3-A5Q6 
       37.71        11.84        13.84        15.48        15.42        15.78 
TCGA-P3-A5QA TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A64Z 
       71.74        47.01        19.00        75.55        13.15        21.07 
TCGA-QK-A6IG TCGA-QK-A6IH TCGA-QK-A8Z9 TCGA-QK-AA3K TCGA-RS-A6TO TCGA-T2-A6WX 
        7.30        21.47        14.76         8.32        12.72         6.87 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JD 
       32.45        13.71         3.12        49.51        74.47        24.30 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-WA-A7GZ TCGA-KU-A66T 
       18.05        13.94        20.55        18.15 

$subtype2
TCGA-BA-5557 TCGA-BA-A4II TCGA-CQ-7063 TCGA-HD-8634 TCGA-BA-4076 TCGA-BA-5151 
       20.48        30.18        70.13        12.66        13.64        23.74 
TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-A6DA TCGA-BA-A6DD 
       42.35        23.84        65.59        14.83        11.54         5.69 
TCGA-BA-A6DE TCGA-BA-A6DJ TCGA-BB-4224 TCGA-BB-7863 TCGA-BB-A5HZ TCGA-C9-A47Z 
       14.47        13.38         9.14        33.70        27.19         6.28 
TCGA-C9-A480 TCGA-CN-4722 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4734 
       12.69        48.76         4.67        12.89        26.86        55.56 
TCGA-CN-4742 TCGA-CN-5359 TCGA-CN-5369 TCGA-CN-5373 TCGA-CN-6020 TCGA-CN-6998 
       13.05        12.39        12.49        52.08         6.74        11.74 
TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5331 TCGA-CQ-6218 TCGA-CQ-6220 TCGA-CQ-6223 
       52.37        54.58        45.99        41.19        32.38        46.95 
TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4CE TCGA-CQ-A4CH TCGA-CR-6471 TCGA-CR-6491 
       53.52        43.10        29.49        12.46        39.52        22.78 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7390 TCGA-CR-7392 TCGA-CR-7394 
        9.27        47.34        24.95        49.58        46.85        44.25 
TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5973 TCGA-CV-5977 
       30.58        17.95        94.88        76.50        86.83        60.49 
TCGA-CV-6436 TCGA-CV-6938 TCGA-CV-6943 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 
       62.43         4.73        19.79         6.08        53.95        10.98 
TCGA-CV-7089 TCGA-CV-7095 TCGA-CV-7099 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7255 
       64.83        18.81         7.99        10.75       130.88         2.10 
TCGA-CV-7411 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-A45O 
       89.33       100.57        56.48       156.49        54.94        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A463 
       21.01       169.38       159.65         1.05         6.51         0.76 
TCGA-CV-A465 TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6K1 TCGA-D6-6516 
        7.07        29.79         6.48        21.24        22.52        25.41 
TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6ES TCGA-F7-A50G TCGA-F7-A50J 
       17.72        12.36        28.77        12.79        20.25        31.13 
TCGA-F7-A61S TCGA-F7-A622 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7917 TCGA-HD-A4C1 
       18.94        11.80        13.38        33.76        27.48         0.36 
TCGA-HD-A6I0 TCGA-IQ-7632 TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67F 
        6.90        14.50        14.37         7.96        30.05        12.62 
TCGA-MZ-A7D7 TCGA-P3-A6T3 TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A6II 
       17.98        18.97         2.04        29.00        16.01         9.34 
TCGA-QK-A6IJ TCGA-QK-A8ZB TCGA-T2-A6WZ TCGA-UF-A7JC TCGA-UF-A7JT 
       12.72        17.82        15.91        17.95        32.65 

$subtype3
TCGA-BA-4077 TCGA-BA-A4IG TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       37.28        28.11         9.07        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CR-6472 TCGA-CX-7082 TCGA-DQ-5629 
       19.82        24.39        48.20        34.52         0.36        30.94 
TCGA-DQ-7589 TCGA-DQ-7593 TCGA-UF-A71D TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-5555 
       46.32        40.24        48.03         9.07        57.93        17.10 
TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6DI TCGA-BA-A6DL TCGA-BB-4217 
       21.17        29.42        20.45        11.05        20.48         6.15 
TCGA-BB-4223 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7864 
      105.90         4.80        18.38        22.42        36.72        50.20 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-8601 TCGA-BB-A6UM TCGA-CN-4731 TCGA-CN-4738 
       44.98        66.28        20.52        12.92        32.81        14.33 
TCGA-CN-4739 TCGA-CN-4741 TCGA-CN-5356 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 
       45.83        73.61        46.32        71.31        56.94        50.07 
TCGA-CN-6012 TCGA-CN-6019 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 
       48.00        34.13        10.45        35.01        25.41        23.57 
TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 
       29.72        21.21         7.40        31.69        12.39        12.07 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-6228 
       23.44        20.88        19.53        10.42        13.25        14.99 
TCGA-CQ-A4C9 TCGA-CR-5243 TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 
       23.24        84.23        54.67        37.87        26.27        58.42 
TCGA-CR-6470 TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6484 
       50.01        36.99        11.90        10.22        11.34        11.64 
TCGA-CR-6487 TCGA-CR-6492 TCGA-CR-7364 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        7.69        15.75        47.18        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 TCGA-CR-7393 
        3.09         0.99        32.78        27.06        12.89        32.65 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 
        5.13         5.95        29.95        48.39       139.43       129.21 
TCGA-CV-5443 TCGA-CV-6433 TCGA-CV-6441 TCGA-CV-6933 TCGA-CV-6935 TCGA-CV-6939 
       91.53        21.07         9.60        90.12         9.70        21.90 
TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6951 TCGA-CV-6962 TCGA-CV-7101 TCGA-CV-7177 
       11.24        42.38        30.08         4.14         5.26        21.80 
TCGA-CV-7242 TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 
       36.00        17.13        95.34        11.87        47.97        49.71 
TCGA-CV-7406 TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7422 
       57.47        17.85         0.46        25.94         0.07        34.09 
TCGA-CV-7424 TCGA-CV-7430 TCGA-CV-7437 TCGA-CV-7446 TCGA-CV-A45W TCGA-CV-A45Z 
       14.89        16.27        16.64        35.93        45.96        48.20 
TCGA-CV-A460 TCGA-CV-A461 TCGA-CX-7086 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-6827 
       60.43        67.86        18.84        23.05         2.53        18.67 
TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7594 TCGA-DQ-7595 
       24.95        23.34        46.45        20.45        40.04        39.12 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50I TCGA-F7-A61V TCGA-H7-A76A TCGA-HD-7754 
       41.59        37.18         3.02        24.95        20.94        25.74 
TCGA-HD-8314 TCGA-HD-A634 TCGA-IQ-A61I TCGA-IQ-A6SG TCGA-KU-A6H7 TCGA-MT-A67D 
       22.03         4.27         0.07        19.04        19.27         1.84 
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-A6T6 TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8Z7 
       12.99        23.15        27.39        21.07        19.73        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-QK-AA3J TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-TN-A7HI 
        5.62        12.20        15.32        16.96         7.10        13.55 
TCGA-TN-A7HJ TCGA-TN-A7HL TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7J9 
       13.25        20.35        64.80        54.67        49.45        44.65 
TCGA-UF-A7JF TCGA-UF-A7JO TCGA-UP-A6WW TCGA-KU-A66S 
       55.43        20.75        17.03        13.35 

$subtype4
TCGA-BA-5559 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-HD-8635 TCGA-BA-6873 
       68.48        11.08        16.73        11.61        22.85         4.01 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BB-8596 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 
        7.10         2.27        71.05        38.04        56.68        52.14 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5364 
       12.99        20.55        27.58        42.02         8.58        16.21 
TCGA-CN-5366 TCGA-CN-5370 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6989 
       11.84         8.52        23.90        47.44        28.04        32.22 
TCGA-CN-6995 TCGA-CN-6996 TCGA-CQ-5325 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 
        3.68        17.42        21.50        70.45        62.37        11.21 
TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CQ-A4C6 
       15.75        66.28        56.58         4.24        38.76        44.48 
TCGA-CR-6474 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7382 
       18.54        12.46        39.16        31.96         9.17        26.17 
TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 
       17.13        47.01        30.02        24.79        35.41       108.95 
TCGA-CV-5435 TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 
       76.24       107.51        80.12        13.35        23.05        48.59 
TCGA-CV-6934 TCGA-CV-6940 TCGA-CV-6950 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-7097 
        2.14        26.43        15.09         7.13         8.42        12.66 
TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7178 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 
       52.31        12.92        71.21        89.65        31.36        18.97 
TCGA-CV-7263 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45R TCGA-CV-A464 
       18.41       153.86         6.38        30.48       180.16        56.61 
TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6515 
       15.25        28.01         3.62        19.92        10.55        13.25 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-5625 
       16.14        24.95        25.32         7.63        58.45        37.25 
TCGA-DQ-5630 TCGA-DQ-7592 TCGA-F7-A620 TCGA-HD-8224 TCGA-HD-A6HZ TCGA-IQ-A61H 
       33.86        37.58        17.85        14.66         3.65        37.41 
TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-QK-A652 TCGA-UF-A71A TCGA-UF-A7JH TCGA-UF-A7JS 
       33.57        10.75        21.21         2.83        29.46        22.36 
TCGA-WA-A7H4 
       14.56 

subtype1 subtype2 subtype3 subtype4 
    0.46     0.36     0.07     2.14 
subtype1 subtype2 subtype3 subtype4 
  210.97   169.38   139.43   180.16 
subtype1 subtype2 subtype3 subtype4 
  19.035   21.010   23.195   23.050 
[1] "0.5 - 211.0 (19.0)" "0.4 - 169.4 (21.0)" "0.1 - 139.4 (23.2)"
[4] "2.1 - 180.2 (23.1)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       5       17        17        74         8         0
  subtype2       8       20        21        57         0         0
  subtype3       4       20        27        75         3         1
  subtype4      10       17        16        47         1         0
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I          5        8        4       10
  STAGE II        17       20       20       17
  STAGE III       17       21       27       16
  STAGE IVA       74       57       75       47
  STAGE IVB        8        0        3        1
  STAGE IVC        0        0        1        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     7 37 17 61
  subtype2    11 30 29 38
  subtype3    17 37 34 48
  subtype4    14 32 19 27
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1        7       11       17       14
  T2          37       30       37       32
  T3          17       29       34       19
  T4          61       38       48       27
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 42 17 48  5
  subtype2 49 15 32  0
  subtype3 52 20 51  3
  subtype4 33 15 38  0
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       42       49       52       33
  N1       17       15       20       15
  N2       48       32       51       38
  N3        5        0        3        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 46  0
  subtype2 50  0
  subtype3 55  1
  subtype4 35  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   46    0
  subtype2   50    0
  subtype3   55    1
  subtype4   35    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       46       50       55       35
  1        0        0        1        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"
D5V7, binary
          cls
clus         0   1
  subtype1  32 104
  subtype2  47  67
  subtype3  29 143
  subtype4  28  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32  104
  subtype2   47   67
  subtype3   29  143
  subtype4   28   70
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       32       47       29       28
  MALE        104       67      143       70
[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"
D5V8, binary
          cls
clus         0   1
  subtype1  39  80
  subtype2  39  65
  subtype3  38 111
  subtype4  45  41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   39   80
  subtype2   39   65
  subtype3   38  111
  subtype4   45   41
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        39       39       38       45
  YES       80       65      111       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 & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                 134
  subtype2                                 114
  subtype3                                 163
  subtype4                                  98
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                 1
  subtype2                                                 0
  subtype3                                                 9
  subtype4                                                 0
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  subtype1                                                         1
  subtype2                                                         0
  subtype3                                                         0
  subtype4                                                         0
D5V9, multiclass
                                                           clus
vv                                                          subtype1 subtype2
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            134      114
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        1        0
                                                           clus
vv                                                          subtype3 subtype4
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            163       98
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                9        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        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"
D5V10, continuous
D5V11, continuous
D5V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                        18
  subtype2                                0     6                         7
  subtype3                                0     2                        18
  subtype4                                1     1                         5
          vv
clus       WHITE
  subtype1   109
  subtype2    98
  subtype3   148
  subtype4    89
D5V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        0        1
  ASIAN                                   2        6        2        1
  BLACK OR AFRICAN AMERICAN              18        7       18        5
  WHITE                                 109       98      148       89
[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"
D5V14, binary
          cls
clus         0   1
  subtype1   8 114
  subtype2   5 105
  subtype3   6 153
  subtype4   6  86
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  114
  subtype2    5  105
  subtype3    6  153
  subtype4    6   86
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            8        5        6        6
  NOT HISPANIC OR LATINO      114      105      153       86
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2        0   1
  subtype1  88  89
  subtype2  57  47
  subtype3 100  72
  subtype4  53  12
subtype1 subtype2 subtype3 subtype4 
     177      104      172       65 
subtype1 subtype2 subtype3 subtype4 
      89       47       72       12 
$subtype1
TCGA-BA-4075 TCGA-BA-5559 TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CQ-A4C7 
        9.30        68.48         9.24        11.08        16.73        11.61 
TCGA-CX-7082 TCGA-HD-8634 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-6873 
        0.36        12.66        22.85         3.35        26.50         4.01 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A8YP TCGA-BB-4224 TCGA-BB-7872 TCGA-BB-8596 
        7.10         2.27        16.41         9.14        38.40        71.05 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4728 TCGA-CN-4733 
        6.28        12.69        38.04         4.67        56.68        52.14 
TCGA-CN-4736 TCGA-CN-4737 TCGA-CN-4740 TCGA-CN-4742 TCGA-CN-5355 TCGA-CN-5358 
       12.99        20.55        27.58        13.05        42.02         8.58 
TCGA-CN-5360 TCGA-CN-5363 TCGA-CN-5364 TCGA-CN-5366 TCGA-CN-5367 TCGA-CN-5370 
       71.31         8.32        16.21        11.84        11.57         8.52 
TCGA-CN-5373 TCGA-CN-5374 TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6018 
       52.08        56.94        23.90        47.44        28.04        19.07 
TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A642 
       34.13        32.22         3.68        17.42        11.74         2.70 
TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 
       20.88        21.50        54.58        70.45        62.37        11.21 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 TCGA-CQ-6229 
       15.75        32.38        66.28        56.58         4.24        38.76 
TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 
       53.52        77.56        44.48        12.46        18.54        16.90 
TCGA-CR-6488 TCGA-CR-6493 TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 
       12.46         9.27        39.16        24.95        31.96         9.17 
TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 
       34.06        26.17        17.13        47.01        30.02        46.85 
TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5434 TCGA-CV-5435 
       32.65        44.25        24.79        35.41       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-6940 TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6956 
       26.43        19.79        15.09        30.08         6.08         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-7255 
       12.92        71.21        89.65        31.36        18.97         2.10 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7423 TCGA-CV-7429 TCGA-CV-7435 
       18.41        57.47        34.09       100.57         3.52       153.86 
TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T 
        6.38        30.48        21.01       169.38       180.16       159.65 
TCGA-CV-A464 TCGA-CV-A465 TCGA-CV-A468 TCGA-CV-A6JN TCGA-CV-A6JT TCGA-CV-A6JU 
       56.61         7.07        15.25        29.79        28.01         3.62 
TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6515 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 
       19.92        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        37.25        33.86        18.02 
TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61W TCGA-F7-A620 
       37.58        40.04        20.25        31.13         0.46        17.85 
TCGA-F7-A622 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8224 TCGA-HD-8314 TCGA-HD-A6HZ 
       11.80        28.47        21.93        14.66        22.03         3.65 
TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-MT-A51X TCGA-P3-A5QA 
       37.71        37.41        33.57        10.75         7.96        71.74 
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        21.21         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        24.30        29.46 
TCGA-UF-A7JS TCGA-WA-A7GZ TCGA-WA-A7H4 
       22.36        20.55        14.56 

$subtype2
TCGA-CN-4727 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 TCGA-DQ-5629 
       51.29         9.07        52.08        35.05        32.48        30.94 
TCGA-DQ-7589 TCGA-UF-A71D TCGA-BA-4074 TCGA-BA-5555 TCGA-BA-6869 TCGA-BA-7269 
       46.32        48.03        15.19        17.10        21.17        41.85 
TCGA-BA-A4IF TCGA-BA-A6D8 TCGA-BA-A6DE TCGA-BA-A6DL TCGA-BB-7862 TCGA-BB-7864 
       29.42        27.95        14.47        20.48        36.72        50.20 
TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-CN-4730 TCGA-CN-4731 
       66.28        24.66        20.52        27.19        26.86        32.81 
TCGA-CN-4738 TCGA-CN-5356 TCGA-CN-6010 TCGA-CN-6012 TCGA-CN-6988 TCGA-CN-A497 
       14.33        46.32        50.07        48.00        10.45        35.01 
TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5324 TCGA-CQ-5332 
        7.40        31.69        12.39        12.07        52.37        10.42 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5247 TCGA-CR-7364 
       13.25        14.99        23.24        31.23        11.77        47.18 
TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7374 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 
        3.45         3.09         0.99        27.06        49.58         5.13 
TCGA-CR-7402 TCGA-CV-5432 TCGA-CV-5441 TCGA-CV-5978 TCGA-CV-6933 TCGA-CV-6935 
       29.95       129.21        94.88         7.07        90.12         9.70 
TCGA-CV-6939 TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6954 TCGA-CV-6960 TCGA-CV-6962 
       21.90        11.24        42.38        65.82        28.34         4.14 
TCGA-CV-7101 TCGA-CV-7177 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        5.26        21.80        36.00        26.20        17.13        95.34 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7409 TCGA-CV-7414 
       11.87        47.97        49.71        35.54        17.85         0.46 
TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7424 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7437 
       25.94         0.07        14.89        54.94        16.27        16.64 
TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45W TCGA-CV-A45Z TCGA-CV-A461 TCGA-D6-6823 
       22.19        35.93        45.96        48.20        67.86        23.05 
TCGA-D6-6824 TCGA-D6-A6EO TCGA-D6-A74Q TCGA-DQ-7595 TCGA-F7-7848 TCGA-F7-A61V 
        2.53        24.95        23.34        39.12        37.18        24.95 
TCGA-IQ-7631 TCGA-IQ-A6SG TCGA-QK-A6VB TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZA 
       38.53        19.04        21.07        12.89         5.62        12.20 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JF 
        3.12        13.55        54.67        49.51        49.45        55.43 
TCGA-UF-A7JO TCGA-KU-A66S 
       20.75        13.35 

$subtype3
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-A6V3 TCGA-CQ-6221 
       37.28        20.48        30.18        25.71        24.39        32.88 
TCGA-CQ-7063 TCGA-CQ-7068 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-7588 TCGA-UF-A7JV 
       70.13        43.04         6.02        34.36        14.04         2.96 
TCGA-BA-4076 TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 
       13.64        23.74        42.35        23.84        65.59        15.52 
TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DJ 
       14.83        12.62        11.54         5.69        11.05        13.38 
TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-A5HY TCGA-BB-A6UO TCGA-CN-4722 TCGA-CN-4723 
        4.41        33.70        10.55         8.81        48.76        55.86 
TCGA-CN-4729 TCGA-CN-4734 TCGA-CN-5359 TCGA-CN-5361 TCGA-CN-5365 TCGA-CN-5369 
       12.89        55.56        12.39        69.70        11.54        12.49 
TCGA-CN-6011 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49A 
       30.67         6.74        38.89        25.41        23.57        17.29 
TCGA-CN-A49B TCGA-CN-A63V TCGA-CQ-5326 TCGA-CQ-5331 TCGA-CQ-5334 TCGA-CQ-6218 
       29.72        22.32         2.93        45.99         4.24        41.19 
TCGA-CQ-6223 TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE 
       46.95        41.88        43.10        29.36        33.60        29.49 
TCGA-CQ-A4CG TCGA-CR-6471 TCGA-CR-6484 TCGA-CR-6491 TCGA-CR-6492 TCGA-CR-7367 
       14.14        39.52        11.64        22.78        15.75        47.34 
TCGA-CR-7373 TCGA-CR-7380 TCGA-CR-7389 TCGA-CR-7395 TCGA-CV-5439 TCGA-CV-5442 
       29.23        19.92        12.89        30.58        17.95        76.50 
TCGA-CV-5973 TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6942 
       86.83        62.43         5.46        20.52         4.73       140.78 
TCGA-CV-6945 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
       12.03        53.95        10.98        64.83       172.67       111.16 
TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7180 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
        7.99         9.01        10.75       130.88        77.16         4.73 
TCGA-CV-7252 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 
        4.96       210.97        89.33         9.67        22.85        25.08 
TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-A45O 
       56.48       156.49        84.49        19.76         7.17        27.98 
TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A463 TCGA-CV-A6JD 
       35.47         1.05         6.51        88.87         0.76         5.98 
TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 
       35.34         6.38         6.48        21.24        23.47        22.52 
TCGA-CV-A6K2 TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6826 TCGA-D6-A4ZB 
       10.42        18.84        25.41         9.60        11.44        12.36 
TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-F7-8298 
       28.77        22.59        13.94        12.10        12.79        32.71 
TCGA-F7-8489 TCGA-F7-A50I TCGA-F7-A61S TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-7774 
       21.63         3.02        18.94        20.25        12.43        13.38 
TCGA-H7-8501 TCGA-H7-8502 TCGA-HD-7229 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-A4C1 
       15.16        15.06        33.76        27.48        27.48         0.36 
TCGA-HD-A633 TCGA-HD-A634 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 
       13.84         4.27         6.90        34.75        15.95        14.50 
TCGA-IQ-A61G TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A67A TCGA-MT-A67D 
       11.84        13.84        15.48        14.37        30.05         1.84 
TCGA-MT-A67F TCGA-MT-A7BN TCGA-MZ-A7D7 TCGA-P3-A5Q6 TCGA-P3-A6T0 TCGA-P3-A6T4 
       12.62        15.42        17.98        15.78        19.00         2.04 
TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VC 
       29.00        16.01        21.07        21.47        12.72        19.73 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WX 
       14.76        17.82         8.32        12.72        16.96         6.87 
TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A7JA 
       15.91        32.45        13.71        13.25        64.80        74.47 
TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JT TCGA-KU-A66T 
       18.05        13.94        32.65        18.15 

$subtype4
TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CR-6472 TCGA-DQ-7593 
        3.55        28.11        19.82        48.20        34.52        40.24 
TCGA-BA-4078 TCGA-BA-5153 TCGA-BA-A4IH TCGA-BB-4217 TCGA-BB-4223 TCGA-BB-4225 
        9.07        57.93        20.45         6.15       105.90         4.80 
TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7866 TCGA-BB-A6UM TCGA-CN-4735 TCGA-CN-4739 
       18.38        22.42        44.98        12.92        57.11        45.83 
TCGA-CN-4741 TCGA-CN-A49C TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CR-5243 TCGA-CR-5248 
       73.61        21.21        23.44        19.53        84.23        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 TCGA-CR-6480 
       37.87        26.27        58.42        50.01        36.99        11.90 
TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7385 
       10.22        11.34         7.69        40.93        35.84        32.78 
TCGA-CR-7399 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5443 TCGA-CV-6433 
        5.95        48.39       139.43        17.16        91.53        21.07 
TCGA-CV-A460 TCGA-CX-A4AQ TCGA-D6-6827 TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7596 
       60.43        51.12        18.67        46.45        20.45        41.59 
TCGA-H7-A76A TCGA-HD-7754 TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MZ-A5BI TCGA-MZ-A6I9 
       20.94        25.74         0.07        19.27         7.13        16.08 
TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T6 TCGA-QK-A6IF 
       29.92        51.25        10.85        36.82        12.99        23.15 
TCGA-QK-A6V9 TCGA-QK-AA3J TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UP-A6WW 
       27.39        15.32         7.10        20.35        17.03 

subtype1 subtype2 subtype3 subtype4 
    0.36     0.07     0.36     0.07 
subtype1 subtype2 subtype3 subtype4 
  180.16   129.21   210.97   139.43 
subtype1 subtype2 subtype3 subtype4 
  21.210   25.445   18.495   23.440 
[1] "0.4 - 180.2 (21.2)" "0.1 - 129.2 (25.4)" "0.4 - 211.0 (18.5)"
[4] "0.1 - 139.4 (23.4)"
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      17       25        32        88         4         0
  subtype2       0       15        18        54         3         1
  subtype3       6       29        25        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        25       15       29        5
  STAGE III       32       18       25        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 23 24 41
  subtype3     9 44 25 78
  subtype4    10 15  8  8
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T0+T1       25        5        9       10
  T2          54       23       44       15
  T3          42       24       25        8
  T4          47       41       78        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 38 12 32  3
  subtype3 70 25 46  1
  subtype4 10  5 20  1
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       58       38       70       10
  N1       25       12       25        5
  N2       71       32       46       20
  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 28  1
  subtype3 70  0
  subtype4 20  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68    0
  subtype2   28    1
  subtype3   70    0
  subtype4   20    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       68       28       70       20
  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  23  81
  subtype3  56 116
  subtype4   4  61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53  126
  subtype2   23   81
  subtype3   56  116
  subtype4    4   61
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       53       23       56        4
  MALE        126       81      116       61
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus        0  1
  subtype1 68 92
  subtype2 29 55
  subtype3 54 98
  subtype4 10 52
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   68   92
  subtype2   29   55
  subtype3   54   98
  subtype4   10   52
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        68       29       54       10
  YES       92       55       98       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"
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                 178
  subtype2                                 100
  subtype3                                 171
  subtype4                                  60
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                 1
  subtype2                                                 4
  subtype3                                                 0
  subtype4                                                 5
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  subtype1                                                         0
  subtype2                                                         0
  subtype3                                                         1
  subtype4                                                         0
D6V9, multiclass
                                                           clus
vv                                                          subtype1 subtype2
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            178      100
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1        4
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        0
                                                           clus
vv                                                          subtype3 subtype4
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            171       60
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                0        5
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        1        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"
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                        15
  subtype3                                1     2                        17
  subtype4                                0     0                         5
          vv
clus       WHITE
  subtype1   153
  subtype2    84
  subtype3   147
  subtype4    60
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       15       17        5
  WHITE                                 153       84      147       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"
D6V14, binary
          cls
clus         0   1
  subtype1  10 159
  subtype2   3  89
  subtype3   8 152
  subtype4   4  58
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   10  159
  subtype2    3   89
  subtype3    8  152
  subtype4    4   58
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO           10        3        8        4
  NOT HISPANIC OR LATINO      159       89      152       58
[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 41 40
  subtype2 90 50
  subtype3 91 41
  subtype4 36 55
  subtype5 42 35
subtype1 subtype2 subtype3 subtype4 subtype5 
      81      140      132       91       77 
subtype1 subtype2 subtype3 subtype4 subtype5 
      40       50       41       55       35 
$subtype1
TCGA-CX-7082 TCGA-DQ-5629 TCGA-H7-A6C5 TCGA-UF-A71D TCGA-4P-AA8J TCGA-BA-4076 
        0.36        30.94        21.11        48.03         3.35        13.64 
TCGA-BA-A6D8 TCGA-BA-A6DL TCGA-BB-7871 TCGA-CN-4722 TCGA-CN-4737 TCGA-CN-4742 
       27.95        20.48        24.66        48.76        20.55        13.05 
TCGA-CN-5356 TCGA-CN-6018 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A497 TCGA-CN-A49A 
       46.32        19.07        10.45        38.89        35.01        17.29 
TCGA-CN-A63T TCGA-CN-A63V TCGA-CQ-5324 TCGA-CQ-5332 TCGA-CQ-6225 TCGA-CQ-7069 
        7.40        22.32        52.37        10.42        13.25        41.88 
TCGA-CQ-7072 TCGA-CQ-A4C9 TCGA-CR-5247 TCGA-CR-7374 TCGA-CR-7388 TCGA-CR-7398 
       77.56        23.24        11.77         0.99        27.06         5.13 
TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6960 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
       11.24        42.38        28.34        26.20        17.13        95.34 
TCGA-CV-7255 TCGA-CV-7409 TCGA-CV-7414 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7423 
        2.10        17.85         0.46        22.85        25.08       100.57 
TCGA-CV-7424 TCGA-CV-7435 TCGA-CV-A45U TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A6JE 
       14.89       153.86        35.47        48.20        67.86        35.34 
TCGA-CV-A6JM TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-D6-6826 TCGA-D6-A4ZB TCGA-D6-A6EP 
        6.38        22.52        10.42        11.44        12.36        13.94 
TCGA-D6-A6ES TCGA-DQ-7595 TCGA-HD-A633 TCGA-IQ-A61O TCGA-MZ-A7D7 TCGA-P3-A6SX 
       12.79        39.12        13.84        13.84        17.98        47.01 
TCGA-P3-A6T4 TCGA-P3-A6T5 TCGA-QK-A64Z TCGA-QK-A6IH TCGA-QK-A8Z7 TCGA-QK-A8Z8 
        2.04        29.00        21.07        21.47        12.89         5.62 
TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M 
       14.76        17.82         8.32        15.91        32.45        13.71 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A7JA TCGA-UF-A7JD 
       13.25        64.80         2.83        49.51        74.47        24.30 
TCGA-UF-A7JK TCGA-KU-A66S TCGA-KU-A66T 
       13.94        13.35        18.15 

$subtype2
TCGA-BA-5557 TCGA-BA-A4II TCGA-BB-A5HU TCGA-CN-4727 TCGA-CQ-7063 TCGA-CR-6478 
       20.48        30.18        25.71        51.29        70.13         6.02 
TCGA-CX-7219 TCGA-DQ-7588 TCGA-DQ-7589 TCGA-HD-8634 TCGA-BA-4074 TCGA-BA-5149 
       34.36        14.04        46.32        12.66        15.19        26.50 
TCGA-BA-5151 TCGA-BA-5152 TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6869 
       23.74        42.35        23.84        65.59        15.52        21.17 
TCGA-BA-6872 TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DJ 
       12.62        11.54         5.69        14.47         7.82        13.38 
TCGA-BB-4217 TCGA-BB-7863 TCGA-BB-7864 TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A5HZ 
        6.15        33.70        50.20        38.40        10.55        27.19 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4726 TCGA-CN-4729 TCGA-CN-4730 
        6.28        12.69        38.04         4.67        12.89        26.86 
TCGA-CN-4731 TCGA-CN-5361 TCGA-CN-5365 TCGA-CN-5366 TCGA-CN-5369 TCGA-CN-5373 
       32.81        69.70        11.54        11.84        12.49        52.08 
TCGA-CN-6011 TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A63U 
       30.67         3.68        11.74        25.41        23.57        31.69 
TCGA-CN-A63W TCGA-CN-A641 TCGA-CN-A642 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5331 
       12.39        12.07         2.70        54.58        70.45        45.99 
TCGA-CQ-5334 TCGA-CQ-6220 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7071 TCGA-CQ-A4C6 
        4.24        32.38        64.87        53.52        43.10        44.48 
TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CQ-A4CH TCGA-CR-6477 TCGA-CR-6491 TCGA-CR-6492 
       29.49        14.14        12.46        16.90        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7373 TCGA-CR-7390 TCGA-CR-7394 TCGA-CR-7395 TCGA-CV-5441 
        9.27        29.23        49.58        44.25        30.58        94.88 
TCGA-CV-5973 TCGA-CV-5977 TCGA-CV-6003 TCGA-CV-6436 TCGA-CV-6945 TCGA-CV-6952 
       86.83        60.49        54.74        62.43        12.03         6.08 
TCGA-CV-7180 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7427 TCGA-CV-7440 TCGA-CV-A45O 
       10.75        89.33         9.67       156.49        22.19        27.98 
TCGA-CV-A45P TCGA-CV-A45Q TCGA-CV-A45V TCGA-CV-A45X TCGA-CV-A463 TCGA-CV-A465 
       21.01       169.38         1.05         6.51         0.76         7.07 
TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CX-7086 TCGA-D6-6516 TCGA-D6-6823 
       29.79         6.48        21.24        18.84        25.41        23.05 
TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-DQ-5631 
       25.32        17.72        22.59        24.95        12.10        18.02 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61W TCGA-F7-A620 
       21.63        20.25        31.13        18.94         0.46        17.85 
TCGA-F7-A622 TCGA-F7-A623 TCGA-F7-A624 TCGA-H7-8501 TCGA-HD-7229 TCGA-HD-7753 
       11.80        20.25        12.43        15.16        33.76        28.47 
TCGA-HD-A4C1 TCGA-HD-A6I0 TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E 
        0.36         6.90        34.75        15.95        14.50        37.71 
TCGA-IQ-A61G TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A6SH TCGA-MT-A51W TCGA-MT-A51X 
       11.84         5.29        13.68        15.48        14.37         7.96 
TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-P3-A5QA TCGA-P3-A6T2 TCGA-P3-A6T3 
       30.05         1.84        12.62        71.74        75.55        18.97 
TCGA-QK-A6IG TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-RS-A6TO TCGA-T2-A6WX 
        7.30         9.34        12.72        19.73        12.72         6.87 
TCGA-UF-A7JC TCGA-UF-A7JJ 
       17.95        18.05 

$subtype3
TCGA-BA-4077 TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-CN-6021 TCGA-CN-6023 
       37.28        68.48         3.55        28.11         9.07        52.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-6221 
       35.05        32.48        19.82        24.39        48.20        32.88 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-DQ-7593 TCGA-UF-A7JV TCGA-BA-4078 TCGA-BA-5153 
       43.04        34.52        40.24         2.96         9.07        57.93 
TCGA-BA-5555 TCGA-BA-6870 TCGA-BA-A4IH TCGA-BA-A6DI TCGA-BA-A8YP TCGA-BB-4223 
       17.10        14.83        20.45        11.05        16.41       105.90 
TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 
        9.14         4.80        18.38        22.42        36.72        44.98 
TCGA-BB-7870 TCGA-BB-8601 TCGA-CN-4723 TCGA-CN-4735 TCGA-CN-4738 TCGA-CN-4739 
       66.28        20.52        55.86        57.11        14.33        45.83 
TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5360 TCGA-CN-5374 TCGA-CN-6010 TCGA-CN-6012 
       73.61        12.39        71.31        56.94        50.07        48.00 
TCGA-CN-6013 TCGA-CN-6019 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63Y TCGA-CN-A6UY 
       23.90        34.13        29.72        21.21        16.57        23.44 
TCGA-CN-A6V6 TCGA-CN-A6V7 TCGA-CQ-6223 TCGA-CQ-6228 TCGA-CQ-A4CI TCGA-CR-5243 
       20.88        19.53        46.95        14.99        31.23        84.23 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6473 
       54.67        37.87        26.27        58.42        50.01        36.99 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6482 TCGA-CR-6487 TCGA-CR-7364 TCGA-CR-7368 
       11.90        10.22        11.34         7.69        47.18        40.93 
TCGA-CR-7369 TCGA-CR-7370 TCGA-CR-7371 TCGA-CR-7385 TCGA-CR-7399 TCGA-CR-7402 
       35.84         3.45         3.09        32.78         5.95        29.95 
TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5442 
       48.39       139.43       129.21       108.95        76.24        76.50 
TCGA-CV-5443 TCGA-CV-6433 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6939 TCGA-CV-7242 
       91.53        21.07         9.70         5.46        21.90        36.00 
TCGA-CV-7253 TCGA-CV-7254 TCGA-CV-7261 TCGA-CV-7407 TCGA-CV-7418 TCGA-CV-7446 
       11.87        47.97        49.71        35.54        25.94        35.93 
TCGA-CV-A45W TCGA-CV-A45Y TCGA-CV-A460 TCGA-CX-A4AQ TCGA-D6-6515 TCGA-D6-6827 
       45.96        88.87        60.43        51.12        13.25        18.67 
TCGA-D6-A6EK TCGA-D6-A74Q TCGA-DQ-7590 TCGA-DQ-7591 TCGA-DQ-7596 TCGA-F7-7848 
       28.77        23.34        46.45        20.45        41.59        37.18 
TCGA-F7-A50I TCGA-H7-7774 TCGA-H7-A76A TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-8314 
        3.02        13.38        20.94        25.74        27.48        22.03 
TCGA-HD-A634 TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MT-A67G TCGA-MT-A7BN TCGA-MZ-A5BI 
        4.27         0.07        19.27         6.25        15.42         7.13 
TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T6 
       16.08        29.92        51.25        10.85        36.82        12.99 
TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A8ZA TCGA-RS-A6TP TCGA-T2-A6X0 TCGA-T3-A92N 
       23.15        27.39        12.20        16.96         7.10         3.12 
TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A719 TCGA-UF-A71E TCGA-UF-A7JF TCGA-UP-A6WW 
       13.55        20.35        54.67        49.45        55.43        17.03 

$subtype4
TCGA-BA-6873 TCGA-BB-4227 TCGA-BB-A6UO TCGA-CN-5370 TCGA-CN-6020 TCGA-CQ-5326 
        4.01         4.41         8.81         8.52         6.74         2.93 
TCGA-CQ-6218 TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CR-6471 TCGA-CR-6474 TCGA-CR-6484 
       41.19        29.36        33.60        39.52        18.54        11.64 
TCGA-CR-7365 TCGA-CR-7367 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 
       39.16        47.34        24.95        31.96         9.17        34.06 
TCGA-CR-7380 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7389 TCGA-CR-7393 
       19.92        26.17        17.13        47.01        12.89        32.65 
TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5966 TCGA-CV-5978 
       24.79        35.41        17.16        17.95        17.92         7.07 
TCGA-CV-5979 TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6938 TCGA-CV-6940 TCGA-CV-6942 
       43.23        90.12        20.52         4.73        26.43       140.78 
TCGA-CV-6943 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6953 TCGA-CV-6954 TCGA-CV-6955 
       19.79        15.09        30.08        53.95        65.82        10.98 
TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7091 
        7.13         8.42         4.14        64.83       172.67       111.16 
TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7102 
       18.81        12.66         7.99         9.01         5.26         1.84 
TCGA-CV-7103 TCGA-CV-7177 TCGA-CV-7178 TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 
       52.31        21.80        71.21       130.88        77.16         4.73 
TCGA-CV-7243 TCGA-CV-7252 TCGA-CV-7410 TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7428 
       31.36         4.96       210.97         0.07        56.48        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7433 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7438 
       16.27        84.49        19.76         7.17        16.64         6.38 
TCGA-CV-A6JD TCGA-CV-A6JZ TCGA-D6-6517 TCGA-D6-6824 TCGA-D6-6825 TCGA-D6-8568 
        5.98        23.47         9.60         2.53        16.14        24.95 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-F7-8298 TCGA-H7-8502 TCGA-HD-7831 TCGA-HD-7917 
       37.25        33.86        32.71        15.06        21.93        27.48 
TCGA-IQ-7631 TCGA-P3-A5Q6 TCGA-P3-A6T0 TCGA-P3-A6T7 TCGA-QK-A6VB TCGA-UF-A7JO 
       38.53        15.78        19.00        16.01        21.07        20.75 
TCGA-UF-A7JT 
       32.65 

$subtype5
TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-HD-8635 TCGA-BA-7269 
        9.24        11.08        16.73        11.61        22.85        41.85 
TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BB-8596 TCGA-CN-4728 TCGA-CN-4733 
       29.42         7.10         2.27        71.05        56.68        52.14 
TCGA-CN-4736 TCGA-CN-4740 TCGA-CN-5355 TCGA-CN-5358 TCGA-CN-5363 TCGA-CN-5364 
       12.99        27.58        42.02         8.58         8.32        16.21 
TCGA-CN-5367 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6989 TCGA-CN-6996 TCGA-CN-A640 
       11.57        47.44        28.04        32.22        17.42         4.41 
TCGA-CQ-5325 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-6219 TCGA-CQ-6222 TCGA-CQ-6224 
       21.50        62.37        11.21        15.75        66.28        56.58 
TCGA-CQ-6227 TCGA-CQ-6229 TCGA-CR-6488 TCGA-CR-7391 TCGA-CR-7392 TCGA-CV-5436 
        4.24        38.76        12.46        30.02        46.85        19.20 
TCGA-CV-5440 TCGA-CV-5444 TCGA-CV-5970 TCGA-CV-5971 TCGA-CV-5976 TCGA-CV-6441 
      107.51        80.12        13.35        23.05        48.59         9.60 
TCGA-CV-6934 TCGA-CV-6961 TCGA-CV-7104 TCGA-CV-7238 TCGA-CV-7247 TCGA-CV-7263 
        2.14         2.50        12.92        89.65        18.97        18.41 
TCGA-CV-7406 TCGA-CV-7422 TCGA-CV-7429 TCGA-CV-7568 TCGA-CV-A45R TCGA-CV-A45T 
       57.47        34.09         3.52        30.48       180.16       159.65 
TCGA-CV-A464 TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7085 
       56.61        15.25        28.01         3.62        19.92        10.55 
TCGA-D6-A6EM TCGA-DQ-5624 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A61V TCGA-HD-8224 
        7.63        58.45        37.58        40.04        24.95        14.66 
TCGA-HD-A6HZ TCGA-IQ-A61H TCGA-IQ-A61J TCGA-KU-A6H8 TCGA-P3-A6T8 TCGA-QK-A652 
        3.65        37.41        33.57        10.75        13.15        21.21 
TCGA-QK-AA3J TCGA-UF-A7J9 TCGA-UF-A7JH TCGA-UF-A7JS TCGA-WA-A7H4 
       15.32        44.65        29.46        22.36        14.56 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.36     0.36     0.07     0.07     2.14 
subtype1 subtype2 subtype3 subtype4 subtype5 
  153.86   169.38   139.43   210.97   180.16 
subtype1 subtype2 subtype3 subtype4 subtype5 
  19.070   19.350   27.435   20.520   21.500 
[1] "0.4 - 153.9 (19.1)" "0.4 - 169.4 (19.4)" "0.1 - 139.4 (27.4)"
[4] "0.1 - 211.0 (20.5)" "2.1 - 180.2 (21.5)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       0        7        13        45         4         1
  subtype2      10       22        26        66         2         0
  subtype3       3       15        13        63         2         0
  subtype4       7       18        16        44         2         0
  subtype5       7       14        11        39         2         0
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I          0       10        3        7        7
  STAGE II         7       22       15       18       14
  STAGE III       13       26       13       16       11
  STAGE IVA       45       66       63       44       39
  STAGE IVB        4        2        2        2        2
  STAGE IVC        1        0        0        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 12 16 40
  subtype2    13 38 31 45
  subtype3    11 35 21 34
  subtype4     9 29 16 33
  subtype5    12 24 15 23
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5
  T0+T1        4       13       11        9       12
  T2          12       38       35       29       24
  T3          16       31       21       16       15
  T4          40       45       34       33       23
[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 32  7 28  2
  subtype2 55 22 40  2
  subtype3 33 12 46  2
  subtype4 28 15 28  1
  subtype5 28 12 29  1
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       32       55       33       28       28
  N1        7       22       12       15       12
  N2       28       40       46       28       29
  N3        2        2        2        1        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"
D7V6, binary
          cls
clus        0  1
  subtype1 26  1
  subtype2 68  0
  subtype3 42  0
  subtype4 25  0
  subtype5 28  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   26    1
  subtype2   68    0
  subtype3   42    0
  subtype4   25    0
  subtype5   28    0
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       26       68       42       25       28
  1        1        0        0        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"
D7V7, binary
          cls
clus         0   1
  subtype1  22  59
  subtype2  48  92
  subtype3  19 113
  subtype4  26  65
  subtype5  26  53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   22   59
  subtype2   48   92
  subtype3   19  113
  subtype4   26   65
  subtype5   26   53
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       22       48       19       26       26
  MALE         59       92      113       65       53
[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"
D7V8, binary
          cls
clus        0  1
  subtype1 29 43
  subtype2 44 87
  subtype3 29 90
  subtype4 27 42
  subtype5 32 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   43
  subtype2   44   87
  subtype3   29   90
  subtype4   27   42
  subtype5   32   38
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        29       44       29       27       32
  YES       43       87       90       42       38
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                  78
  subtype2                                 140
  subtype3                                 125
  subtype4                                  91
  subtype5                                  78
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                 2
  subtype2                                                 0
  subtype3                                                 7
  subtype4                                                 0
  subtype5                                                 1
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  subtype1                                                         1
  subtype2                                                         0
  subtype3                                                         0
  subtype4                                                         0
  subtype5                                                         0
D7V9, multiclass
                                                           clus
vv                                                          subtype1 subtype2
  HEAD & NECK SQUAMOUS CELL CARCINOMA                             78      140
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        1        0
                                                           clus
vv                                                          subtype3 subtype4
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            125       91
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                7        0
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        0
                                                           clus
vv                                                          subtype5
  HEAD & NECK SQUAMOUS CELL CARCINOMA                             78
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V10, continuous
D7V11, continuous
D7V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        12
  subtype2                                0     9                        11
  subtype3                                1     0                        13
  subtype4                                0     1                         5
  subtype5                                1     0                         6
          vv
clus       WHITE
  subtype1    64
  subtype2   116
  subtype3   117
  subtype4    82
  subtype5    69
D7V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1        0        1
  ASIAN                                   1        9        0        1        0
  BLACK OR AFRICAN AMERICAN              12       11       13        5        6
  WHITE                                  64      116      117       82       69
[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"
D7V14, binary
          cls
clus         0   1
  subtype1   2  69
  subtype2   7 129
  subtype3   4 118
  subtype4   6  78
  subtype5   6  67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   69
  subtype2    7  129
  subtype3    4  118
  subtype4    6   78
  subtype5    6   67
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        7        4        6        6
  NOT HISPANIC OR LATINO       69      129      118       78       67
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1  94  97
  subtype2  85  59
  subtype3 121  65
subtype1 subtype2 subtype3 
     191      144      186 
subtype1 subtype2 subtype3 
      97       59       65 
$subtype1
TCGA-BA-5559 TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CX-7082 
       68.48         9.24        11.08        16.73        11.61         0.36 
TCGA-HD-8634 TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-6873 
       12.66        22.85         3.35        26.50        12.62         4.01 
TCGA-BA-A4IF TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A8YP TCGA-BB-7872 TCGA-BB-8596 
       29.42         7.10         2.27        16.41        38.40        71.05 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-4725 TCGA-CN-4728 TCGA-CN-4733 TCGA-CN-4736 
        6.28        12.69        38.04        56.68        52.14        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        42.02         8.58        71.31 
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        52.08 
TCGA-CN-6013 TCGA-CN-6016 TCGA-CN-6017 TCGA-CN-6019 TCGA-CN-6989 TCGA-CN-6995 
       23.90        47.44        28.04        34.13        32.22         3.68 
TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49A TCGA-CN-A63V TCGA-CN-A640 TCGA-CN-A642 
       17.42        11.74        17.29        22.32         4.41         2.70 
TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 
       20.88        21.50        54.58        70.45        62.37        11.21 
TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6227 
        4.24        15.75        32.38        66.28        56.58         4.24 
TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4C6 TCGA-CQ-A4CE 
       38.76        64.87        53.52        77.56        44.48        29.49 
TCGA-CQ-A4CH TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 TCGA-CR-7372 
       12.46        18.54        16.90        12.46        39.16        24.95 
TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 
       31.96         9.17        34.06        26.17        17.13        47.01 
TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 TCGA-CR-7397 TCGA-CR-7401 
       30.02        46.85        32.65        44.25        24.79        35.41 
TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 TCGA-CV-5436 TCGA-CV-5440 TCGA-CV-5444 
      129.21       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-6935 TCGA-CV-6940 TCGA-CV-6943 
       54.74         9.60         2.14         9.70        26.43        19.79 
TCGA-CV-6945 TCGA-CV-6950 TCGA-CV-6951 TCGA-CV-6952 TCGA-CV-6956 TCGA-CV-6959 
       12.03        15.09        30.08         6.08         7.13         8.42 
TCGA-CV-6961 TCGA-CV-7095 TCGA-CV-7097 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 
        2.50        18.81        12.66         1.84        52.31        12.92 
TCGA-CV-7178 TCGA-CV-7180 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7253 
       71.21        10.75        89.65        31.36        18.97        11.87 
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-7423 TCGA-CV-7429 TCGA-CV-7433 TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45P 
      100.57         3.52        19.76         6.38        30.48        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A464 TCGA-CV-A465 
      169.38       180.16       159.65         1.05        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6515 
       15.25        28.01         3.62        19.92        10.55        13.25 
TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM TCGA-DQ-5624 
       16.14        24.95        25.32        17.72         7.63        58.45 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-5631 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-A61V 
       37.25        33.86        18.02        37.58        40.04        24.95 
TCGA-F7-A61W TCGA-F7-A620 TCGA-F7-A622 TCGA-HD-7753 TCGA-HD-7831 TCGA-HD-8224 
        0.46        17.85        11.80        28.47        21.93        14.66 
TCGA-HD-8314 TCGA-HD-A6HZ TCGA-IQ-7630 TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J 
       22.03         3.65        15.95        37.71        37.41        33.57 
TCGA-IQ-A61K TCGA-IQ-A61L TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-P3-A5QA 
        5.29        13.68        10.75         7.96        30.05        71.74 
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        21.21         7.30 
TCGA-QK-A6II TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-UF-A71A TCGA-UF-A7J9 TCGA-UF-A7JC 
        9.34        14.76        15.32         2.83        44.65        17.95 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS TCGA-UF-A7JT TCGA-WA-A7H4 
       24.30        29.46        22.36        32.65        14.56 

$subtype2
TCGA-BB-A5HU TCGA-CN-6992 TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-CR-6478 TCGA-DQ-5629 
       25.71        35.05        24.39        32.88         6.02        30.94 
TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-UF-A71D TCGA-BA-4076 TCGA-BA-5152 TCGA-BA-5555 
       14.04        21.11        48.03        13.64        42.35        17.10 
TCGA-BA-5556 TCGA-BA-5558 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A6D8 TCGA-BA-A6DE 
       23.84        65.59        14.83        41.85        27.95        14.47 
TCGA-BA-A6DF TCGA-BA-A6DL TCGA-BB-4227 TCGA-BB-7863 TCGA-BB-7870 TCGA-BB-A5HY 
        7.82        20.48         4.41        33.70        66.28        10.55 
TCGA-BB-A5HZ TCGA-CN-4722 TCGA-CN-4723 TCGA-CN-4729 TCGA-CN-4730 TCGA-CN-4738 
       27.19        48.76        55.86        12.89        26.86        14.33 
TCGA-CN-4739 TCGA-CN-5356 TCGA-CN-5361 TCGA-CN-5365 TCGA-CN-5369 TCGA-CN-6010 
       45.83        46.32        69.70        11.54        12.49        50.07 
TCGA-CN-6011 TCGA-CN-6018 TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-6994 TCGA-CN-A63T 
       30.67        19.07         6.74        10.45        38.89         7.40 
TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A641 TCGA-CQ-5332 TCGA-CQ-6223 TCGA-CQ-6225 
       31.69        12.39        12.07        10.42        46.95        13.25 
TCGA-CQ-7069 TCGA-CQ-7071 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CR-6482 TCGA-CR-6484 
       41.88        43.10        23.24        33.60        11.34        11.64 
TCGA-CR-7364 TCGA-CR-7370 TCGA-CR-7374 TCGA-CR-7388 TCGA-CR-7390 TCGA-CR-7398 
       47.18         3.45         0.99        27.06        49.58         5.13 
TCGA-CR-7399 TCGA-CR-7402 TCGA-CV-5431 TCGA-CV-5439 TCGA-CV-5441 TCGA-CV-5978 
        5.95        29.95        17.16        17.95        94.88         7.07 
TCGA-CV-6933 TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6948 TCGA-CV-6953 TCGA-CV-6954 
       90.12        20.52        11.24        42.38        53.95        65.82 
TCGA-CV-7091 TCGA-CV-7101 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7242 TCGA-CV-7245 
      111.16         5.26        77.16         4.73        36.00        26.20 
TCGA-CV-7248 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7261 TCGA-CV-7409 TCGA-CV-7411 
       17.13        95.34         4.96        49.71        17.85        89.33 
TCGA-CV-7413 TCGA-CV-7415 TCGA-CV-7416 TCGA-CV-7418 TCGA-CV-7421 TCGA-CV-7424 
        9.67        22.85        25.08        25.94         0.07        14.89 
TCGA-CV-7425 TCGA-CV-7435 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45U TCGA-CV-A45W 
       56.48       153.86        22.19        35.93        35.47        45.96 
TCGA-CV-A45X TCGA-CV-A461 TCGA-CV-A6JE TCGA-CV-A6JM TCGA-CV-A6JY TCGA-CV-A6K2 
        6.51        67.86        35.34         6.38        21.24        10.42 
TCGA-CX-7086 TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB TCGA-D6-A6ES TCGA-D6-A74Q 
       18.84        11.44        18.67        12.36        12.79        23.34 
TCGA-DQ-7595 TCGA-F7-8298 TCGA-F7-A624 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-IQ-7631 
       39.12        32.71        12.43         0.36        13.84        38.53 
TCGA-IQ-7632 TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-MT-A67D TCGA-MT-A7BN TCGA-MZ-A7D7 
       14.50        13.84        15.48         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        21.47        12.72        21.07 
TCGA-QK-A6VC TCGA-QK-A8Z7 TCGA-QK-A8Z8 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-RS-A6TO 
       19.73        12.89         5.62        17.82         8.32        12.72 
TCGA-T2-A6X2 TCGA-T3-A92M TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B 
       32.45        13.71        13.25        64.80        54.67        49.51 
TCGA-UF-A7JA TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO TCGA-KU-A66S TCGA-KU-A66T 
       74.47        18.05        13.94        20.75        13.35        18.15 

$subtype3
TCGA-BA-4077 TCGA-BA-5557 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-4727 
       37.28        20.48         3.55        28.11        30.18        51.29 
TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-7063 
        9.07        52.08        32.48        19.82        48.20        70.13 
TCGA-CQ-7068 TCGA-CR-6472 TCGA-CX-7219 TCGA-DQ-7589 TCGA-DQ-7593 TCGA-UF-A7JV 
       43.04        34.52        34.36        46.32        40.24         2.96 
TCGA-BA-4074 TCGA-BA-4078 TCGA-BA-5151 TCGA-BA-5153 TCGA-BA-6868 TCGA-BA-6869 
       15.19         9.07        23.74        57.93        15.52        21.17 
TCGA-BA-A4IH TCGA-BA-A6DA TCGA-BA-A6DD TCGA-BA-A6DI TCGA-BA-A6DJ TCGA-BB-4217 
       20.45        11.54         5.69        11.05        13.38         6.15 
TCGA-BB-4223 TCGA-BB-4224 TCGA-BB-4225 TCGA-BB-4228 TCGA-BB-7861 TCGA-BB-7862 
      105.90         9.14         4.80        18.38        22.42        36.72 
TCGA-BB-7864 TCGA-BB-7866 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A6UO TCGA-CN-4726 
       50.20        44.98        24.66        20.52         8.81         4.67 
TCGA-CN-4731 TCGA-CN-4735 TCGA-CN-4741 TCGA-CN-5359 TCGA-CN-5374 TCGA-CN-6012 
       32.81        57.11        73.61        12.39        56.94        48.00 
TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B TCGA-CN-A49C TCGA-CN-A63Y 
       35.01        25.41        23.57        29.72        21.21        16.57 
TCGA-CN-A6UY TCGA-CN-A6V7 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-5331 TCGA-CQ-6218 
       23.44        19.53        52.37         2.93        45.99        41.19 
TCGA-CQ-6228 TCGA-CQ-A4CB TCGA-CQ-A4CG TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5247 
       14.99        29.36        14.14        31.23        84.23        11.77 
TCGA-CR-5248 TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 
       54.67        37.87        26.27        58.42        50.01        39.52 
TCGA-CR-6473 TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
       36.99        11.90        10.22         7.69        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7371 TCGA-CR-7373 
        9.27        47.34        40.93        35.84         3.09        29.23 
TCGA-CR-7380 TCGA-CR-7385 TCGA-CR-7389 TCGA-CR-7395 TCGA-CR-7404 TCGA-CV-5430 
       19.92        32.78        12.89        30.58        48.39       139.43 
TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5973 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6936 
       76.50        91.53        86.83        21.07        62.43         5.46 
TCGA-CV-6938 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6962 
        4.73        21.90       140.78        10.98        28.34         4.14 
TCGA-CV-7089 TCGA-CV-7090 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7177 TCGA-CV-7183 
       64.83       172.67         7.99         9.01        21.80       130.88 
TCGA-CV-7254 TCGA-CV-7410 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
       47.97       210.97       156.49        54.94        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-A45O TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 
        7.17        16.64        27.98        88.87        48.20        60.43 
TCGA-CV-A463 TCGA-CV-A6JD TCGA-CV-A6JN TCGA-CV-A6JO TCGA-CV-A6JZ TCGA-CV-A6K1 
        0.76         5.98        29.79         6.48        23.47        22.52 
TCGA-CX-A4AQ TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6824 TCGA-D6-A6EK 
       51.12        25.41         9.60        23.05         2.53        28.77 
TCGA-D6-A6EN TCGA-D6-A6EO TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-DQ-7590 TCGA-DQ-7591 
       22.59        24.95        13.94        12.10        46.45        20.45 
TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J 
       41.59        37.18        21.63        20.25         3.02        31.13 
TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-7774 TCGA-H7-8501 TCGA-H7-8502 TCGA-H7-A76A 
       18.94        20.25        13.38        15.16        15.06        20.94 
TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 TCGA-HD-7917 TCGA-HD-A634 TCGA-HD-A6I0 
       33.76        25.74        27.48        27.48         4.27         6.90 
TCGA-HL-7533 TCGA-IQ-A61G TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67F 
       34.75        11.84         0.07        19.27        14.37        12.62 
TCGA-MT-A67G TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QE 
        6.25         7.13        16.08        29.92        15.78        51.25 
TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-P3-A6T7 TCGA-QK-A6IF 
       10.85        36.82         2.04        12.99        16.01        23.15 
TCGA-QK-A6V9 TCGA-QK-A8ZA TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X0 
       27.39        12.20        16.96         6.87        15.91         7.10 
TCGA-T3-A92N TCGA-TN-A7HI TCGA-TN-A7HL TCGA-UF-A71E TCGA-UF-A7JF TCGA-UP-A6WW 
        3.12        13.55        20.35        49.45        55.43        17.03 

subtype1 subtype2 subtype3 
    0.36     0.07     0.07 
subtype1 subtype2 subtype3 
  180.16   153.86   210.97 
subtype1 subtype2 subtype3 
  20.880   20.635   22.685 
[1] "0.4 - 180.2 (20.9)" "0.1 - 153.9 (20.6)" "0.1 - 211.0 (22.7)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      19       31        31        94         5         0
  subtype2       3       18        20        80         5         1
  subtype3       5       27        28        83         2         0
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         19        3        5
  STAGE II        31       18       27
  STAGE III       31       20       28
  STAGE IVA       94       80       83
  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 30 27 66
  subtype3    17 50 31 54
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       27        5       17
  T2          58       30       50
  T3          41       27       31
  T4          55       66       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 15 40  4
  subtype3 48 28 58  1
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       67       61       48
  N1       25       15       28
  N2       73       40       58
  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 51  1
  subtype3 64  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74    0
  subtype2   51    1
  subtype3   64    0
   clus
vv  subtype1 subtype2 subtype3
  0       74       51       64
  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  97
  subtype3  36 150
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   58  135
  subtype2   47   97
  subtype3   36  150
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       58       47       36
  MALE        135       97      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"
D8V8, binary
          cls
clus         0   1
  subtype1  74  96
  subtype2  39  82
  subtype3  48 122
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   74   96
  subtype2   39   82
  subtype3   48  122
     clus
vv    subtype1 subtype2 subtype3
  NO        74       39       48
  YES       96       82      122
[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 & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                 191
  subtype2                                 141
  subtype3                                 180
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                 2
  subtype2                                                 2
  subtype3                                                 6
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         0
D8V9, multiclass
                                                           clus
vv                                                          subtype1 subtype2
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            191      141
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2        2
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        1
                                                           clus
vv                                                          subtype3
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            180
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                6
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        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"
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                        20
  subtype3                                1     1                        15
          vv
clus       WHITE
  subtype1   165
  subtype2   118
  subtype3   165
D8V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   8        2        1
  BLACK OR AFRICAN AMERICAN              12       20       15
  WHITE                                 165      118      165
[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   4 128
  subtype3   9 164
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  169
  subtype2    4  128
  subtype3    9  164
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           12        4        9
  NOT HISPANIC OR LATINO      169      128      164
[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  73  71
  subtype2 120  67
  subtype3  85  59
subtype1 subtype2 subtype3 
     144      187      144 
subtype1 subtype2 subtype3 
      71       67       59 
$subtype1
TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-DQ-7589 TCGA-HD-8635 
        9.24        11.08        16.73        11.61        46.32        22.85 
TCGA-4P-AA8J TCGA-BA-7269 TCGA-BA-A6DB TCGA-BB-7871 TCGA-BB-8596 TCGA-BB-A6UO 
        3.35        41.85         7.10        24.66        71.05         8.81 
TCGA-CN-4733 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5370 TCGA-CN-6016 TCGA-CN-6017 
       52.14        13.05         8.58         8.52        47.44        28.04 
TCGA-CN-6018 TCGA-CN-6019 TCGA-CN-6020 TCGA-CN-6994 TCGA-CN-6996 TCGA-CN-A49A 
       19.07        34.13         6.74        38.89        17.42        17.29 
TCGA-CN-A63V TCGA-CQ-5326 TCGA-CQ-5329 TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 
       22.32         2.93        70.45        62.37        11.21         4.24 
TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7064 
       15.75        32.38        66.28        56.58        38.76        64.87 
TCGA-CQ-7069 TCGA-CQ-7072 TCGA-CQ-A4CB TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6488 
       41.88        77.56        29.36        11.77        18.54        12.46 
TCGA-CR-7365 TCGA-CR-7372 TCGA-CR-7376 TCGA-CR-7377 TCGA-CR-7379 TCGA-CR-7380 
       39.16        24.95        31.96         9.17        34.06        19.92 
TCGA-CR-7382 TCGA-CR-7383 TCGA-CR-7386 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7397 
       26.17        17.13        47.01        30.02        46.85        24.79 
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-5978 TCGA-CV-5979 TCGA-CV-6441 TCGA-CV-6934 
       13.35        23.05         7.07        43.23         9.60         2.14 
TCGA-CV-6937 TCGA-CV-6941 TCGA-CV-6942 TCGA-CV-6943 TCGA-CV-6945 TCGA-CV-6950 
       20.52        11.24       140.78        19.79        12.03        15.09 
TCGA-CV-6951 TCGA-CV-6954 TCGA-CV-6956 TCGA-CV-6959 TCGA-CV-6961 TCGA-CV-7090 
       30.08        65.82         7.13         8.42         2.50       172.67 
TCGA-CV-7095 TCGA-CV-7102 TCGA-CV-7103 TCGA-CV-7104 TCGA-CV-7177 TCGA-CV-7178 
       18.81         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7183 TCGA-CV-7235 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 
      130.88        77.16         4.73        89.65        31.36        18.97 
TCGA-CV-7263 TCGA-CV-7406 TCGA-CV-7407 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7414 
       18.41        57.47        35.54       210.97        89.33         0.46 
TCGA-CV-7415 TCGA-CV-7421 TCGA-CV-7422 TCGA-CV-7424 TCGA-CV-7429 TCGA-CV-7433 
       22.85         0.07        34.09        14.89         3.52        19.76 
TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A460 TCGA-CV-A464 TCGA-CV-A468 
      153.86         6.38        30.48        60.43        56.61        15.25 
TCGA-CX-7085 TCGA-D6-6824 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A6EM TCGA-D6-A6EP 
       10.55         2.53        24.95        25.32         7.63        13.94 
TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7594 TCGA-F7-8298 TCGA-H7-8502 TCGA-H7-A76A 
       37.25        33.86        40.04        32.71        15.06        20.94 
TCGA-HD-7831 TCGA-HD-8224 TCGA-HD-8314 TCGA-IQ-7631 TCGA-IQ-A61H TCGA-IQ-A61J 
       21.93        14.66        22.03        38.53        37.41        33.57 
TCGA-KU-A6H8 TCGA-P3-A6SX TCGA-P3-A6T0 TCGA-P3-A6T2 TCGA-P3-A6T8 TCGA-QK-A6VB 
       10.75        47.01        19.00        75.55        13.15        21.07 
TCGA-QK-A8Z7 TCGA-QK-A8Z9 TCGA-QK-A8ZB TCGA-QK-AA3K TCGA-T3-A92M TCGA-UF-A7J9 
       12.89        14.76        17.82         8.32        13.71        44.65 
TCGA-UF-A7JA TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JK TCGA-UF-A7JT TCGA-WA-A7H4 
       74.47        24.30        29.46        13.94        32.65        14.56 

$subtype2
TCGA-BA-5557 TCGA-BA-A4IG TCGA-BA-A4II TCGA-BB-A5HU TCGA-CQ-6221 TCGA-CQ-7068 
       20.48        28.11        30.18        25.71        32.88        43.04 
TCGA-DQ-7588 TCGA-H7-A6C5 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-5149 TCGA-BA-5152 
       14.04        21.11        48.03         2.96        26.50        42.35 
TCGA-BA-6869 TCGA-BA-A4IF TCGA-BA-A4IH TCGA-BA-A6D8 TCGA-BA-A6DA TCGA-BA-A6DD 
       21.17        29.42        20.45        27.95        11.54         5.69 
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-BA-A8YP TCGA-BB-7864 TCGA-BB-7870 TCGA-BB-7872 TCGA-BB-A5HY TCGA-BB-A5HZ 
       16.41        50.20        66.28        38.40        10.55        27.19 
TCGA-C9-A47Z TCGA-C9-A480 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
        6.28        12.69        35.01        25.41        23.57        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A640 
       21.21         7.40        31.69        12.39        16.57         4.41 
TCGA-CN-A641 TCGA-CN-A642 TCGA-CN-A6V6 TCGA-CQ-5325 TCGA-CQ-5331 TCGA-CQ-7065 
       12.07         2.70        20.88        21.50        45.99        53.52 
TCGA-CQ-7071 TCGA-CQ-A4C6 TCGA-CQ-A4C9 TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG 
       43.10        44.48        23.24        33.60        29.49        14.14 
TCGA-CQ-A4CH TCGA-CQ-A4CI TCGA-CR-6477 TCGA-CR-6492 TCGA-CR-6493 TCGA-CV-5432 
       12.46        31.23        16.90        15.75         9.27       129.21 
TCGA-CV-5441 TCGA-CV-5442 TCGA-CV-5976 TCGA-CV-5977 TCGA-CV-7409 TCGA-CV-7413 
       94.88        76.50        48.59        60.49        17.85         9.67 
TCGA-CV-7416 TCGA-CV-7423 TCGA-CV-7425 TCGA-CV-7427 TCGA-CV-A45O TCGA-CV-A45P 
       25.08       100.57        56.48       156.49        27.98        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45U TCGA-CV-A45V TCGA-CV-A45W 
      169.38       180.16       159.65        35.47         1.05        45.96 
TCGA-CV-A45X TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A465 
        6.51        88.87        48.20        67.86         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        28.01 
TCGA-CV-A6JU TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K0 TCGA-CV-A6K1 TCGA-CV-A6K2 
        3.62        21.24        23.47        19.92        22.52        10.42 
TCGA-CX-7086 TCGA-CX-A4AQ TCGA-D6-A4Z9 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN 
       18.84        51.12        17.72        12.36        28.77        22.59 
TCGA-D6-A6EO TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5631 TCGA-DQ-7590 TCGA-DQ-7591 
       24.95        12.10        12.79        18.02        46.45        20.45 
TCGA-DQ-7592 TCGA-F7-A50G TCGA-F7-A50I TCGA-F7-A50J TCGA-F7-A61S TCGA-F7-A61V 
       37.58        20.25         3.02        31.13        18.94        24.95 
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-HD-7753 TCGA-HD-7754 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A634 
       15.16        28.47        25.74         0.36        13.84         4.27 
TCGA-HD-A6HZ TCGA-HD-A6I0 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61E TCGA-IQ-A61G 
        3.65         6.90        15.95        14.50        37.71        11.84 
TCGA-IQ-A61I TCGA-IQ-A61K TCGA-IQ-A61L TCGA-IQ-A61O TCGA-IQ-A6SH TCGA-KU-A6H7 
        0.07         5.29        13.68        13.84        15.48        19.27 
TCGA-MT-A51W TCGA-MT-A51X TCGA-MT-A67A TCGA-MT-A67D TCGA-MT-A67F TCGA-MT-A67G 
       14.37         7.96        30.05         1.84        12.62         6.25 
TCGA-MT-A7BN TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5Q6 TCGA-P3-A5QA 
       15.42        16.08        17.98        29.92        15.78        71.74 
TCGA-P3-A5QE TCGA-P3-A5QF TCGA-P3-A6SW TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T6 
       51.25        10.85        36.82        18.97        29.00        12.99 
TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A652 TCGA-QK-A6IF TCGA-QK-A6IG TCGA-QK-A6IH 
       16.01        21.07        21.21        23.15         7.30        21.47 
TCGA-QK-A6II TCGA-QK-A6IJ TCGA-QK-A6VC TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-RS-A6TO 
        9.34        12.72        19.73         5.62        12.20        12.72 
TCGA-RS-A6TP TCGA-T2-A6WX TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92N TCGA-TN-A7HI 
       16.96         6.87        15.91        32.45         3.12        13.55 
TCGA-TN-A7HJ TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71A TCGA-UF-A71B TCGA-UF-A71E 
       13.25        64.80        54.67         2.83        49.51        49.45 
TCGA-UF-A7JC TCGA-UF-A7JF TCGA-UF-A7JJ TCGA-UF-A7JO TCGA-UF-A7JS TCGA-KU-A66S 
       17.95        55.43        18.05        20.75        22.36        13.35 
TCGA-KU-A66T 
       18.15 

$subtype3
TCGA-BA-5559 TCGA-BA-6871 TCGA-CN-6021 TCGA-CN-6023 TCGA-CN-6992 TCGA-CN-6997 
       68.48         3.55         9.07        52.08        35.05        32.48 
TCGA-CN-A6V1 TCGA-CN-A6V3 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CR-6472 TCGA-CR-6478 
       19.82        24.39        48.20        70.13        34.52         6.02 
TCGA-CX-7082 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7593 TCGA-BA-5555 TCGA-BA-5556 
        0.36        34.36        30.94        40.24        17.10        23.84 
TCGA-BA-5558 TCGA-BA-6868 TCGA-BA-6870 TCGA-BA-6872 TCGA-BA-6873 TCGA-BB-4217 
       65.59        15.52        14.83        12.62         4.01         6.15 
TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 TCGA-BB-7866 TCGA-BB-8601 TCGA-CN-4738 
        4.41        22.42        36.72        44.98        20.52        14.33 
TCGA-CN-4739 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 TCGA-CN-6988 
       45.83        50.07        30.67        48.00        23.90        10.45 
TCGA-CN-6995 TCGA-CN-6998 TCGA-CN-A6UY TCGA-CQ-5324 TCGA-CQ-5327 TCGA-CQ-5332 
        3.68        11.74        23.44        52.37        54.58        10.42 
TCGA-CQ-6218 TCGA-CQ-6223 TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CR-5243 TCGA-CR-5248 
       41.19        46.95        13.25        14.99        84.23        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-7364 
       11.90        10.22        11.64         7.69        22.78        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-7390 TCGA-CR-7393 
        0.99        32.78        27.06        12.89        49.58        32.65 
TCGA-CR-7394 TCGA-CR-7395 TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 
       44.25        30.58         5.13         5.95        29.95        48.39 
TCGA-CV-5430 TCGA-CV-5431 TCGA-CV-5435 TCGA-CV-5439 TCGA-CV-5443 TCGA-CV-5973 
      139.43        17.16        76.24        17.95        91.53        86.83 
TCGA-CV-6003 TCGA-CV-6433 TCGA-CV-6436 TCGA-CV-6935 TCGA-CV-6936 TCGA-CV-6939 
       54.74        21.07        62.43         9.70         5.46        21.90 
TCGA-CV-6940 TCGA-CV-6948 TCGA-CV-6952 TCGA-CV-6953 TCGA-CV-6955 TCGA-CV-6960 
       26.43        42.38         6.08        53.95        10.98        28.34 
TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7091 TCGA-CV-7097 TCGA-CV-7099 TCGA-CV-7100 
        4.14        64.83       111.16        12.66         7.99         9.01 
TCGA-CV-7101 TCGA-CV-7180 TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7248 TCGA-CV-7250 
        5.26        10.75        36.00        26.20        17.13        95.34 
TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7255 TCGA-CV-7261 TCGA-CV-7418 TCGA-CV-7428 
        4.96        11.87         2.10        49.71        25.94        54.94 
TCGA-CV-7430 TCGA-CV-7432 TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-7446 
       16.27        84.49         7.17        16.64        22.19        35.93 
TCGA-D6-6515 TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-6826 
       13.25        25.41         9.60        23.05        16.14        11.44 
TCGA-D6-6827 TCGA-D6-A74Q TCGA-DQ-5624 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 
       18.67        23.34        58.45        39.12        41.59        37.18 
TCGA-F7-8489 TCGA-HD-7229 TCGA-HD-7832 TCGA-HD-7917 TCGA-HL-7533 TCGA-MZ-A5BI 
       21.63        33.76        27.48        27.48        34.75         7.13 
TCGA-P3-A6T4 TCGA-QK-A6V9 TCGA-QK-AA3J TCGA-T2-A6X0 TCGA-TN-A7HL TCGA-UP-A6WW 
        2.04        27.39        15.32         7.10        20.35        17.03 

subtype1 subtype2 subtype3 
    0.07     0.07     0.36 
subtype1 subtype2 subtype3 
  210.97   180.16   139.43 
subtype1 subtype2 subtype3 
  22.175   19.730   24.900 
[1] "0.1 - 211.0 (22.2)" "0.1 - 180.2 (19.7)" "0.4 - 139.4 (24.9)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1       9       25        23        78         3         0
  subtype2       8       26        34        87         6         1
  subtype3       8       21        17        65         1         0
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I          9        8        8
  STAGE II        25       26       21
  STAGE III       23       34       17
  STAGE IVA       78       87       65
  STAGE IVB        3        6        1
  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    14 42 29 53
  subtype2    20 55 33 60
  subtype3    12 28 28 45
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       14       20       12
  T2          42       55       28
  T3          29       33       28
  T4          53       60       45
[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 48 21 58  1
  subtype2 68 28 56  4
  subtype3 45 16 40  1
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       48       68       45
  N1       21       28       16
  N2       58       56       40
  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"
D9V6, binary
          cls
clus        0  1
  subtype1 45  0
  subtype2 99  1
  subtype3 31  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   45    0
  subtype2   99    1
  subtype3   31    0
   clus
vv  subtype1 subtype2 subtype3
  0       45       99       31
  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"
D9V7, binary
          cls
clus         0   1
  subtype1  43 101
  subtype2  54 135
  subtype3  33 111
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43  101
  subtype2   54  135
  subtype3   33  111
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       43       54       33
  MALE        101      135      111
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus         0   1
  subtype1  53  69
  subtype2  51 127
  subtype3  42  79
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   53   69
  subtype2   51  127
  subtype3   42   79
     clus
vv    subtype1 subtype2 subtype3
  NO        53       51       42
  YES       69      127       79
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                 142
  subtype2                                 181
  subtype3                                 143
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                 2
  subtype2                                                 7
  subtype3                                                 1
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         0
D9V9, multiclass
                                                           clus
vv                                                          subtype1 subtype2
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            142      181
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2        7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        1
                                                           clus
vv                                                          subtype3
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            143
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        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"
D9V10, continuous
D9V11, continuous
D9V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        14
  subtype2                                2     8                        15
  subtype3                                0     2                        15
          vv
clus       WHITE
  subtype1   123
  subtype2   156
  subtype3   126
D9V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        2        0
  ASIAN                                   1        8        2
  BLACK OR AFRICAN AMERICAN              14       15       15
  WHITE                                 123      156      126
[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"
D9V14, binary
          cls
clus         0   1
  subtype1   8 127
  subtype2   9 161
  subtype3   7 129
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    8  127
  subtype2    9  161
  subtype3    7  129
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            8        9        7
  NOT HISPANIC OR LATINO      127      161      129
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(10) Variable = MIRSEQ_MATURE_CHIERARCHICAL
D10V1, survival
          sevent
clus2        0   1
  subtype1  89  83
  subtype2  59  45
  subtype3 130  69
subtype1 subtype2 subtype3 
     172      104      199 
subtype1 subtype2 subtype3 
      83       45       69 
$subtype1
TCGA-BA-5557 TCGA-CN-6022 TCGA-CN-6024 TCGA-CQ-7067 TCGA-CQ-A4C7 TCGA-CX-7082 
       20.48         9.24        11.08        16.73        11.61         0.36 
TCGA-HD-8635 TCGA-4P-AA8J TCGA-BA-5149 TCGA-BA-6872 TCGA-BA-6873 TCGA-BA-A4IF 
       22.85         3.35        26.50        12.62         4.01        29.42 
TCGA-BA-A6DB TCGA-BA-A6DG TCGA-BA-A8YP TCGA-BB-7872 TCGA-BB-8596 TCGA-C9-A480 
        7.10         2.27        16.41        38.40        71.05        12.69 
TCGA-CN-4733 TCGA-CN-4742 TCGA-CN-5358 TCGA-CN-5370 TCGA-CN-6016 TCGA-CN-6017 
       52.14        13.05         8.58         8.52        47.44        28.04 
TCGA-CN-6019 TCGA-CN-6994 TCGA-CN-6995 TCGA-CN-6996 TCGA-CN-6998 TCGA-CN-A49A 
       34.13        38.89         3.68        17.42        11.74        17.29 
TCGA-CN-A63V TCGA-CN-A640 TCGA-CN-A642 TCGA-CQ-5325 TCGA-CQ-5327 TCGA-CQ-5329 
       22.32         4.41         2.70        21.50        54.58        70.45 
TCGA-CQ-5330 TCGA-CQ-5333 TCGA-CQ-5334 TCGA-CQ-6219 TCGA-CQ-6220 TCGA-CQ-6222 
       62.37        11.21         4.24        15.75        32.38        66.28 
TCGA-CQ-6224 TCGA-CQ-6229 TCGA-CQ-7064 TCGA-CQ-7065 TCGA-CQ-7072 TCGA-CQ-A4C6 
       56.58        38.76        64.87        53.52        77.56        44.48 
TCGA-CQ-A4CH TCGA-CR-5247 TCGA-CR-6474 TCGA-CR-6477 TCGA-CR-6488 TCGA-CR-7365 
       12.46        11.77        18.54        16.90        12.46        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-7390 TCGA-CR-7391 TCGA-CR-7392 TCGA-CR-7393 TCGA-CR-7394 
       47.01        49.58        30.02        46.85        32.65        44.25 
TCGA-CR-7395 TCGA-CR-7397 TCGA-CR-7401 TCGA-CV-5432 TCGA-CV-5434 TCGA-CV-5435 
       30.58        24.79        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-6937 TCGA-CV-6940 TCGA-CV-6941 TCGA-CV-6943 TCGA-CV-6950 
        9.70        20.52        26.43        11.24        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-7177 TCGA-CV-7178 
       12.66         1.84        52.31        12.92        21.80        71.21 
TCGA-CV-7180 TCGA-CV-7236 TCGA-CV-7238 TCGA-CV-7243 TCGA-CV-7247 TCGA-CV-7248 
       10.75         4.73        89.65        31.36        18.97        17.13 
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-7423 TCGA-CV-7433 TCGA-CV-7435 TCGA-CV-7438 TCGA-CV-7568 TCGA-CV-A45P 
      100.57        19.76       153.86         6.38        30.48        21.01 
TCGA-CV-A45Q TCGA-CV-A45R TCGA-CV-A45T TCGA-CV-A45V TCGA-CV-A464 TCGA-CV-A465 
      169.38       180.16       159.65         1.05        56.61         7.07 
TCGA-CV-A468 TCGA-CV-A6JT TCGA-CV-A6JU TCGA-CV-A6K0 TCGA-CX-7085 TCGA-D6-6515 
       15.25        28.01         3.62        19.92        10.55        13.25 
TCGA-D6-6823 TCGA-D6-6825 TCGA-D6-8568 TCGA-D6-8569 TCGA-D6-A4Z9 TCGA-D6-A6EM 
       23.05        16.14        24.95        25.32        17.72         7.63 
TCGA-DQ-5624 TCGA-DQ-5625 TCGA-DQ-5630 TCGA-DQ-7592 TCGA-DQ-7594 TCGA-F7-8298 
       58.45        37.25        33.86        37.58        40.04        32.71 
TCGA-F7-A50J TCGA-F7-A61V TCGA-F7-A620 TCGA-F7-A622 TCGA-HD-7831 TCGA-HD-8224 
       31.13        24.95        17.85        11.80        21.93        14.66 
TCGA-HD-8314 TCGA-HD-A6HZ TCGA-IQ-A61E TCGA-IQ-A61H TCGA-IQ-A61J TCGA-IQ-A61K 
       22.03         3.65        37.71        37.41        33.57         5.29 
TCGA-IQ-A61L TCGA-KU-A6H8 TCGA-MT-A51X TCGA-MT-A67A TCGA-P3-A6SX TCGA-P3-A6T8 
       13.68        10.75         7.96        30.05        47.01        13.15 
TCGA-QK-A652 TCGA-QK-A6II TCGA-QK-A8Z9 TCGA-QK-AA3J TCGA-UF-A71A TCGA-UF-A7J9 
       21.21         9.34        14.76        15.32         2.83        44.65 
TCGA-UF-A7JD TCGA-UF-A7JH TCGA-UF-A7JS TCGA-WA-A7H4 
       24.30        29.46        22.36        14.56 

$subtype2
TCGA-BB-A5HU TCGA-CN-A6V3 TCGA-CQ-6221 TCGA-DQ-7588 TCGA-BA-5152 TCGA-BA-A6DD 
       25.71        24.39        32.88        14.04        42.35         5.69 
TCGA-BA-A6DE TCGA-BA-A6DF TCGA-BA-A6DI TCGA-BB-4217 TCGA-BB-7864 TCGA-BB-A5HY 
       14.47         7.82        11.05         6.15        50.20        10.55 
TCGA-BB-A6UO TCGA-CN-6018 TCGA-CQ-5324 TCGA-CQ-5326 TCGA-CQ-7069 TCGA-CQ-7071 
        8.81        19.07        52.37         2.93        41.88        43.10 
TCGA-CQ-A4CB TCGA-CQ-A4CD TCGA-CQ-A4CE TCGA-CQ-A4CG TCGA-CR-7380 TCGA-CV-5441 
       29.36        33.60        29.49        14.14        19.92        94.88 
TCGA-CV-6945 TCGA-CV-7409 TCGA-CV-7410 TCGA-CV-7411 TCGA-CV-7413 TCGA-CV-7415 
       12.03        17.85       210.97        89.33         9.67        22.85 
TCGA-CV-7416 TCGA-CV-7421 TCGA-CV-7425 TCGA-CV-7429 TCGA-CV-A45U TCGA-CV-A45X 
       25.08         0.07        56.48         3.52        35.47         6.51 
TCGA-CV-A45Y TCGA-CV-A45Z TCGA-CV-A460 TCGA-CV-A6JD TCGA-CV-A6JE TCGA-CV-A6JM 
       88.87        48.20        60.43         5.98        35.34         6.38 
TCGA-CV-A6JO TCGA-CV-A6JY TCGA-CV-A6JZ TCGA-CV-A6K1 TCGA-CV-A6K2 TCGA-CX-7086 
        6.48        21.24        23.47        22.52        10.42        18.84 
TCGA-CX-A4AQ TCGA-D6-A6EP TCGA-D6-A6EQ TCGA-D6-A6ES TCGA-DQ-5631 TCGA-DQ-7590 
       51.12        13.94        12.10        12.79        18.02        46.45 
TCGA-F7-8489 TCGA-F7-A50G TCGA-F7-A61W TCGA-F7-A624 TCGA-H7-8501 TCGA-H7-8502 
       21.63        20.25         0.46        12.43        15.16        15.06 
TCGA-H7-A76A TCGA-HD-7753 TCGA-HD-7917 TCGA-HD-A4C1 TCGA-HD-A633 TCGA-HD-A6I0 
       20.94        28.47        27.48         0.36        13.84         6.90 
TCGA-HL-7533 TCGA-IQ-7630 TCGA-IQ-7632 TCGA-IQ-A61G TCGA-IQ-A61O TCGA-IQ-A6SH 
       34.75        15.95        14.50        11.84        13.84        15.48 
TCGA-MT-A67D TCGA-MT-A67G TCGA-P3-A5Q6 TCGA-P3-A5QA TCGA-P3-A6SW TCGA-P3-A6T0 
        1.84         6.25        15.78        71.74        36.82        19.00 
TCGA-P3-A6T2 TCGA-P3-A6T3 TCGA-P3-A6T5 TCGA-P3-A6T7 TCGA-QK-A64Z TCGA-QK-A6IG 
       75.55        18.97        29.00        16.01        21.07         7.30 
TCGA-QK-A6IH TCGA-QK-A6IJ TCGA-QK-A6VB TCGA-QK-A6VC TCGA-QK-A8ZB TCGA-QK-AA3K 
       21.47        12.72        21.07        19.73        17.82         8.32 
TCGA-RS-A6TO TCGA-RS-A6TP TCGA-T2-A6WZ TCGA-T2-A6X2 TCGA-T3-A92M TCGA-T3-A92N 
       12.72        16.96        15.91        32.45        13.71         3.12 
TCGA-TN-A7HJ TCGA-UF-A7JA TCGA-UF-A7JC TCGA-UF-A7JJ TCGA-UF-A7JK TCGA-UF-A7JO 
       13.25        74.47        17.95        18.05        13.94        20.75 
TCGA-UF-A7JT TCGA-KU-A66T 
       32.65        18.15 

$subtype3
TCGA-BA-5559 TCGA-BA-6871 TCGA-BA-A4IG TCGA-BA-A4II TCGA-CN-6021 TCGA-CN-6023 
       68.48         3.55        28.11        30.18         9.07        52.08 
TCGA-CN-6992 TCGA-CN-6997 TCGA-CN-A6V1 TCGA-CQ-5323 TCGA-CQ-7063 TCGA-CQ-7068 
       35.05        32.48        19.82        48.20        70.13        43.04 
TCGA-CR-6472 TCGA-CR-6478 TCGA-CX-7219 TCGA-DQ-5629 TCGA-DQ-7589 TCGA-DQ-7593 
       34.52         6.02        34.36        30.94        46.32        40.24 
TCGA-H7-A6C5 TCGA-UF-A71D TCGA-UF-A7JV TCGA-BA-5555 TCGA-BA-5556 TCGA-BA-5558 
       21.11        48.03         2.96        17.10        23.84        65.59 
TCGA-BA-6868 TCGA-BA-6869 TCGA-BA-6870 TCGA-BA-7269 TCGA-BA-A4IH TCGA-BA-A6D8 
       15.52        21.17        14.83        41.85        20.45        27.95 
TCGA-BA-A6DA TCGA-BA-A6DJ TCGA-BA-A6DL TCGA-BB-4227 TCGA-BB-7861 TCGA-BB-7862 
       11.54        13.38        20.48         4.41        22.42        36.72 
TCGA-BB-7866 TCGA-BB-7870 TCGA-BB-7871 TCGA-BB-8601 TCGA-BB-A5HZ TCGA-C9-A47Z 
       44.98        66.28        24.66        20.52        27.19         6.28 
TCGA-CN-4738 TCGA-CN-4739 TCGA-CN-6010 TCGA-CN-6011 TCGA-CN-6012 TCGA-CN-6013 
       14.33        45.83        50.07        30.67        48.00        23.90 
TCGA-CN-6020 TCGA-CN-6988 TCGA-CN-A497 TCGA-CN-A498 TCGA-CN-A499 TCGA-CN-A49B 
        6.74        10.45        35.01        25.41        23.57        29.72 
TCGA-CN-A49C TCGA-CN-A63T TCGA-CN-A63U TCGA-CN-A63W TCGA-CN-A63Y TCGA-CN-A641 
       21.21         7.40        31.69        12.39        16.57        12.07 
TCGA-CN-A6UY TCGA-CN-A6V6 TCGA-CQ-5331 TCGA-CQ-5332 TCGA-CQ-6218 TCGA-CQ-6223 
       23.44        20.88        45.99        10.42        41.19        46.95 
TCGA-CQ-6225 TCGA-CQ-6228 TCGA-CQ-A4C9 TCGA-CQ-A4CI TCGA-CR-5243 TCGA-CR-5248 
       13.25        14.99        23.24        31.23        84.23        54.67 
TCGA-CR-5249 TCGA-CR-5250 TCGA-CR-6467 TCGA-CR-6470 TCGA-CR-6471 TCGA-CR-6473 
       37.87        26.27        58.42        50.01        39.52        36.99 
TCGA-CR-6480 TCGA-CR-6481 TCGA-CR-6484 TCGA-CR-6487 TCGA-CR-6491 TCGA-CR-6492 
       11.90        10.22        11.64         7.69        22.78        15.75 
TCGA-CR-6493 TCGA-CR-7364 TCGA-CR-7367 TCGA-CR-7368 TCGA-CR-7369 TCGA-CR-7370 
        9.27        47.18        47.34        40.93        35.84         3.45 
TCGA-CR-7371 TCGA-CR-7373 TCGA-CR-7374 TCGA-CR-7385 TCGA-CR-7388 TCGA-CR-7389 
        3.09        29.23         0.99        32.78        27.06        12.89 
TCGA-CR-7398 TCGA-CR-7399 TCGA-CR-7402 TCGA-CR-7404 TCGA-CV-5430 TCGA-CV-5431 
        5.13         5.95        29.95        48.39       139.43        17.16 
TCGA-CV-5439 TCGA-CV-5442 TCGA-CV-5443 TCGA-CV-5973 TCGA-CV-5978 TCGA-CV-6433 
       17.95        76.50        91.53        86.83         7.07        21.07 
TCGA-CV-6436 TCGA-CV-6936 TCGA-CV-6939 TCGA-CV-6942 TCGA-CV-6948 TCGA-CV-6953 
       62.43         5.46        21.90       140.78        42.38        53.95 
TCGA-CV-6954 TCGA-CV-6955 TCGA-CV-6960 TCGA-CV-6962 TCGA-CV-7089 TCGA-CV-7090 
       65.82        10.98        28.34         4.14        64.83       172.67 
TCGA-CV-7091 TCGA-CV-7099 TCGA-CV-7100 TCGA-CV-7101 TCGA-CV-7183 TCGA-CV-7235 
      111.16         7.99         9.01         5.26       130.88        77.16 
TCGA-CV-7242 TCGA-CV-7245 TCGA-CV-7250 TCGA-CV-7252 TCGA-CV-7253 TCGA-CV-7261 
       36.00        26.20        95.34         4.96        11.87        49.71 
TCGA-CV-7418 TCGA-CV-7424 TCGA-CV-7427 TCGA-CV-7428 TCGA-CV-7430 TCGA-CV-7432 
       25.94        14.89       156.49        54.94        16.27        84.49 
TCGA-CV-7434 TCGA-CV-7437 TCGA-CV-7440 TCGA-CV-7446 TCGA-CV-A45O TCGA-CV-A45W 
        7.17        16.64        22.19        35.93        27.98        45.96 
TCGA-CV-A461 TCGA-CV-A463 TCGA-CV-A6JN TCGA-D6-6516 TCGA-D6-6517 TCGA-D6-6824 
       67.86         0.76        29.79        25.41         9.60         2.53 
TCGA-D6-6826 TCGA-D6-6827 TCGA-D6-A4ZB TCGA-D6-A6EK TCGA-D6-A6EN TCGA-D6-A6EO 
       11.44        18.67        12.36        28.77        22.59        24.95 
TCGA-D6-A74Q TCGA-DQ-7591 TCGA-DQ-7595 TCGA-DQ-7596 TCGA-F7-7848 TCGA-F7-A50I 
       23.34        20.45        39.12        41.59        37.18         3.02 
TCGA-F7-A61S TCGA-F7-A623 TCGA-H7-7774 TCGA-HD-7229 TCGA-HD-7754 TCGA-HD-7832 
       18.94        20.25        13.38        33.76        25.74        27.48 
TCGA-HD-A634 TCGA-IQ-7631 TCGA-IQ-A61I TCGA-KU-A6H7 TCGA-MT-A51W TCGA-MT-A67F 
        4.27        38.53         0.07        19.27        14.37        12.62 
TCGA-MT-A7BN TCGA-MZ-A5BI TCGA-MZ-A6I9 TCGA-MZ-A7D7 TCGA-P3-A5Q5 TCGA-P3-A5QE 
       15.42         7.13        16.08        17.98        29.92        51.25 
TCGA-P3-A5QF TCGA-P3-A6T4 TCGA-P3-A6T6 TCGA-QK-A6IF TCGA-QK-A6V9 TCGA-QK-A8Z7 
       10.85         2.04        12.99        23.15        27.39        12.89 
TCGA-QK-A8Z8 TCGA-QK-A8ZA TCGA-T2-A6WX TCGA-T2-A6X0 TCGA-TN-A7HI TCGA-TN-A7HL 
        5.62        12.20         6.87         7.10        13.55        20.35 
TCGA-UF-A718 TCGA-UF-A719 TCGA-UF-A71B TCGA-UF-A71E TCGA-UF-A7JF TCGA-UP-A6WW 
       64.80        54.67        49.51        49.45        55.43        17.03 
TCGA-KU-A66S 
       13.35 

subtype1 subtype2 subtype3 
    0.36     0.07     0.07 
subtype1 subtype2 subtype3 
  180.16   210.97   172.67 
subtype1 subtype2 subtype3 
  21.650   18.035   23.840 
[1] "0.4 - 180.2 (21.6)" "0.1 - 211.0 (18.0)" "0.1 - 172.7 (23.8)"
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IVA STAGE IVB STAGE IVC
  subtype1      16       32        32        79         4         0
  subtype2       2       13        13        61         4         0
  subtype3       7       27        29        90         2         1
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         16        2        7
  STAGE II        32       13       27
  STAGE III       32       13       29
  STAGE IVA       79       61       90
  STAGE IVB        4        4        2
  STAGE IVC        0        0        1
[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    24 54 39 46
  subtype2     6 23 17 49
  subtype3    16 48 34 63
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T0+T1       24        6       16
  T2          54       23       48
  T3          39       17       34
  T4          46       49       63
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 64 24 61  2
  subtype2 37 13 38  2
  subtype3 60 28 55  2
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       64       37       60
  N1       24       13       28
  N2       61       38       55
  N3        2        2        2
[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 65  0
  subtype2 54  0
  subtype3 56  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   65    0
  subtype2   54    0
  subtype3   56    1
   clus
vv  subtype1 subtype2 subtype3
  0       65       54       56
  1        0        0        1
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus         0   1
  subtype1  57 117
  subtype2  26  78
  subtype3  47 152
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   57  117
  subtype2   26   78
  subtype3   47  152
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       57       26       47
  MALE        117       78      152
[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"
D10V8, binary
          cls
clus         0   1
  subtype1  69  81
  subtype2  26  70
  subtype3  51 124
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   81
  subtype2   26   70
  subtype3   51  124
     clus
vv    subtype1 subtype2 subtype3
  NO        69       26       51
  YES       81       70      124
[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 & NECK SQUAMOUS CELL CARCINOMA
  subtype1                                 172
  subtype2                                 102
  subtype3                                 192
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE
  subtype1                                                 2
  subtype2                                                 1
  subtype3                                                 7
          vv
clus       HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT
  subtype1                                                         0
  subtype2                                                         1
  subtype3                                                         0
D10V9, multiclass
                                                           clus
vv                                                          subtype1 subtype2
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            172      102
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                2        1
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        0        1
                                                           clus
vv                                                          subtype3
  HEAD & NECK SQUAMOUS CELL CARCINOMA                            192
  HEAD & NECK SQUAMOUS CELL CARCINOMA BASALOID TYPE                7
  HEAD & NECK SQUAMOUS CELL CARCINOMA, SPINDLE CELL VARIANT        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"
D10V10, continuous
D10V11, continuous
D10V12, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     6                        10
  subtype2                                1     1                        13
  subtype3                                0     4                        21
          vv
clus       WHITE
  subtype1   151
  subtype2    84
  subtype3   170
D10V13, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   6        1        4
  BLACK OR AFRICAN AMERICAN              10       13       21
  WHITE                                 151       84      170
[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  12 155
  subtype2   4  91
  subtype3   8 171
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   12  155
  subtype2    4   91
  subtype3    8  171
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO           12        4        8
  NOT HISPANIC OR LATINO      155       91      171
[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"
