[1] "ofn"        "-oTKIRP-TP"
[1] "opt"                    "-OPAGGREGRATED_CLUSTER"
[1] "tl" ""  
[1] "dx" ""  
[1] "opt"                 "AGGREGRATED_CLUSTER"
[1] "dx" ""  
[1] "cfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/Append_Data/KIRP-TP/15081779/KIRP-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/KIRP-TP/15098835/KIRP-TP.mergedcluster.txt"

nPatients in clinical file=271, in cluster file=291, common to both=271
[1]  10 271
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
104  72  44  49 
  1   2   3   4 
104  72  44  49 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3 
 72  67 116 
  1   2   3 
 72  67 116 
[1] "RPPA_CNMF"
[1] 3
 1  2  3 
71 85 48 
 1  2  3 
71 85 48 
[1] "RPPA_CHIERARCHICAL"
[1] 3
 1  2  3  4  5  6  7 
16 22 41 34 26 40 25 
 1  2  3  4  5  6  7 
16 22 41 34 26 40 25 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4 
32 94 58 86 
 1  2  3  4 
32 94 58 86 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
107 119  44 
  1   2   3 
107 119  44 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3 
 80 100  91 
  1   2   3 
 80 100  91 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
 1  2  3  4 
50 61 77 83 
 1  2  3  4 
50 61 77 83 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
 1  2  3 
63 79 66 
 1  2  3 
63 79 66 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
 1  2  3  4 
92 71 15 30 
 1  2  3  4 
92 71 15 30 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                        
 [2] "VITAL_STATUS"                          
 [3] "DAYS_TO_DEATH"                         
 [4] "DAYS_TO_LAST_FOLLOWUP"                 
 [5] "PRIMARY_SITE_OF_DISEASE"               
 [6] "NEOPLASM_DISEASESTAGE"                 
 [7] "PATHOLOGY_T_STAGE"                     
 [8] "PATHOLOGY_N_STAGE"                     
 [9] "PATHOLOGY_M_STAGE"                     
[10] "DCC_UPLOAD_DATE"                       
[11] "GENDER"                                
[12] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"  
[13] "DAYS_TO_LAST_KNOWN_ALIVE"              
[14] "RADIATION_THERAPY"                     
[15] "KARNOFSKY_PERFORMANCE_SCORE"           
[16] "HISTOLOGICAL_TYPE"                     
[17] "RADIATIONS_RADIATION_REGIMENINDICATION"
[18] "NUMBER_PACK_YEARS_SMOKED"              
[19] "YEAR_OF_TOBACCO_SMOKING_ONSET"         
[20] "RACE"                                  
[21] "ETHNICITY"                             
[22] "BATCH_NUMBER"                          

Input Data has 22 rows and 271 columns.

[1] "Batch" "22"   
[1] "Last Follow UP"
Variable 1:'YEARS_TO_BIRTH':	nDistinctValues=54,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 2:'VITAL_STATUS':	nDistinctValues=2,	numeric=TRUE,	binary=TRUE,	exclude=FALSE.
Variable 3:'DAYS_TO_DEATH':	nDistinctValues=35,	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=221,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'PRIMARY_SITE_OF_DISEASE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "PRIMARY_SITE_OF_DISEASE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'NEOPLASM_DISEASESTAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=12,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'DCC_UPLOAD_DATE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 11:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 12:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 13:'DAYS_TO_LAST_KNOWN_ALIVE':	nDistinctValues=8,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DAYS_?TO', vnms) to deal with survival parameters seperately"
Variable 14:'RADIATION_THERAPY':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATION_THERAPY is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 15:'KARNOFSKY_PERFORMANCE_SCORE':	nDistinctValues=6,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'HISTOLOGICAL_TYPE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "HISTOLOGICAL_TYPE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 17:'RADIATIONS_RADIATION_REGIMENINDICATION':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "RADIATIONS_RADIATION_REGIMENINDICATION is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 18:'NUMBER_PACK_YEARS_SMOKED':	nDistinctValues=35,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 19:'YEAR_OF_TOBACCO_SMOKING_ONSET':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 20:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 21:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 22:'BATCH_NUMBER':	nDistinctValues=26,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] NA
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 271 columns, 1 survival variables, and 11 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"                "NEOPLASM_DISEASESTAGE"        
 [3] "PATHOLOGY_T_STAGE"             "PATHOLOGY_N_STAGE"            
 [5] "PATHOLOGY_M_STAGE"             "GENDER"                       
 [7] "KARNOFSKY_PERFORMANCE_SCORE"   "NUMBER_PACK_YEARS_SMOKED"     
 [9] "YEAR_OF_TOBACCO_SMOKING_ONSET" "RACE"                         
[11] "ETHNICITY"                    
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
NEOPLASM_DISEASESTAGE, nv=4, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
178  29  54   2 
[1] "table(vv)"
vv
   T1    T2 T3+T4 
  178    29    56 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
178  29  54   2 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


   T1    T2 T3+T4 
  178    29    56 
PATHOLOGY_N_STAGE, nv=3, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
N0 N1 N2 
45 22  4 
[1] "table(vv)"
vv
N0 N1 N2 
45 22  4 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
N0 N1 N2 
45 22  4 

$nClasses
[1] 3

$ClinVariableType
[1] "multiclass(3)"


N0 N1 N2 
45 22  4 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
KARNOFSKY_PERFORMANCE_SCORE, nv=6, binary=FALSE, numeric=TRUE
NUMBER_PACK_YEARS_SMOKED, nv=35, binary=FALSE, numeric=TRUE
YEAR_OF_TOBACCO_SMOKING_ONSET, nv=33, 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 88 13
  subtype2 60  6
  subtype3 38  3
  subtype4 36 12
subtype1 subtype2 subtype3 subtype4 
     101       66       41       48 
subtype1 subtype2 subtype3 subtype4 
      13        6        3       12 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JK 
        7.04        59.01        67.30        75.42        35.67        38.99 
TCGA-2Z-A9JL TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JT TCGA-4A-A93X TCGA-4A-A93Y 
       26.43        24.33        31.20        22.49        12.82        11.57 
TCGA-A4-7287 TCGA-A4-7583 TCGA-A4-7585 TCGA-A4-7915 TCGA-A4-7996 TCGA-A4-7997 
       19.63         0.10        35.18         0.23        16.64        30.48 
TCGA-A4-8312 TCGA-A4-8516 TCGA-A4-A48D TCGA-AL-3467 TCGA-AL-3473 TCGA-B1-5398 
       23.28         0.76        12.46        58.45        25.08        19.56 
TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A5W8 TCGA-B9-A5W9 
       16.87        16.77         0.46        12.46         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        12.30        86.76        19.27        63.72        22.92 
TCGA-BQ-5880 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5889 
       43.20        40.83        26.04        26.04        25.35        10.88 
TCGA-BQ-7044 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 
      123.62        93.34        44.84        61.28        49.84        26.27 
TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 TCGA-DW-7834 TCGA-DW-7838 
       20.12        11.28         7.63         7.17       129.86        24.46 
TCGA-DW-7839 TCGA-DW-7841 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5902 
       13.78        14.63        80.88        61.02        54.90        19.00 
TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-G7-6797 TCGA-GL-7773 TCGA-GL-8500 
        0.43        48.62        34.82        25.15        12.92        27.65 
TCGA-GL-A4EM TCGA-GL-A9DC TCGA-GL-A9DE TCGA-IA-A40X TCGA-IA-A83S TCGA-IA-A83T 
        1.05         0.89         4.60        19.99        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-MH-A560 TCGA-MH-A561 TCGA-MH-A854 TCGA-MH-A855 
       67.17        22.26        30.38        27.65         0.36        12.13 
TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       25.97        21.44        99.78        42.94         6.61        92.58 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-SX-A7SL TCGA-SX-A7SM 
       52.27        50.60        78.90        12.85        27.06        11.93 
TCGA-SX-A7SO TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-WN-A9G9 TCGA-WN-AB4C 
       38.63        14.83        21.93         0.53        26.01        29.00 
TCGA-Y8-A894 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RZ TCGA-Y8-A8S1 
       18.64        18.05        15.62         6.74        13.28 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JM 
       75.55        58.22         4.57        34.85        56.81        30.71 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-A4-7288 
       29.36        25.58         5.29        16.18         0.13        61.05 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8517 TCGA-A4-A6HP 
       19.13         0.89        25.64        23.31        19.63        12.46 
TCGA-AL-3468 TCGA-AL-3472 TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B3-3925 
       76.64        30.35        21.67        24.56         3.55        33.83 
TCGA-B3-4104 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-A5W7 TCGA-B9-A8YH 
       34.49        50.50        26.40         1.15        19.23        17.49 
TCGA-BQ-5891 TCGA-BQ-7051 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7840 
        0.95        50.40        11.61        13.61        37.55         3.75 
TCGA-DW-7842 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LE 
        3.02        34.19        24.89        39.25         6.38        80.65 
TCGA-GL-A59R TCGA-HE-A5NH TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-IZ-A6M8 TCGA-IZ-A6M9 
       12.43        13.41        56.75        21.34        16.34        12.36 
TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A562 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVL 
       34.29        27.78        20.25        15.48        87.22        16.01 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SU 
       47.90        47.44        33.04        19.00        26.47        43.76 
TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       38.86        30.67        27.39        12.99        25.28         6.02 

$subtype3
TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-A4-7286 TCGA-A4-8311 TCGA-A4-8518 TCGA-A4-8630 
      100.27        56.91        18.21        23.97        19.73        14.33 
TCGA-A4-A4ZT TCGA-AL-3471 TCGA-AT-A5NU TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-A6W5 
       16.96        13.55         2.20         6.58        30.58        10.16 
TCGA-B9-4114 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-7268 TCGA-BQ-5881 TCGA-BQ-7045 
       28.18        15.12        43.99        22.06        47.80        48.26 
TCGA-BQ-7046 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7836 TCGA-DW-7963 TCGA-DZ-6133 
       96.92         7.04         3.81        35.93        40.77        51.19 
TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-A8LB TCGA-GL-6846 TCGA-GL-A59T TCGA-GL-A9DD 
        2.40        51.78        17.98       194.79        17.95        11.21 
TCGA-HE-A5NI TCGA-HE-A5NL TCGA-KV-A6GE TCGA-KV-A74V TCGA-PJ-A5Z9 TCGA-SX-A7SP 
       11.84         5.49        29.10        11.41        17.75        16.31 
TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PS TCGA-UZ-A9PV TCGA-Y8-A895 
       48.30        60.03        52.11        25.68        15.91 

$subtype4
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-A4-8098 TCGA-A4-A57E TCGA-A4-A5DU TCGA-A4-A5XZ 
       54.64        51.52        29.46         8.48        16.31        15.75 
TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-7332 
        8.28        12.99         9.63        44.61        49.25         7.33 
TCGA-B3-3926 TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-A44B TCGA-BQ-5877 TCGA-BQ-5882 
       10.09        20.61         0.46         2.10         8.88        21.63 
TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5890 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 
       30.28        13.25         7.66        11.97         7.92         2.76 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 
       79.86        10.68        13.08         1.18         4.01        11.05 
TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-7966 TCGA-HE-A5NF 
       13.68        25.84        17.33        16.90         3.68        68.12 
TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40Y TCGA-J7-8537 TCGA-KV-A6GD TCGA-P4-A5EB 
       73.25        16.80         2.04         0.13        11.97        84.95 
TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SQ TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-Y8-A896 
       14.07        28.80        41.62        18.02        86.27        18.64 

subtype1 subtype2 subtype3 subtype4 
    0.10     0.13     2.20     0.13 
subtype1 subtype2 subtype3 subtype4 
  129.86    87.22   194.79    86.27 
subtype1 subtype2 subtype3 subtype4 
  23.280   25.085   19.730   13.875 
[1] "0.1 - 129.9 (23.3)" "0.1 - 87.2 (25.1)"  "2.2 - 194.8 (19.7)"
[4] "0.1 - 86.3 (13.9)" 
D1V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      64       10        22        2
  subtype2      53        6         6        1
  subtype3      34        3         2        2
  subtype4      16        2        19        9
D1V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         64       53       34       16
  STAGE II        10        6        3        2
  STAGE III       22        6        2       19
  STAGE IV         2        1        2        9
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 68  8    21
  subtype2 55 10     6
  subtype3 35  5     4
  subtype4 18  6    25
D1V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          68       55       35       18
  T2           8       10        5        6
  T3+T4       21        6        4       25
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 19  8  1
  subtype2 10  1  0
  subtype3  7  1  0
  subtype4  9 12  3
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       19       10        7        9
  N1        8        1        1       12
  N2        1        0        0        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus        0  1
  subtype1 40  2
  subtype2 22  1
  subtype3 14  0
  subtype4 14  6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   40    2
  subtype2   22    1
  subtype3   14    0
  subtype4   14    6
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       40       22       14       14
  1        2        1        0        6
[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 33 71
  subtype2  9 63
  subtype3  8 36
  subtype4 22 27
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   33   71
  subtype2    9   63
  subtype3    8   36
  subtype4   22   27
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       33        9        8       22
  MALE         71       63       36       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, continuous
D1V9, continuous
D1V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        26
  subtype2                                1     1                        17
  subtype3                                1     0                         6
  subtype4                                0     3                        11
          vv
clus       WHITE
  subtype1    73
  subtype2    49
  subtype3    35
  subtype4    30
D1V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   1        1        0        3
  BLACK OR AFRICAN AMERICAN              26       17        6       11
  WHITE                                  73       49       35       30
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V12, binary
          cls
clus        0  1
  subtype1  7 79
  subtype2  2 64
  subtype3  2 37
  subtype4  1 40
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   79
  subtype2    2   64
  subtype3    2   37
  subtype4    1   40
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            7        2        2        1
  NOT HISPANIC OR LATINO       79       64       37       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  60   8
  subtype2  48  17
  subtype3 102   7
subtype1 subtype2 subtype3 
      68       65      109 
subtype1 subtype2 subtype3 
       8       17        7 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J9 TCGA-2Z-A9JI TCGA-2Z-A9JJ 
        7.04        75.55       100.27        75.42        51.52        35.67 
TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JT TCGA-4A-A93Y TCGA-A4-7286 
       38.99        30.71        24.33        22.49        11.57        18.21 
TCGA-A4-7287 TCGA-A4-7585 TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A48D TCGA-AL-7173 
       19.63        35.18        23.28        19.73        12.46        44.61 
TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A5W8 
       19.56        16.87        16.77         0.46        12.46         6.81 
TCGA-B9-A69E TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5888 
       14.86        47.80        40.83        26.04        30.28        13.25 
TCGA-BQ-5889 TCGA-BQ-7045 TCGA-BQ-7049 TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 
       10.88        48.26        44.84        26.27         7.63         7.04 
TCGA-BQ-7062 TCGA-DW-7838 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 
        3.81        24.46        14.63        40.77        80.88        61.02 
TCGA-EV-5903 TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6792 TCGA-G7-6796 TCGA-GL-A4EM 
       24.89        13.08         0.43        48.62        34.82         1.05 
TCGA-GL-A9DD TCGA-HE-A5NF TCGA-HE-A5NK TCGA-IA-A83S TCGA-IA-A83T TCGA-IZ-A6M8 
       11.21        68.12        73.25        85.78        88.24        16.34 
TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A560 TCGA-MH-A855 TCGA-MH-A857 TCGA-P4-A5ED 
        0.13        11.97        30.38        12.13        21.44        92.58 
TCGA-PJ-A5Z8 TCGA-SX-A7SP TCGA-UZ-A9PM TCGA-UZ-A9PN TCGA-WN-A9G9 TCGA-WN-AB4C 
       12.85        16.31        14.83        21.93        26.01        29.00 
TCGA-Y8-A896 TCGA-Y8-A8S1 
       18.64        13.28 

$subtype2
TCGA-2Z-A9J2 TCGA-2Z-A9J8 TCGA-2Z-A9JG TCGA-2Z-A9JO TCGA-4A-A93X TCGA-A4-7915 
       59.01        67.30        54.64        31.20        12.82         0.23 
TCGA-A4-8098 TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-A5DJ TCGA-B9-A44B 
       29.46         8.48         8.28        12.99        49.25         2.10 
TCGA-B9-A5W9 TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 
        0.16        12.30        86.76        19.27         8.88        63.72 
TCGA-BQ-5879 TCGA-BQ-5880 TCGA-BQ-5882 TCGA-BQ-5886 TCGA-BQ-5887 TCGA-BQ-5890 
       22.92        43.20        21.63        26.04        25.35         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 
        0.95        11.97         7.92         2.76       123.62        96.92 
TCGA-BQ-7048 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 
       93.34        61.28        50.40        49.84        20.12        11.28 
TCGA-BQ-7061 TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 
        7.17        79.86        10.68         1.18         4.01        11.05 
TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A9DE TCGA-IA-A40X 
       13.68        16.90       194.79         3.68         4.60        19.99 
TCGA-IA-A40Y TCGA-IZ-8195 TCGA-P4-A5E6 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5EB 
        2.04        22.26        99.78        42.94         6.61        84.95 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-P4-AAVO TCGA-PJ-A8JU TCGA-Q2-A5QZ TCGA-SX-A7SM 
       52.27        50.60        78.90        12.49        14.07        11.93 
TCGA-SX-A7SO TCGA-UN-AAZ9 TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-Y8-A8RZ 
       38.63        18.02        86.27        52.11         6.74 

$subtype3
TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JD TCGA-2Z-A9JE TCGA-2Z-A9JL 
       58.22        56.91         4.57        34.85        56.81        26.43 
TCGA-2Z-A9JP TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-A4-7288 
       29.36        25.58         5.29        16.18         0.13        61.05 
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8310 
        0.10        19.13         0.89        16.64        30.48        25.64 
TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 TCGA-A4-A4ZT 
       23.97        23.31         0.76        19.63        14.33        16.96 
TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AT-A5NU TCGA-B1-7332 TCGA-B1-A47M 
       16.31        15.75        12.46         2.20         7.33        21.67 
TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-A6W5 TCGA-B9-5155 TCGA-B9-5156 
       24.56         3.55         6.58        10.16        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 
       22.06        19.23        17.49        11.61        13.61       129.86 
TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6133 
       35.93        37.55        13.78         3.75         3.02        51.19 
TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6795 
       54.90        34.19        19.00         2.40        51.78        39.25 
TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC TCGA-G7-A8LE 
       25.15        25.84         6.38        17.98        17.33        80.65 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-HE-A5NH 
       12.92        27.65        12.43        17.95         0.89        13.41 
TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A83W TCGA-IZ-8196 
       11.84        56.75         5.49        16.80        67.17        21.34 
TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 
       12.36        29.10        11.41        34.29        27.78        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVL 
       20.25         0.36        25.97        15.48        87.22        16.01 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A71W 
       17.75        47.90        47.44        33.04        28.80        26.89 
TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       27.06        19.00        41.62        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       60.03         0.53        38.86        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY 
       12.99        18.64        15.91        18.05        15.62        25.28 
TCGA-Y8-A8S0 
        6.02 

subtype1 subtype2 subtype3 
    0.13     0.16     0.10 
subtype1 subtype2 subtype3 
  100.27   194.79   129.86 
subtype1 subtype2 subtype3 
   22.21    19.99    19.63 
[1] "0.1 - 100.3 (22.2)" "0.2 - 194.8 (20.0)" "0.1 - 129.9 (19.6)"
D2V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      48        8        11        2
  subtype2      21        4        29        9
  subtype3      95        6         8        2
D2V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         48       21       95
  STAGE II         8        4        6
  STAGE III       11       29        8
  STAGE IV         2        9        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"
          vv
clus       T1 T2 T3+T4
  subtype1 50  5    14
  subtype2 23  7    33
  subtype3 98 10     7
D2V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          50       23       98
  T2           5        7       10
  T3+T4       14       33        7
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 13  3  1
  subtype2 15 18  3
  subtype3 15  0  0
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       13       15       15
  N1        3       18        0
  N2        1        3        0
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus        0  1
  subtype1 29  1
  subtype2 23  6
  subtype3 29  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29    1
  subtype2   23    6
  subtype3   29    1
   clus
vv  subtype1 subtype2 subtype3
  0       29       23       29
  1        1        6        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"
D2V7, binary
          cls
clus        0  1
  subtype1 19 53
  subtype2 28 39
  subtype3 22 94
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   19   53
  subtype2   28   39
  subtype3   22   94
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       19       28       22
  MALE         53       39       94
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, continuous
D2V9, continuous
D2V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     3                        18
  subtype2                                0     1                        17
  subtype3                                1     1                        18
          vv
clus       WHITE
  subtype1    46
  subtype2    46
  subtype3    88
D2V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        0        1
  ASIAN                                   3        1        1
  BLACK OR AFRICAN AMERICAN              18       17       18
  WHITE                                  46       46       88
[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"
D2V12, binary
          cls
clus        0  1
  subtype1  1 60
  subtype2  5 47
  subtype3  6 99
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   60
  subtype2    5   47
  subtype3    6   99
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        5        6
  NOT HISPANIC OR LATINO       60       47       99
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 58 10
  subtype2 71 10
  subtype3 40  5
subtype1 subtype2 subtype3 
      68       81       45 
subtype1 subtype2 subtype3 
      10       10        5 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JI TCGA-A4-7583 
        7.04        75.55       100.27        56.91        51.52         0.10 
TCGA-A4-8517 TCGA-AL-3473 TCGA-AL-7173 TCGA-AL-A5DJ TCGA-B1-A47M TCGA-B1-A47O 
       19.63        25.08        44.61        49.25        21.67        16.87 
TCGA-B1-A657 TCGA-B3-8121 TCGA-B3-A6W5 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W7 
        6.58        12.46        10.16        43.99         2.10        19.23 
TCGA-B9-A5W8 TCGA-B9-A8YH TCGA-BQ-5879 TCGA-BQ-5882 TCGA-BQ-5887 TCGA-BQ-5888 
        6.81        17.49        22.92        21.63        25.35        13.25 
TCGA-BQ-5889 TCGA-BQ-7049 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7840 TCGA-DW-7841 
       10.88        44.84        37.55        24.46         3.75        14.63 
TCGA-DW-7963 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5903 TCGA-F9-A4JJ 
       40.77        80.88        61.02        54.90        24.89        10.68 
TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6795 TCGA-G7-6796 TCGA-GL-7773 
       13.08         0.43         4.01        39.25        34.82        12.92 
TCGA-GL-A59R TCGA-GL-A9DC TCGA-GL-A9DD TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ 
       12.43         0.89        11.21        13.41        11.84        56.75 
TCGA-HE-A5NK TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40Y TCGA-IA-A83W TCGA-IZ-8195 
       73.25         5.49        16.80         2.04        67.17        22.26 
TCGA-J7-8537 TCGA-P4-A5E6 TCGA-P4-A5EA TCGA-P4-A5ED TCGA-PJ-A5Z8 TCGA-PJ-A5Z9 
        0.13        99.78         6.61        92.58        12.85        17.75 
TCGA-SX-A71U TCGA-SX-A7SN TCGA-SX-A7SP TCGA-SX-A7SR TCGA-WN-A9G9 TCGA-Y8-A895 
       33.04        19.00        16.31        26.47        26.01        15.91 
TCGA-Y8-A896 TCGA-Y8-A897 
       18.64        18.05 

$subtype2
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9J8 TCGA-2Z-A9J9 TCGA-2Z-A9JE TCGA-2Z-A9JJ 
       58.22         4.57        67.30        75.42        56.81        35.67 
TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-4A-A93W TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-7996 
       26.43        25.58         0.13         0.89         0.23        16.64 
TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A57E TCGA-AL-3472 
       30.48        23.97         0.76        14.33         8.48        30.35 
TCGA-B1-7332 TCGA-B1-A47N TCGA-B1-A654 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W9 
        7.33        24.56         3.55        15.12        22.06         0.16 
TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5885 TCGA-BQ-5891 TCGA-BQ-7050 TCGA-BQ-7051 
        8.88        63.72        30.28         0.95        61.28        50.40 
TCGA-BQ-7062 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7839 TCGA-DW-7842 
        3.81        11.61        13.61       129.86        13.78         3.02 
TCGA-DZ-6131 TCGA-DZ-6133 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7VF TCGA-F9-A8NY 
       79.86        51.19        34.19        19.00         2.40         1.18 
TCGA-G7-6792 TCGA-G7-6797 TCGA-G7-7501 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
       48.62        25.15        13.68        25.84         6.38        17.98 
TCGA-G7-A8LC TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-8500 
       17.33        16.90        80.65       194.79         3.68        27.65 
TCGA-IZ-8196 TCGA-KV-A6GD TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55Z TCGA-MH-A562 
       21.34        11.97        29.10        11.41        27.78        20.25 
TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-SX-A71R TCGA-SX-A7SM TCGA-SX-A7SQ TCGA-SX-A7SS 
       87.22        42.94        47.90        11.93        41.62        48.30 
TCGA-UN-AAZ9 TCGA-UZ-A9PK TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-UZ-A9PR 
       18.02        60.03        21.93         0.53        86.27        38.86 
TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 
       52.11        30.67        25.68        27.39        12.99        18.64 
TCGA-Y8-A8RY TCGA-Y8-A8RZ TCGA-Y8-A8S0 
       25.28         6.74         6.02 

$subtype3
TCGA-2Z-A9JD TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JT TCGA-4A-A93X TCGA-4A-A93Y 
       34.85        31.20        29.36        22.49        12.82        11.57 
TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-8098 TCGA-B1-5398 TCGA-B9-A69E TCGA-B9-A8YI 
       61.05        35.18        29.46        19.56        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5890 TCGA-BQ-5892 
       86.76        43.20        47.80        40.83         7.66        11.97 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 TCGA-BQ-7053 
        7.92         2.76       123.62        96.92        93.34        49.84 
TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7061 
       26.27        20.12        11.28         7.63         7.04         7.17 
TCGA-G7-6790 TCGA-G7-6793 TCGA-GL-A4EM TCGA-GL-A9DE TCGA-HE-A5NF TCGA-IA-A40X 
       51.78        11.05         1.05         4.60        68.12        19.99 
TCGA-IZ-A6M8 TCGA-MH-A560 TCGA-MH-A855 TCGA-P4-A5EB TCGA-PJ-A8JU TCGA-Q2-A5QZ 
       16.34        30.38        12.13        84.95        12.49        14.07 
TCGA-SX-A7SO TCGA-UZ-A9PM TCGA-Y8-A8S1 
       38.63        14.83        13.28 

subtype1 subtype2 subtype3 
    0.10     0.13     1.05 
subtype1 subtype2 subtype3 
  100.27   194.79   123.62 
subtype1 subtype2 subtype3 
   18.82    22.06    19.99 
[1] "0.1 - 100.3 (18.8)" "0.1 - 194.8 (22.1)" "1.1 - 123.6 (20.0)"
D3V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      41        7        17        3
  subtype2      57        6        14        7
  subtype3      28        2        12        3
D3V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         41       57       28
  STAGE II         7        6        2
  STAGE III       17       14       12
  STAGE IV         3        7        3
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 45  7    19
  subtype2 57 13    15
  subtype3 29  2    15
D3V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          45       57       29
  T2           7       13        2
  T3+T4       19       15       15
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 17  6  2
  subtype2 17 10  0
  subtype3  8  3  2
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17       17        8
  N1        6       10        3
  N2        2        0        2
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 24  1
  subtype2 26  5
  subtype3 19  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    1
  subtype2   26    5
  subtype3   19    2
   clus
vv  subtype1 subtype2 subtype3
  0       24       26       19
  1        1        5        2
[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"
D3V7, binary
          cls
clus        0  1
  subtype1 18 53
  subtype2 24 61
  subtype3 14 34
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   18   53
  subtype2   24   61
  subtype3   14   34
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       18       24       14
  MALE         53       61       34
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, continuous
D3V9, continuous
D3V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     3                        15
  subtype2                                0     2                        18
  subtype3                                1     0                        11
          vv
clus       WHITE
  subtype1    45
  subtype2    63
  subtype3    33
D3V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        1
  ASIAN                                   3        2        0
  BLACK OR AFRICAN AMERICAN              15       18       11
  WHITE                                  45       63       33
[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"
D3V12, binary
          cls
clus        0  1
  subtype1  1 56
  subtype2  1 75
  subtype3  2 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   56
  subtype2    1   75
  subtype3    2   37
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            1        1        2
  NOT HISPANIC OR LATINO       56       75       37
[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(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 15  0
  subtype2 20  1
  subtype3 35  4
  subtype4 31  1
  subtype5 15 11
  subtype6 34  3
  subtype7 19  5
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
      15       21       39       32       26       37       24 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       0        1        4        1       11        3        5 
$subtype1
TCGA-2K-A9WE TCGA-A4-7583 TCGA-B3-A6W5 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7838 
        7.04         0.10        10.16         7.63         3.81        24.46 
TCGA-DZ-6132 TCGA-G7-7502 TCGA-GL-A9DC TCGA-HE-A5NH TCGA-KV-A6GD TCGA-P4-A5E7 
       80.88        25.84         0.89        13.41        11.97        87.22 
TCGA-PJ-A5Z9 TCGA-UZ-A9PK TCGA-UZ-A9PS 
       17.75        60.03        52.11 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JI TCGA-B1-A47M TCGA-B1-A47O 
       75.55       100.27        56.91        51.52        21.67        16.87 
TCGA-B1-A657 TCGA-B9-5156 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-5888 TCGA-DW-7837 
        6.58        43.99        19.23        17.49        13.25        37.55 
TCGA-DW-7841 TCGA-DZ-6134 TCGA-EV-5903 TCGA-GL-7773 TCGA-HE-A5NL TCGA-IA-A40Y 
       14.63        61.02        24.89        12.92         5.49         2.04 
TCGA-SX-A71U TCGA-SX-A7SP TCGA-WN-A9G9 
       33.04        16.31        26.01 

$subtype3
TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JL TCGA-2Z-A9JQ TCGA-4A-A93W TCGA-A4-7734 
       58.22         4.57        26.43        25.58         0.13         0.89 
TCGA-A4-7996 TCGA-A4-8311 TCGA-AL-3472 TCGA-B1-A47N TCGA-B1-A654 TCGA-B9-5155 
       16.64        23.97        30.35        24.56         3.55        15.12 
TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5901 
       11.61        13.61       129.86         3.02        51.19        34.19 
TCGA-EV-5902 TCGA-F9-A7VF TCGA-G7-6797 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE 
       19.00         2.40        25.15         6.38        17.98        80.65 
TCGA-GL-8500 TCGA-HE-A5NI TCGA-IZ-8196 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A562 
       27.65        11.84        21.34        29.10        11.41        20.25 
TCGA-SX-A71R TCGA-SX-A7SQ TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       47.90        41.62        38.86        30.67        25.68        27.39 
TCGA-UZ-A9Q0 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       12.99        25.28         6.02 

$subtype4
TCGA-2Z-A9J8 TCGA-2Z-A9JE TCGA-2Z-A9JT TCGA-A4-7997 TCGA-A4-8516 TCGA-A4-8630 
       67.30        56.81        22.49        30.48         0.76        14.33 
TCGA-A4-A57E TCGA-B1-7332 TCGA-B9-7268 TCGA-B9-A5W9 TCGA-BQ-5878 TCGA-BQ-5885 
        8.48         7.33        22.06         0.16        63.72        30.28 
TCGA-BQ-5891 TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7053 TCGA-BQ-7056 
        0.95        96.92        61.28        50.40        49.84        20.12 
TCGA-DW-7839 TCGA-G7-6792 TCGA-G7-7501 TCGA-G7-A8LC TCGA-GL-6846 TCGA-IA-A40U 
       13.78        48.62        13.68        17.33       194.79        16.80 
TCGA-IA-A40X TCGA-MH-A55Z TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-UN-AAZ9 TCGA-UZ-A9PP 
       19.99        27.78        99.78        84.95        18.02         0.53 
TCGA-Y8-A894 TCGA-Y8-A8RZ 
       18.64         6.74 

$subtype5
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-A4-7915 TCGA-AL-7173 TCGA-B3-8121 TCGA-BQ-5877 
       75.42        35.67         0.23        44.61        12.46         8.88 
TCGA-BQ-5879 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7049 TCGA-DZ-6135 
       22.92        11.97         7.92         2.76        44.84        54.90 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LD TCGA-GL-7966 
       10.68         1.18         4.01        11.05        16.90         3.68 
TCGA-P4-A5E8 TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SS TCGA-UZ-A9PN 
       42.94        12.85        14.07        11.93        48.30        21.93 
TCGA-UZ-A9PQ TCGA-Y8-A897 
       86.27        18.05 

$subtype6
TCGA-2Z-A9JD TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7288 
       34.85        31.20        29.36        12.82        11.57        61.05 
TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8517 TCGA-B1-5398 TCGA-B9-A69E TCGA-B9-A8YI 
       35.18        29.46        19.63        19.56        14.86        12.30 
TCGA-BQ-5875 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5883 TCGA-BQ-5890 TCGA-BQ-7044 
       86.76        43.20        47.80        40.83         7.66       123.62 
TCGA-BQ-7048 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-7963 
       93.34        26.27        11.28         7.04         7.17        40.77 
TCGA-G7-6790 TCGA-GL-A4EM TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-IZ-8195 
       51.78         1.05        11.21         4.60        68.12        22.26 
TCGA-IZ-A6M8 TCGA-MH-A560 TCGA-MH-A855 TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-UZ-A9PM 
       16.34        30.38        12.13        12.49        38.63        14.83 
TCGA-Y8-A8S1 
       13.28 

$subtype7
TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B9-A44B TCGA-B9-A5W8 TCGA-BQ-5882 TCGA-BQ-5887 
       25.08        49.25         2.10         6.81        21.63        25.35 
TCGA-BQ-5889 TCGA-DW-7840 TCGA-DZ-6131 TCGA-F9-A7Q0 TCGA-F9-A97G TCGA-G7-6795 
       10.88         3.75        79.86        13.08         0.43        39.25 
TCGA-G7-6796 TCGA-GL-A59R TCGA-HE-A5NJ TCGA-HE-A5NK TCGA-IA-A83W TCGA-J7-8537 
       34.82        12.43        56.75        73.25        67.17         0.13 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-SX-A7SN TCGA-SX-A7SR TCGA-Y8-A895 TCGA-Y8-A896 
        6.61        92.58        19.00        26.47        15.91        18.64 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
    0.10     2.04     0.13     0.16     0.23     1.05     0.13 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
   87.22   100.27   129.86   194.79    86.27   123.62    92.58 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
  13.410   21.670   23.970   21.090   13.460   22.260   20.315 
[1] "0.1 - 87.2 (13.4)"  "2.0 - 100.3 (21.7)" "0.1 - 129.9 (24.0)"
[4] "0.2 - 194.8 (21.1)" "0.2 - 86.3 (13.5)"  "1.1 - 123.6 (22.3)"
[7] "0.1 - 92.6 (20.3)" 
D4V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      14        2         0        0
  subtype2      16        1         4        0
  subtype3      35        1         2        2
  subtype4      19        3        10        2
  subtype5       9        1         8        8
  subtype6      25        3         9        0
  subtype7       8        4        10        1
D4V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  STAGE I         14       16       35       19        9       25        8
  STAGE II         2        1        1        3        1        3        4
  STAGE III        0        4        2       10        8        9       10
  STAGE IV         0        0        2        2        8        0        1
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 14  2     0
  subtype2 17  1     4
  subtype3 35  5     1
  subtype4 20  4    10
  subtype5  9  3    14
  subtype6 26  3     9
  subtype7 10  4    11
D4V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  T1          14       17       35       20        9       26       10
  T2           2        1        5        4        3        3        4
  T3+T4        0        4        1       10       14        9       11
[1] 3 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  2  0  0
  subtype2  5  1  0
  subtype3  5  0  0
  subtype4 11  4  0
  subtype5  4 10  3
  subtype6  7  1  1
  subtype7  8  3  0
D4V5, multiclass
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       2        6        5       15       17        9       11 
 [1] "subtype2" "subtype6" "subtype3" "subtype6" "subtype5" "subtype4"
 [7] "subtype3" "subtype7" "subtype5" "subtype6" "subtype2" "subtype2"
[13] "subtype4" "subtype5" "subtype4" "subtype5" "subtype6" "subtype7"
[19] "subtype4" "subtype7" "subtype2" "subtype7" "subtype6" "subtype4"
[25] "subtype5" "subtype5" "subtype5" "subtype6" "subtype4" "subtype4"
[31] "subtype4" "subtype6" "subtype6" "subtype7" "subtype5" "subtype7"
[37] "subtype5" "subtype5" "subtype7" "subtype4" "subtype5" "subtype4"
[43] "subtype5" "subtype7" "subtype4" "subtype2" "subtype7" "subtype4"
[49] "subtype7" "subtype3" "subtype4" "subtype5" "subtype7" "subtype3"
[55] "subtype5" "subtype2" "subtype5" "subtype4" "subtype6" "subtype5"
[61] "subtype3" "subtype5" "subtype4"
    clus
vv   subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  N0        5        5       11        4        7        8
  N1        1        0        4       10        1        3
  N2        0        0        0        3        1        0
[1] 3 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V6, binary
          cls
clus        0  1
  subtype1  5  0
  subtype2  5  0
  subtype3 13  1
  subtype4 12  1
  subtype5  8  5
  subtype6 14  0
  subtype7 12  1
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    5    0
  subtype2    5    0
  subtype3   13    1
  subtype4   12    1
  subtype5    8    5
  subtype6   14    0
  subtype7   12    1
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  0        5        5       13       12        8       14       12
  1        0        0        1        1        5        0        1
[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"
D4V7, binary
          cls
clus        0  1
  subtype1  4 12
  subtype2  4 18
  subtype3  8 33
  subtype4 13 21
  subtype5 14 12
  subtype6  9 31
  subtype7  4 21
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   12
  subtype2    4   18
  subtype3    8   33
  subtype4   13   21
  subtype5   14   12
  subtype6    9   31
  subtype7    4   21
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7
  FEMALE        4        4        8       13       14        9        4
  MALE         12       18       33       21       12       31       21
[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"
D4V8, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       2        6       13        7        5        5        5 
 [1] "subtype6" "subtype6" "subtype3" "subtype4" "subtype4" "subtype3"
 [7] "subtype3" "subtype3" "subtype2" "subtype4" "subtype7" "subtype2"
[13] "subtype3" "subtype6" "subtype3" "subtype3" "subtype2" "subtype6"
[19] "subtype5" "subtype7" "subtype3" "subtype4" "subtype3" "subtype3"
[25] "subtype4" "subtype5" "subtype3" "subtype4" "subtype4" "subtype2"
[31] "subtype7" "subtype5" "subtype3" "subtype2" "subtype5" "subtype7"
[37] "subtype6" "subtype2" "subtype3" "subtype7" "subtype5"
D4V9, continuous
D4V10, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 subtype7 
       2        4       12        7        5        9        3 
 [1] "subtype3" "subtype3" "subtype4" "subtype6" "subtype2" "subtype6"
 [7] "subtype3" "subtype6" "subtype4" "subtype3" "subtype5" "subtype3"
[13] "subtype6" "subtype3" "subtype6" "subtype7" "subtype4" "subtype3"
[19] "subtype5" "subtype3" "subtype2" "subtype6" "subtype3" "subtype4"
[25] "subtype4" "subtype6" "subtype5" "subtype2" "subtype5" "subtype7"
[31] "subtype5" "subtype6" "subtype6" "subtype3" "subtype3" "subtype2"
[37] "subtype4" "subtype7" "subtype3" "subtype4"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     0                         4
  subtype2                                0     0                         5
  subtype3                                0     0                         6
  subtype4                                0     1                         8
  subtype5                                0     1                         8
  subtype6                                1     0                        10
  subtype7                                0     3                         3
          vv
clus       WHITE
  subtype1     9
  subtype2    16
  subtype3    33
  subtype4    24
  subtype5    15
  subtype6    28
  subtype7    16
D4V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4 subtype5
  AMERICAN INDIAN OR ALASKA NATIVE        0        0        0        0        0
  ASIAN                                   0        0        0        1        1
  BLACK OR AFRICAN AMERICAN               4        5        6        8        8
  WHITE                                   9       16       33       24       15
                                  clus
vv                                 subtype6 subtype7
  AMERICAN INDIAN OR ALASKA NATIVE        1        0
  ASIAN                                   0        3
  BLACK OR AFRICAN AMERICAN              10        3
  WHITE                                  28       16
[1] 4 7
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V12, binary
          cls
clus        0  1
  subtype1  0 13
  subtype2  0 19
  subtype3  0 36
  subtype4  2 28
  subtype5  1 20
  subtype6  0 33
  subtype7  1 19
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   13
  subtype2    0   19
  subtype3    0   36
  subtype4    2   28
  subtype5    1   20
  subtype6    0   33
  subtype7    1   19
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            0        0        0        2        1        0
  NOT HISPANIC OR LATINO       13       19       36       28       20       33
                        clus
vv                       subtype7
  HISPANIC OR LATINO            1
  NOT HISPANIC OR LATINO       19
[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(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 24  5
  subtype2 82  7
  subtype3 51  4
  subtype4 66 18
subtype1 subtype2 subtype3 subtype4 
      29       89       55       84 
subtype1 subtype2 subtype3 subtype4 
       5        7        4       18 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-A4-7997 TCGA-AL-7173 TCGA-B1-A657 
        7.04        26.43        30.71        30.48        44.61         6.58 
TCGA-B3-8121 TCGA-B9-4114 TCGA-B9-5156 TCGA-BQ-5889 TCGA-BQ-7045 TCGA-BQ-7049 
       12.46        28.18        43.99        10.88        48.26        44.84 
TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7834 TCGA-DW-7837 TCGA-DW-7838 TCGA-DW-7841 
        7.63         3.81       129.86        37.55        24.46        14.63 
TCGA-DZ-6132 TCGA-DZ-6134 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5903 TCGA-G7-6792 
       80.88        61.02        54.90        34.19        24.89        48.62 
TCGA-GL-A9DD TCGA-IA-A83T TCGA-IA-A83W TCGA-KV-A6GD TCGA-Y8-A898 
       11.21        88.24        67.17        11.97        15.62 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JQ TCGA-2Z-A9JR 
       75.55        58.22         4.57        56.81        25.58         5.29 
TCGA-2Z-A9JS TCGA-4A-A93W TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-8311 
       16.18         0.13         0.10        19.13         0.89        23.97 
TCGA-A4-8515 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A6HP TCGA-AL-3468 
       23.31        14.33        16.96        16.31        12.46        76.64 
TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 
       13.55        30.35         2.20        21.67        24.56         3.55 
TCGA-B3-3925 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-4617 
       33.83        10.16        50.50        26.40         0.46         1.15 
TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-DW-5560 TCGA-DW-5561 
       15.12        22.06        19.23        17.49        11.61        13.61 
TCGA-DW-7836 TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6133 TCGA-EV-5902 
       35.93        13.78         3.75         3.02        51.19        19.00 
TCGA-F9-A7VF TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB 
        2.40        39.25        25.15        25.84         6.38        17.98 
TCGA-G7-A8LE TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A9DC TCGA-HE-A5NH TCGA-HE-A5NI 
       80.65        27.65        12.43         0.89        13.41        11.84 
TCGA-HE-A5NJ TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 
       56.75        21.34        12.36        34.29        27.78        27.65 
TCGA-MH-A562 TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-AAVL 
       20.25         0.36        25.97        15.48        87.22        16.01 
TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL 
       17.75        47.90        47.44        33.04        26.89        27.06 
TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK 
       19.00        41.62        26.47        48.30        43.76        60.03 
TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 
        0.53        38.86        30.67        25.68        27.39        12.99 
TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        15.91        18.05        25.28         6.02 

$subtype3
TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JD TCGA-2Z-A9JG 
       59.01       100.27        56.91        67.30        34.85        54.64 
TCGA-2Z-A9JP TCGA-2Z-A9JT TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-7996 
       29.36        22.49        18.21        61.05        35.18        16.64 
TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A5XZ 
       25.64         0.76        19.63        19.73        12.46        15.75 
TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B1-A656 TCGA-B3-4103 
       25.08        19.56         7.33        16.77         0.46        30.58 
TCGA-B9-A5W8 TCGA-B9-A8YI TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5886 TCGA-BQ-5890 
        6.81        12.30        43.20        47.80        26.04         7.66 
TCGA-BQ-7046 TCGA-BQ-7051 TCGA-BQ-7060 TCGA-DW-7963 TCGA-G7-6790 TCGA-G7-6796 
       96.92        50.40         7.04        40.77        51.78        34.82 
TCGA-GL-A59T TCGA-GL-A9DE TCGA-HE-A5NF TCGA-HE-A5NL TCGA-IA-A40U TCGA-IA-A40X 
       17.95         4.60        68.12         5.49        16.80        19.99 
TCGA-IA-A83S TCGA-IZ-A6M8 TCGA-KV-A6GE TCGA-KV-A74V TCGA-P4-A5E6 TCGA-P4-A5EB 
       85.78        16.34        29.10        11.41        99.78        84.95 
TCGA-P4-AAVK TCGA-P4-AAVM TCGA-SX-A71V TCGA-SX-A7SP TCGA-UZ-A9PM TCGA-WN-A9G9 
       52.27        50.60        28.80        16.31        14.83        26.01 
TCGA-Y8-A8RZ 
        6.74 

$subtype4
TCGA-2Z-A9J9 TCGA-2Z-A9JI TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO 
       75.42        51.52        35.67        38.99        24.33        31.20 
TCGA-4A-A93X TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8098 TCGA-A4-8312 
       12.82        11.57        19.63         0.23        29.46        23.28 
TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3467 TCGA-AL-A5DJ 
        8.48         8.28        12.99         9.63        58.45        49.25 
TCGA-B1-A47O TCGA-B3-3926 TCGA-B3-4104 TCGA-B9-4116 TCGA-B9-A44B TCGA-B9-A5W9 
       16.87        10.09        34.49        20.61         2.10         0.16 
TCGA-B9-A69E TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5878 TCGA-BQ-5879 
       14.86        86.76        19.27         8.88        63.72        22.92 
TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5887 TCGA-BQ-5888 
       21.63        40.83        26.04        30.28        25.35        13.25 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7044 TCGA-BQ-7048 
        0.95        11.97         7.92         2.76       123.62        93.34 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7055 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7061 
       61.28        49.84        26.27        20.12        11.28         7.17 
TCGA-DZ-6131 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY TCGA-F9-A97G TCGA-G7-6789 
       79.86        10.68        13.08         1.18         0.43         4.01 
TCGA-G7-6793 TCGA-G7-7501 TCGA-G7-A8LC TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-7773 
       11.05        13.68        17.33        16.90       194.79        12.92 
TCGA-GL-7966 TCGA-GL-A4EM TCGA-HE-A5NK TCGA-IA-A40Y TCGA-IZ-8195 TCGA-J7-8537 
        3.68         1.05        73.25         2.04        22.26         0.13 
TCGA-MH-A560 TCGA-MH-A855 TCGA-MH-A857 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       30.38        12.13        21.44        42.94         6.61        92.58 
TCGA-P4-AAVO TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UN-AAZ9 
       78.90        12.85        14.07        11.93        38.63        18.02 
TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-AB4C TCGA-Y8-A896 TCGA-Y8-A8S1 
       21.93        86.27        52.11        29.00        18.64        13.28 

subtype1 subtype2 subtype3 subtype4 
    3.81     0.10     0.46     0.13 
subtype1 subtype2 subtype3 subtype4 
  129.86    87.22   100.27   194.79 
subtype1 subtype2 subtype3 subtype4 
  30.480   19.230   25.640   18.955 
[1] "3.8 - 129.9 (30.5)" "0.1 - 87.2 (19.2)"  "0.5 - 100.3 (25.6)"
[4] "0.1 - 194.8 (19.0)"
D5V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      26        2         0        2
  subtype2      74        5         7        2
  subtype3      37        8         9        0
  subtype4      31        6        33       10
D5V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         26       74       37       31
  STAGE II         2        5        8        6
  STAGE III        0        7        9       33
  STAGE IV         2        2        0       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       T1 T2 T3+T4
  subtype1 27  2     2
  subtype2 76 11     6
  subtype3 39  7     9
  subtype4 35  9    39
D5V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          27       76       39       35
  T2           2       11        7        9
  T3+T4        2        6        9       39
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1  4  1  1
  subtype2 12  1  0
  subtype3 13  2  0
  subtype4 16 18  3
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0        4       12       13       16
  N1        1        1        2       18
  N2        1        0        0        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 13  1
  subtype2 27  1
  subtype3 17  0
  subtype4 34  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   13    1
  subtype2   27    1
  subtype3   17    0
  subtype4   34    7
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       13       27       17       34
  1        1        1        0        7
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1  4 28
  subtype2 18 76
  subtype3  9 49
  subtype4 41 45
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   28
  subtype2   18   76
  subtype3    9   49
  subtype4   41   45
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        4       18        9       41
  MALE         28       76       49       45
[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, continuous
D5V9, continuous
D5V10, continuous
[1] "Remove cluster labels:" "subtype1"              
clus
subtype1 subtype2 subtype3 subtype4 
       2       23       11       16 
 [1] "subtype2" "subtype2" "subtype3" "subtype3" "subtype4" "subtype4"
 [7] "subtype4" "subtype2" "subtype4" "subtype3" "subtype4" "subtype4"
[13] "subtype2" "subtype2" "subtype2" "subtype4" "subtype2" "subtype3"
[19] "subtype4" "subtype4" "subtype2" "subtype4" "subtype2" "subtype4"
[25] "subtype2" "subtype3" "subtype2" "subtype2" "subtype3" "subtype3"
[31] "subtype2" "subtype4" "subtype2" "subtype2" "subtype2" "subtype2"
[37] "subtype4" "subtype2" "subtype2" "subtype3" "subtype3" "subtype2"
[43] "subtype4" "subtype2" "subtype3" "subtype4" "subtype2" "subtype4"
[49] "subtype2" "subtype3"
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         8
  subtype2                                1     0                        19
  subtype3                                1     0                        10
  subtype4                                0     4                        23
          vv
clus       WHITE
  subtype1    20
  subtype2    68
  subtype3    45
  subtype4    55
D5V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   1        0        0        4
  BLACK OR AFRICAN AMERICAN               8       19       10       23
  WHITE                                  20       68       45       55
[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"
D5V12, binary
          cls
clus        0  1
  subtype1  1 24
  subtype2  5 82
  subtype3  2 49
  subtype4  4 66
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   24
  subtype2    5   82
  subtype3    2   49
  subtype4    4   66
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        5        2        4
  NOT HISPANIC OR LATINO       24       82       49       66
[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  89  14
  subtype2 105   8
  subtype3  29  12
subtype1 subtype2 subtype3 
     103      113       41 
subtype1 subtype2 subtype3 
      14        8       12 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J8 TCGA-2Z-A9JD TCGA-2Z-A9JG 
        7.04        59.01       100.27        67.30        34.85        54.64 
TCGA-2Z-A9JI TCGA-2Z-A9JK TCGA-2Z-A9JO TCGA-2Z-A9JP TCGA-2Z-A9JT TCGA-4A-A93X 
       51.52        38.99        31.20        29.36        22.49        12.82 
TCGA-4A-A93Y TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7585 TCGA-A4-8098 TCGA-A4-8310 
       11.57        18.21        61.05        35.18        29.46        25.64 
TCGA-A4-8517 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5Y0 TCGA-A4-A5Y1 
       19.63        19.73        12.46         8.48         8.28        12.99 
TCGA-AL-3466 TCGA-AL-3473 TCGA-AL-A5DJ TCGA-B1-5398 TCGA-B1-A47O TCGA-B1-A655 
        9.63        25.08        49.25        19.56        16.87        16.77 
TCGA-B1-A656 TCGA-B3-4103 TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A5W8 TCGA-B9-A5W9 
        0.46        30.58         0.46         2.10         6.81         0.16 
TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5876 TCGA-BQ-5878 TCGA-BQ-5880 
       14.86        12.30        86.76        19.27        63.72        43.20 
TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5887 
       47.80        21.63        26.04        30.28        26.04        25.35 
TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7048 
        7.66         0.95        11.97       123.62        96.92        93.34 
TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       61.28        49.84        20.12        11.28         7.63         7.04 
TCGA-BQ-7061 TCGA-BQ-7062 TCGA-DW-7838 TCGA-DW-7963 TCGA-DZ-6131 TCGA-DZ-6134 
        7.17         3.81        24.46        40.77        79.86        61.02 
TCGA-F9-A97G TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A4EM 
        0.43        34.82        13.68        16.90       194.79         1.05 
TCGA-GL-A59T TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NF TCGA-IA-A40X TCGA-IA-A40Y 
       17.95        11.21         4.60        68.12        19.99         2.04 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-A6M8 TCGA-J7-8537 TCGA-KV-A6GD 
       85.78        88.24        22.26        16.34         0.13        11.97 
TCGA-MH-A560 TCGA-MH-A855 TCGA-P4-A5E6 TCGA-P4-A5EB TCGA-P4-AAVK TCGA-P4-AAVM 
       30.38        12.13        99.78        84.95        52.27        50.60 
TCGA-P4-AAVO TCGA-Q2-A5QZ TCGA-SX-A71V TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SP 
       78.90        14.07        28.80        11.93        38.63        16.31 
TCGA-UZ-A9PM TCGA-UZ-A9PQ TCGA-UZ-A9PS TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A8RZ 
       14.83        86.27        52.11        26.01        29.00         6.74 
TCGA-Y8-A8S1 
       13.28 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JL 
       75.55        58.22        56.91         4.57        56.81        26.43 
TCGA-2Z-A9JM TCGA-2Z-A9JQ TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-4A-A93W TCGA-A4-7583 
       30.71        25.58         5.29        16.18         0.13         0.10 
TCGA-A4-7732 TCGA-A4-7734 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8311 TCGA-A4-8515 
       19.13         0.89        16.64        30.48        23.97        23.31 
TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP 
        0.76        14.33        16.96        16.31        15.75        12.46 
TCGA-AL-3467 TCGA-AL-3468 TCGA-AL-3471 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-7332 
       58.45        76.64        13.55        30.35         2.20         7.33 
TCGA-B1-A47M TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 TCGA-B3-3925 TCGA-B3-A6W5 
       21.67        24.56         3.55         6.58        33.83        10.16 
TCGA-B9-4113 TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-5156 
       50.50        28.18        26.40         1.15        15.12        43.99 
TCGA-B9-7268 TCGA-B9-A5W7 TCGA-B9-A8YH TCGA-BQ-7045 TCGA-BQ-7051 TCGA-DW-5560 
       22.06        19.23        17.49        48.26        50.40        11.61 
TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
       13.61       129.86        35.93        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7842 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 
       14.63         3.02        51.19        54.90        34.19        19.00 
TCGA-EV-5903 TCGA-F9-A7VF TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-6797 
       24.89         2.40        51.78        48.62        39.25        25.15 
TCGA-G7-7502 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LE TCGA-GL-8500 TCGA-GL-A59R 
       25.84         6.38        17.98        80.65        27.65        12.43 
TCGA-GL-A9DC TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NJ TCGA-HE-A5NL TCGA-IA-A40U 
        0.89        13.41        11.84        56.75         5.49        16.80 
TCGA-IA-A83W TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W 
       67.17        21.34        12.36        29.10        11.41        34.29 
TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 TCGA-MH-A854 TCGA-O9-A75Z TCGA-PJ-A5Z9 
       27.78        27.65        20.25         0.36        15.48        17.75 
TCGA-SX-A71R TCGA-SX-A71S TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN 
       47.90        47.44        33.04        26.89        27.06        19.00 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PP 
       41.62        26.47        48.30        43.76        60.03         0.53 
TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX TCGA-UZ-A9Q0 TCGA-Y8-A894 
       38.86        30.67        25.68        27.39        12.99        18.64 
TCGA-Y8-A895 TCGA-Y8-A897 TCGA-Y8-A898 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       15.91        18.05        15.62        25.28         6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JN TCGA-A4-7287 TCGA-A4-7915 TCGA-A4-8312 
       75.42        35.67        24.33        19.63         0.23        23.28 
TCGA-AL-7173 TCGA-B3-3926 TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-4116 TCGA-BQ-5877 
       44.61        10.09        34.49        12.46        20.61         8.88 
TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 
       22.92        40.83        13.25        10.88         7.92         2.76 
TCGA-BQ-7049 TCGA-BQ-7055 TCGA-DZ-6132 TCGA-F9-A4JJ TCGA-F9-A7Q0 TCGA-F9-A8NY 
       44.84        26.27        80.88        10.68        13.08         1.18 
TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-A8LC TCGA-GL-7773 TCGA-GL-7966 TCGA-HE-A5NK 
        4.01        11.05        17.33        12.92         3.68        73.25 
TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-A5ED 
       25.97        21.44        87.22        42.94         6.61        92.58 
TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-UN-AAZ9 TCGA-UZ-A9PN TCGA-Y8-A896 
       16.01        12.85        18.02        21.93        18.64 

subtype1 subtype2 subtype3 
    0.13     0.10     0.23 
subtype1 subtype2 subtype3 
  194.79   129.86    92.58 
subtype1 subtype2 subtype3 
   22.26    22.06    18.64 
[1] "0.1 - 194.8 (22.3)" "0.1 - 129.9 (22.1)" "0.2 - 92.6 (18.6)" 
D6V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      53       10        32        4
  subtype2      94        8         8        2
  subtype3      21        3         9        8
D6V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         53       94       21
  STAGE II        10        8        3
  STAGE III       32        8        9
  STAGE IV         4        2        8
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 56 11    33
  subtype2 98 14     7
  subtype3 23  4    16
D6V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          56       98       23
  T2          11       14        4
  T3+T4       33        7       16
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 23 12  1
  subtype2 19  0  0
  subtype3  3 10  3
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       23       19        3
  N1       12        0       10
  N2        1        0        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus        0  1
  subtype1 38  3
  subtype2 36  1
  subtype3 17  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   38    3
  subtype2   36    1
  subtype3   17    5
   clus
vv  subtype1 subtype2 subtype3
  0       38       36       17
  1        3        1        5
[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"
D6V7, binary
          cls
clus        0  1
  subtype1 27 80
  subtype2 21 98
  subtype3 24 20
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   27   80
  subtype2   21   98
  subtype3   24   20
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       27       21       24
  MALE         80       98       20
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, continuous
D6V9, continuous
D6V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     2                        23
  subtype2                                1     1                        25
  subtype3                                0     2                        12
          vv
clus       WHITE
  subtype1    78
  subtype2    84
  subtype3    26
D6V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   2        1        2
  BLACK OR AFRICAN AMERICAN              23       25       12
  WHITE                                  78       84       26
[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"
D6V12, binary
          cls
clus         0   1
  subtype1   4  88
  subtype2   4 103
  subtype3   4  30
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    4   88
  subtype2    4  103
  subtype3    4   30
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            4        4        4
  NOT HISPANIC OR LATINO       88      103       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"

Clustering(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 69  8
  subtype2 85  8
  subtype3 70 18
subtype1 subtype2 subtype3 
      77       93       88 
subtype1 subtype2 subtype3 
       8        8       18 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9J8 TCGA-2Z-A9JD 
        7.04        59.01       100.27        56.91        67.30        34.85 
TCGA-2Z-A9JK TCGA-2Z-A9JL TCGA-4A-A93X TCGA-A4-7585 TCGA-A4-7997 TCGA-A4-8098 
       38.99        26.43        12.82        35.18        30.48        29.46 
TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8518 TCGA-A4-A48D TCGA-A4-A57E TCGA-A4-A5XZ 
       25.64         0.76        19.73        12.46         8.48        15.75 
TCGA-A4-A5Y0 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-7332 TCGA-B1-A655 TCGA-B3-3925 
        8.28        25.08        19.56         7.33        16.77        33.83 
TCGA-B9-4114 TCGA-B9-4115 TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A44B TCGA-B9-A5W8 
       28.18        26.40         0.46        43.99         2.10         6.81 
TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5881 
       17.49        12.30        86.76        63.72        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       21.63        26.04        26.04         7.66         0.95        11.97 
TCGA-BQ-7050 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7062 TCGA-DW-7837 
       61.28        50.40        11.28         7.63         3.81        37.55 
TCGA-DW-7840 TCGA-DW-7841 TCGA-DW-7963 TCGA-DZ-6135 TCGA-F9-A97G TCGA-G7-6790 
        3.75        14.63        40.77        54.90         0.43        51.78 
TCGA-G7-6792 TCGA-G7-7501 TCGA-GL-A9DD TCGA-GL-A9DE TCGA-HE-A5NL TCGA-IA-A83S 
       48.62        13.68        11.21         4.60         5.49        85.78 
TCGA-IA-A83W TCGA-IZ-A6M8 TCGA-KV-A74V TCGA-MH-A560 TCGA-MH-A855 TCGA-P4-A5E6 
       67.17        16.34        11.41        30.38        12.13        99.78 
TCGA-P4-A5EB TCGA-P4-AAVM TCGA-PJ-A8JU TCGA-SX-A7SO TCGA-SX-A7SP TCGA-UZ-A9PM 
       84.95        50.60        12.49        38.63        16.31        14.83 
TCGA-UZ-A9PR TCGA-UZ-A9Q0 TCGA-WN-A9G9 TCGA-Y8-A897 TCGA-Y8-A8RZ 
       38.86        12.99        26.01        18.05         6.74 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J7 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI 
       75.55        58.22         4.57        56.81        54.64        51.52 
TCGA-2Z-A9JP TCGA-2Z-A9JR TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7286 TCGA-A4-7288 
       29.36         5.29        16.18        22.49        18.21        61.05 
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
        0.10        19.13        16.64        23.97        23.31        19.63 
TCGA-A4-8630 TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A6HP TCGA-AL-3467 TCGA-AL-3468 
       14.33        16.96        16.31        12.46        58.45        76.64 
TCGA-AL-3471 TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47O TCGA-B3-3926 TCGA-B3-A6W5 
       13.55        49.25         2.20        16.87        10.09        10.16 
TCGA-B9-4113 TCGA-B9-4116 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 TCGA-B9-A5W7 
       50.50        20.61         1.15        15.12        22.06        19.23 
TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5885 TCGA-BQ-5888 TCGA-BQ-5893 TCGA-BQ-7044 
        0.16        14.86        30.28        13.25         7.92       123.62 
TCGA-BQ-7046 TCGA-BQ-7055 TCGA-DW-7839 TCGA-DZ-6133 TCGA-EV-5902 TCGA-F9-A7Q0 
       96.92        26.27        13.78        51.19        19.00        13.08 
TCGA-F9-A7VF TCGA-F9-A8NY TCGA-G7-6795 TCGA-G7-6797 TCGA-G7-A8LB TCGA-G7-A8LC 
        2.40         1.18        39.25        25.15        17.98        17.33 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59R TCGA-GL-A59T TCGA-GL-A9DC TCGA-HE-A5NF 
       12.92        27.65        12.43        17.95         0.89        68.12 
TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NK TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       13.41        11.84        73.25        16.80        19.99         2.04 
TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-MH-A55W TCGA-MH-A55Z TCGA-MH-A561 TCGA-MH-A562 
       12.36        29.10        34.29        27.78        27.65        20.25 
TCGA-MH-A854 TCGA-P4-A5ED TCGA-P4-AAVO TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U 
        0.36        92.58        78.90        17.75        47.90        33.04 
TCGA-SX-A71V TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS 
       28.80        27.06        19.00        41.62        26.47        48.30 
TCGA-UN-AAZ9 TCGA-UZ-A9PS TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-WN-AB4C TCGA-Y8-A894 
       18.02        52.11        30.67        25.68        29.00        18.64 
TCGA-Y8-A896 TCGA-Y8-A8RY TCGA-Y8-A8S0 
       18.64        25.28         6.02 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ 
       75.42        35.67        30.71        24.33        31.20        25.58 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8312 
        0.13        11.57        19.63         0.89         0.23        23.28 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-A47M TCGA-B1-A47N 
       12.99         9.63        30.35        44.61        21.67        24.56 
TCGA-B1-A654 TCGA-B1-A656 TCGA-B1-A657 TCGA-B3-4103 TCGA-B3-4104 TCGA-B3-8121 
        3.55         0.46         6.58        30.58        34.49        12.46 
TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5889 
       19.27         8.88        22.92        40.83        25.35        10.88 
TCGA-BQ-5894 TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7056 
        2.76        48.26        93.34        44.84        49.84        20.12 
TCGA-BQ-7060 TCGA-BQ-7061 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7834 TCGA-DW-7836 
        7.04         7.17        11.61        13.61       129.86        35.93 
TCGA-DW-7838 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 
       24.46         3.02        79.86        80.88        61.02        34.19 
TCGA-EV-5903 TCGA-F9-A4JJ TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7502 
       24.89        10.68         4.01        11.05        34.82        25.84 
TCGA-G7-A4TM TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM 
        6.38        16.90        80.65       194.79         3.68         1.05 
TCGA-HE-A5NJ TCGA-IA-A83T TCGA-IZ-8195 TCGA-IZ-8196 TCGA-J7-8537 TCGA-KV-A6GD 
       56.75        88.24        22.26        21.34         0.13        11.97 
TCGA-MH-A856 TCGA-MH-A857 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-P4-A5E8 TCGA-P4-A5EA 
       25.97        21.44        15.48        87.22        42.94         6.61 
TCGA-P4-AAVK TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S TCGA-SX-A71W 
       52.27        16.01        12.85        14.07        47.44        26.89 
TCGA-SX-A7SM TCGA-SX-A7SU TCGA-UZ-A9PK TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ 
       11.93        43.76        60.03        21.93         0.53        86.27 
TCGA-UZ-A9PX TCGA-Y8-A895 TCGA-Y8-A898 TCGA-Y8-A8S1 
       27.39        15.91        15.62        13.28 

subtype1 subtype2 subtype3 
    0.43     0.10     0.13 
subtype1 subtype2 subtype3 
  100.27   123.62   194.79 
subtype1 subtype2 subtype3 
  21.630   19.630   22.095 
[1] "0.4 - 100.3 (21.6)" "0.1 - 123.6 (19.6)" "0.1 - 194.8 (22.1)"
D7V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      45       11        18        1
  subtype2      69        5        14        4
  subtype3      55        5        17        9
D7V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         45       69       55
  STAGE II        11        5        5
  STAGE III       18       14       17
  STAGE IV         1        4        9
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 47 13    17
  subtype2 73 10    16
  subtype3 58  6    23
D7V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          47       73       58
  T2          13       10        6
  T3+T4       17       16       23
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 19  4  1
  subtype2 13  4  0
  subtype3 13 14  3
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       19       13       13
  N1        4        4       14
  N2        1        0        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 28  1
  subtype2 27  3
  subtype3 36  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    1
  subtype2   27    3
  subtype3   36    5
   clus
vv  subtype1 subtype2 subtype3
  0       28       27       36
  1        1        3        5
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 16 64
  subtype2 27 73
  subtype3 30 61
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   64
  subtype2   27   73
  subtype3   30   61
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       16       27       30
  MALE         64       73       61
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, continuous
D7V9, continuous
D7V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                        23
  subtype2                                1     2                        15
  subtype3                                1     2                        22
          vv
clus       WHITE
  subtype1    53
  subtype2    75
  subtype3    61
D7V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1
  ASIAN                                   1        2        2
  BLACK OR AFRICAN AMERICAN              23       15       22
  WHITE                                  53       75       61
[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"
D7V12, binary
          cls
clus        0  1
  subtype1  3 68
  subtype2  3 83
  subtype3  6 71
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   68
  subtype2    3   83
  subtype3    6   71
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        3        6
  NOT HISPANIC OR LATINO       68       83       71
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2       0  1
  subtype1 40  9
  subtype2 52  3
  subtype3 67  7
  subtype4 65 15
subtype1 subtype2 subtype3 subtype4 
      49       55       74       80 
subtype1 subtype2 subtype3 subtype4 
       9        3        7       15 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J8 TCGA-2Z-A9JD TCGA-2Z-A9JK 
        7.04        59.01       100.27        67.30        34.85        38.99 
TCGA-2Z-A9JL TCGA-A4-7585 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8518 TCGA-A4-A5Y0 
       26.43        35.18        30.48        29.46        19.73         8.28 
TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 TCGA-B9-5156 
       12.99         9.63        25.08        19.56        33.83        43.99 
TCGA-B9-A5W8 TCGA-BQ-5878 TCGA-BQ-5880 TCGA-BQ-5885 TCGA-BQ-5886 TCGA-BQ-5890 
        6.81        63.72        43.20        30.28        26.04         7.66 
TCGA-BQ-5891 TCGA-BQ-5892 TCGA-BQ-7051 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7061 
        0.95        11.97        50.40        11.28         7.63         7.17 
TCGA-DZ-6135 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-7501 TCGA-GL-A9DD 
       54.90         0.43        51.78        48.62        13.68        11.21 
TCGA-IA-A83S TCGA-IA-A83T TCGA-IA-A83W TCGA-MH-A55Z TCGA-MH-A562 TCGA-MH-A855 
       85.78        88.24        67.17        27.78        20.25        12.13 
TCGA-P4-A5EB TCGA-P4-AAVM TCGA-SX-A7SM TCGA-SX-A7SO TCGA-UZ-A9PM TCGA-WN-A9G9 
       84.95        50.60        11.93        38.63        14.83        26.01 
TCGA-Y8-A8RZ 
        6.74 

$subtype2
TCGA-2Z-A9J1 TCGA-2Z-A9JE TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JP TCGA-2Z-A9JR 
       75.55        56.81        54.64        51.52        29.36         5.29 
TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-8310 TCGA-A4-8516 TCGA-A4-8630 TCGA-A4-A48D 
       12.82        18.21        25.64         0.76        14.33        12.46 
TCGA-A4-A57E TCGA-AL-3467 TCGA-B1-7332 TCGA-B1-A655 TCGA-B9-4114 TCGA-B9-4115 
        8.48        58.45         7.33        16.77        28.18        26.40 
TCGA-B9-4116 TCGA-B9-4117 TCGA-B9-A44B TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5875 
       20.61         0.46         2.10        17.49        12.30        86.76 
TCGA-BQ-5876 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7050 
       19.27        47.80        21.63       123.62        96.92        61.28 
TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-5561 TCGA-DW-7837 TCGA-DW-7839 TCGA-DW-7840 
        7.04         3.81        13.61        37.55        13.78         3.75 
TCGA-DW-7841 TCGA-DW-7963 TCGA-EV-5902 TCGA-G7-A4TM TCGA-GL-A9DC TCGA-GL-A9DE 
       14.63        40.77        19.00         6.38         0.89         4.60 
TCGA-HE-A5NK TCGA-IA-A40X TCGA-IZ-A6M8 TCGA-MH-A560 TCGA-O9-A75Z TCGA-P4-AAVK 
       73.25        19.99        16.34        30.38        15.48        52.27 
TCGA-P4-AAVO TCGA-PJ-A8JU TCGA-SX-A7SL TCGA-SX-A7SP TCGA-UZ-A9PR TCGA-UZ-A9PS 
       78.90        12.49        27.06        16.31        38.86        52.11 
TCGA-UZ-A9PX 
       27.39 

$subtype3
TCGA-2Z-A9J3 TCGA-2Z-A9J6 TCGA-2Z-A9J7 TCGA-2Z-A9JS TCGA-2Z-A9JT TCGA-A4-7288 
       58.22        56.91         4.57        16.18        22.49        61.05 
TCGA-A4-7583 TCGA-A4-7732 TCGA-A4-7996 TCGA-A4-8311 TCGA-A4-8515 TCGA-A4-8517 
        0.10        19.13        16.64        23.97        23.31        19.63 
TCGA-A4-A4ZT TCGA-A4-A5DU TCGA-A4-A5XZ TCGA-A4-A6HP TCGA-AL-3468 TCGA-AL-3471 
       16.96        16.31        15.75        12.46        76.64        13.55 
TCGA-AL-A5DJ TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A47O TCGA-B1-A657 TCGA-B3-3926 
       49.25         2.20        24.56        16.87         6.58        10.09 
TCGA-B3-4103 TCGA-B3-A6W5 TCGA-B9-4113 TCGA-B9-4617 TCGA-B9-5155 TCGA-B9-7268 
       30.58        10.16        50.50         1.15        15.12        22.06 
TCGA-B9-A5W7 TCGA-BQ-5888 TCGA-BQ-7055 TCGA-DZ-6133 TCGA-F9-A7Q0 TCGA-F9-A7VF 
       19.23        13.25        26.27        51.19        13.08         2.40 
TCGA-G7-6796 TCGA-G7-6797 TCGA-G7-7502 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-8500 
       34.82        25.15        25.84        17.98        17.33        27.65 
TCGA-GL-A59R TCGA-GL-A59T TCGA-HE-A5NF TCGA-HE-A5NH TCGA-HE-A5NI TCGA-HE-A5NL 
       12.43        17.95        68.12        13.41        11.84         5.49 
TCGA-IA-A40U TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A55W TCGA-MH-A854 
       16.80        12.36        29.10        11.41        34.29         0.36 
TCGA-P4-A5E6 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71V TCGA-SX-A7SN 
       99.78        17.75        47.90        33.04        28.80        19.00 
TCGA-SX-A7SQ TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU TCGA-UN-AAZ9 TCGA-UZ-A9PU 
       41.62        26.47        48.30        43.76        18.02        30.67 
TCGA-UZ-A9PV TCGA-UZ-A9Q0 TCGA-Y8-A894 TCGA-Y8-A895 TCGA-Y8-A896 TCGA-Y8-A897 
       25.68        12.99        18.64        15.91        18.64        18.05 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$subtype4
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-2Z-A9JQ 
       75.42        35.67        30.71        24.33        31.20        25.58 
TCGA-4A-A93W TCGA-4A-A93Y TCGA-A4-7287 TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-8312 
        0.13        11.57        19.63         0.89         0.23        23.28 
TCGA-AL-3472 TCGA-AL-7173 TCGA-B1-A47M TCGA-B1-A654 TCGA-B1-A656 TCGA-B3-4104 
       30.35        44.61        21.67         3.55         0.46        34.49 
TCGA-B3-8121 TCGA-B9-A5W9 TCGA-B9-A69E TCGA-BQ-5877 TCGA-BQ-5879 TCGA-BQ-5883 
       12.46         0.16        14.86         8.88        22.92        40.83 
TCGA-BQ-5884 TCGA-BQ-5887 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 TCGA-BQ-7045 
       26.04        25.35        10.88         7.92         2.76        48.26 
TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-DW-5560 TCGA-DW-7834 
       93.34        44.84        49.84        20.12        11.61       129.86 
TCGA-DW-7836 TCGA-DW-7838 TCGA-DW-7842 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 
       35.93        24.46         3.02        79.86        80.88        61.02 
TCGA-EV-5901 TCGA-EV-5903 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 
       34.19        24.89        10.68         1.18         4.01        11.05 
TCGA-G7-6795 TCGA-G7-A8LD TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7773 TCGA-GL-7966 
       39.25        16.90        80.65       194.79        12.92         3.68 
TCGA-GL-A4EM TCGA-HE-A5NJ TCGA-IA-A40Y TCGA-IZ-8195 TCGA-IZ-8196 TCGA-J7-8537 
        1.05        56.75         2.04        22.26        21.34         0.13 
TCGA-KV-A6GD TCGA-MH-A561 TCGA-MH-A856 TCGA-MH-A857 TCGA-P4-A5E7 TCGA-P4-A5E8 
       11.97        27.65        25.97        21.44        87.22        42.94 
TCGA-P4-A5EA TCGA-P4-A5ED TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71S 
        6.61        92.58        16.01        12.85        14.07        47.44 
TCGA-SX-A71W TCGA-UZ-A9PK TCGA-UZ-A9PN TCGA-UZ-A9PP TCGA-UZ-A9PQ TCGA-WN-AB4C 
       26.89        60.03        21.93         0.53        86.27        29.00 
TCGA-Y8-A898 TCGA-Y8-A8S1 
       15.62        13.28 

subtype1 subtype2 subtype3 subtype4 
    0.43     0.46     0.10     0.13 
subtype1 subtype2 subtype3 subtype4 
  100.27   123.62    99.78   194.79 
subtype1 subtype2 subtype3 subtype4 
   26.43    19.27    18.64    22.59 
[1] "0.4 - 100.3 (26.4)" "0.5 - 123.6 (19.3)" "0.1 - 99.8 (18.6)" 
[4] "0.1 - 194.8 (22.6)"
D8V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      22       10        14        2
  subtype2      42        2         7        1
  subtype3      58        5         9        2
  subtype4      47        4        19        9
D8V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         22       42       58       47
  STAGE II        10        2        5        4
  STAGE III       14        7        9       19
  STAGE IV         2        1        2        9
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 24  8    15
  subtype2 44  6     8
  subtype3 61  9     7
  subtype4 49  6    26
D8V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          24       44       61       49
  T2           8        6        9        6
  T3+T4       15        8        7       26
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 12  6  1
  subtype2  9  0  0
  subtype3 12  2  0
  subtype4 12 14  3
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       12        9       12       12
  N1        6        0        2       14
  N2        1        0        0        3
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus        0  1
  subtype1 21  2
  subtype2 16  1
  subtype3 23  1
  subtype4 31  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    2
  subtype2   16    1
  subtype3   23    1
  subtype4   31    5
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       21       16       23       31
  1        2        1        1        5
[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"
D8V7, binary
          cls
clus        0  1
  subtype1  7 43
  subtype2 15 46
  subtype3 17 60
  subtype4 34 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    7   43
  subtype2   15   46
  subtype3   17   60
  subtype4   34   49
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE        7       15       17       34
  MALE         43       46       60       49
[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"
D8V8, continuous
D8V9, continuous
D8V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                0     1                         9
  subtype2                                1     0                        21
  subtype3                                1     1                        10
  subtype4                                0     3                        20
          vv
clus       WHITE
  subtype1    39
  subtype2    35
  subtype3    59
  subtype4    56
D8V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        0        1        1        0
  ASIAN                                   1        0        1        3
  BLACK OR AFRICAN AMERICAN               9       21       10       20
  WHITE                                  39       35       59       56
[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"
D8V12, binary
          cls
clus        0  1
  subtype1  1 44
  subtype2  3 49
  subtype3  2 66
  subtype4  6 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   44
  subtype2    3   49
  subtype3    2   66
  subtype4    6   63
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        3        2        6
  NOT HISPANIC OR LATINO       44       49       66       63
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 55  6
  subtype2 71  3
  subtype3 43 21
subtype1 subtype2 subtype3 
      61       74       64 
subtype1 subtype2 subtype3 
       6        3       21 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J2 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JD 
        7.04        75.55        59.01       100.27        56.91        34.85 
TCGA-2Z-A9JI TCGA-2Z-A9JO TCGA-2Z-A9JT TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7288 
       51.52        31.20        22.49        12.82        18.21        61.05 
TCGA-A4-7585 TCGA-A4-7996 TCGA-A4-7997 TCGA-A4-8098 TCGA-A4-8517 TCGA-A4-8518 
       35.18        16.64        30.48        29.46        19.63        19.73 
TCGA-A4-A57E TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3473 TCGA-B1-5398 TCGA-B1-A47O 
        8.48        15.75         8.28        25.08        19.56        16.87 
TCGA-B9-4117 TCGA-B9-5156 TCGA-B9-A69E TCGA-B9-A8YI TCGA-BQ-5880 TCGA-BQ-5881 
        0.46        43.99        14.86        12.30        43.20        47.80 
TCGA-BQ-5882 TCGA-BQ-5884 TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-5892 
       21.63        26.04        26.04         7.66         0.95        11.97 
TCGA-BQ-7046 TCGA-BQ-7050 TCGA-BQ-7055 TCGA-BQ-7058 TCGA-BQ-7059 TCGA-BQ-7060 
       96.92        61.28        26.27        11.28         7.63         7.04 
TCGA-BQ-7062 TCGA-DZ-6131 TCGA-F9-A97G TCGA-G7-6790 TCGA-G7-6796 TCGA-G7-7501 
        3.81        79.86         0.43        51.78        34.82        13.68 
TCGA-GL-A9DD TCGA-GL-A9DE TCGA-IA-A40X TCGA-MH-A855 TCGA-P4-AAVK TCGA-P4-AAVM 
       11.21         4.60        19.99        12.13        52.27        50.60 
TCGA-SX-A7SO TCGA-SX-A7SP TCGA-WN-A9G9 TCGA-WN-AB4C TCGA-Y8-A897 TCGA-Y8-A8RZ 
       38.63        16.31        26.01        29.00        18.05         6.74 
TCGA-Y8-A8S1 
       13.28 

$subtype2
TCGA-2Z-A9J3 TCGA-2Z-A9J9 TCGA-2Z-A9JG TCGA-2Z-A9JL TCGA-2Z-A9JP TCGA-2Z-A9JQ 
       58.22        75.42        54.64        26.43        29.36        25.58 
TCGA-2Z-A9JR TCGA-4A-A93W TCGA-A4-8310 TCGA-A4-8312 TCGA-A4-8515 TCGA-A4-8516 
        5.29         0.13        25.64        23.28        23.31         0.76 
TCGA-A4-8630 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47N TCGA-B1-A654 TCGA-B1-A657 
       14.33        30.35         2.20        24.56         3.55         6.58 
TCGA-B3-3925 TCGA-B9-4115 TCGA-B9-5155 TCGA-B9-A5W9 TCGA-B9-A8YH TCGA-BQ-5878 
       33.83        26.40        15.12         0.16        17.49        63.72 
TCGA-BQ-7044 TCGA-BQ-7051 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 TCGA-DW-7837 
      123.62        50.40        11.61        13.61        35.93        37.55 
TCGA-DW-7839 TCGA-DW-7840 TCGA-DW-7842 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5902 
       13.78         3.75         3.02        51.19        54.90        19.00 
TCGA-F9-A7Q0 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-A4TM TCGA-G7-A8LB TCGA-G7-A8LC 
       13.08        48.62        39.25         6.38        17.98        17.33 
TCGA-GL-7773 TCGA-GL-8500 TCGA-GL-A59T TCGA-GL-A9DC TCGA-HE-A5NJ TCGA-IA-A40U 
       12.92        27.65        17.95         0.89        56.75        16.80 
TCGA-IA-A40Y TCGA-IZ-8196 TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A854 
        2.04        21.34        12.36        29.10        11.41         0.36 
TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E6 TCGA-PJ-A5Z9 TCGA-SX-A71R TCGA-SX-A71S 
       25.97        15.48        99.78        17.75        47.90        47.44 
TCGA-SX-A71U TCGA-SX-A7SL TCGA-SX-A7SN TCGA-SX-A7SR TCGA-SX-A7SS TCGA-SX-A7SU 
       33.04        27.06        19.00        26.47        48.30        43.76 
TCGA-UZ-A9PK TCGA-UZ-A9PP TCGA-UZ-A9PR TCGA-UZ-A9PU TCGA-UZ-A9PV TCGA-UZ-A9PX 
       60.03         0.53        38.86        30.67        25.68        27.39 
TCGA-Y8-A8RY TCGA-Y8-A8S0 
       25.28         6.02 

$subtype3
TCGA-2Z-A9JJ TCGA-2Z-A9JK TCGA-2Z-A9JM TCGA-2Z-A9JN TCGA-4A-A93Y TCGA-A4-7287 
       35.67        38.99        30.71        24.33        11.57        19.63 
TCGA-A4-7734 TCGA-A4-7915 TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-7173 TCGA-B1-A656 
        0.89         0.23        12.99         9.63        44.61         0.46 
TCGA-B3-4104 TCGA-B3-8121 TCGA-B9-A44B TCGA-BQ-5876 TCGA-BQ-5877 TCGA-BQ-5879 
       34.49        12.46         2.10        19.27         8.88        22.92 
TCGA-BQ-5883 TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5893 TCGA-BQ-5894 
       40.83        25.35        13.25        10.88         7.92         2.76 
TCGA-BQ-7045 TCGA-BQ-7048 TCGA-BQ-7049 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7061 
       48.26        93.34        44.84        49.84        20.12         7.17 
TCGA-DW-7834 TCGA-DW-7838 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5901 TCGA-EV-5903 
      129.86        24.46        80.88        61.02        34.19        24.89 
TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-7502 TCGA-G7-A8LD 
       10.68         1.18         4.01        11.05        25.84        16.90 
TCGA-G7-A8LE TCGA-GL-6846 TCGA-GL-7966 TCGA-GL-A4EM TCGA-IA-A83S TCGA-IA-A83T 
       80.65       194.79         3.68         1.05        85.78        88.24 
TCGA-IA-A83W TCGA-IZ-8195 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A857 TCGA-P4-A5E7 
       67.17        22.26         0.13        11.97        21.44        87.22 
TCGA-P4-A5E8 TCGA-P4-A5EA TCGA-P4-AAVL TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A71W 
       42.94         6.61        16.01        12.85        14.07        26.89 
TCGA-SX-A7SM TCGA-UZ-A9PN TCGA-UZ-A9PQ TCGA-Y8-A898 
       11.93        21.93        86.27        15.62 

subtype1 subtype2 subtype3 
    0.43     0.13     0.13 
subtype1 subtype2 subtype3 
  100.27   123.62   194.79 
subtype1 subtype2 subtype3 
   19.99    24.92    20.78 
[1] "0.4 - 100.3 (20.0)" "0.1 - 123.6 (24.9)" "0.1 - 194.8 (20.8)"
D9V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      37        5        13        1
  subtype2      62        4        10        1
  subtype3      29        6        18       11
D9V3, multiclass
           clus
vv          subtype1 subtype2 subtype3
  STAGE I         37       62       29
  STAGE II         5        4        6
  STAGE III       13       10       18
  STAGE IV         1        1       11
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3+T4
  subtype1 39  7    14
  subtype2 64  6     9
  subtype3 31  5    26
D9V4, multiclass
       clus
vv      subtype1 subtype2 subtype3
  T1          39       64       31
  T2           7        6        5
  T3+T4       14        9       26
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 17  2  1
  subtype2 12  3  0
  subtype3  8 16  3
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       17       12        8
  N1        2        3       16
  N2        1        0        3
[1] 3 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus        0  1
  subtype1 23  1
  subtype2 24  0
  subtype3 26  7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   23    1
  subtype2   24    0
  subtype3   26    7
   clus
vv  subtype1 subtype2 subtype3
  0       23       24       26
  1        1        0        7
[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 17 46
  subtype2 13 66
  subtype3 28 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   46
  subtype2   13   66
  subtype3   28   38
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       17       13       28
  MALE         46       66       38
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, continuous
D9V9, continuous
D9V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                1     1                        10
  subtype2                                1     2                        14
  subtype3                                0     2                        15
          vv
clus       WHITE
  subtype1    49
  subtype2    58
  subtype3    46
D9V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3
  AMERICAN INDIAN OR ALASKA NATIVE        1        1        0
  ASIAN                                   1        2        2
  BLACK OR AFRICAN AMERICAN              10       14       15
  WHITE                                  49       58       46
[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"
D9V12, binary
          cls
clus        0  1
  subtype1  3 51
  subtype2  4 67
  subtype3  3 50
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   51
  subtype2    4   67
  subtype3    3   50
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        4        3
  NOT HISPANIC OR LATINO       51       67       50
[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 83  4
  subtype2 50 20
  subtype3  7  6
  subtype4 29  0
subtype1 subtype2 subtype3 subtype4 
      87       70       13       29 
subtype1 subtype2 subtype3 subtype4 
       4       20        6        0 
$subtype1
TCGA-2K-A9WE TCGA-2Z-A9J1 TCGA-2Z-A9J3 TCGA-2Z-A9J5 TCGA-2Z-A9J6 TCGA-2Z-A9JD 
        7.04        75.55        58.22       100.27        56.91        34.85 
TCGA-2Z-A9JG TCGA-2Z-A9JI TCGA-2Z-A9JL TCGA-2Z-A9JM TCGA-2Z-A9JP TCGA-2Z-A9JR 
       54.64        51.52        26.43        30.71        29.36         5.29 
TCGA-2Z-A9JT TCGA-4A-A93X TCGA-A4-7286 TCGA-A4-7288 TCGA-A4-7996 TCGA-A4-7997 
       22.49        12.82        18.21        61.05        16.64        30.48 
TCGA-A4-8098 TCGA-A4-8310 TCGA-A4-8515 TCGA-A4-8516 TCGA-A4-8517 TCGA-A4-8630 
       29.46        25.64        23.31         0.76        19.63        14.33 
TCGA-A4-A5XZ TCGA-A4-A5Y0 TCGA-AL-3473 TCGA-B1-5398 TCGA-B3-3925 TCGA-B9-4115 
       15.75         8.28        25.08        19.56        33.83        26.40 
TCGA-B9-4117 TCGA-B9-5155 TCGA-B9-5156 TCGA-B9-A8YH TCGA-B9-A8YI TCGA-BQ-5878 
        0.46        15.12        43.99        17.49        12.30        63.72 
TCGA-BQ-5886 TCGA-BQ-5890 TCGA-BQ-5891 TCGA-BQ-7044 TCGA-BQ-7046 TCGA-BQ-7051 
       26.04         7.66         0.95       123.62        96.92        50.40 
TCGA-BQ-7055 TCGA-BQ-7059 TCGA-BQ-7060 TCGA-BQ-7062 TCGA-DW-7837 TCGA-DW-7839 
       26.27         7.63         7.04         3.81        37.55        13.78 
TCGA-DW-7840 TCGA-DZ-6133 TCGA-DZ-6135 TCGA-EV-5901 TCGA-EV-5902 TCGA-F9-A7Q0 
        3.75        51.19        54.90        34.19        19.00        13.08 
TCGA-G7-6790 TCGA-G7-6792 TCGA-G7-6795 TCGA-G7-A8LB TCGA-G7-A8LC TCGA-GL-8500 
       51.78        48.62        39.25        17.98        17.33        27.65 
TCGA-GL-A59T TCGA-GL-A9DC TCGA-GL-A9DE TCGA-IA-A40U TCGA-IA-A40X TCGA-IA-A40Y 
       17.95         0.89         4.60        16.80        19.99         2.04 
TCGA-IA-A83W TCGA-IZ-A6M9 TCGA-KV-A6GE TCGA-KV-A74V TCGA-MH-A855 TCGA-P4-A5E6 
       67.17        12.36        29.10        11.41        12.13        99.78 
TCGA-P4-AAVM TCGA-SX-A71R TCGA-SX-A71U TCGA-SX-A71W TCGA-SX-A7SL TCGA-SX-A7SN 
       50.60        47.90        33.04        26.89        27.06        19.00 
TCGA-SX-A7SR TCGA-SX-A7SS TCGA-UZ-A9PK TCGA-UZ-A9PP TCGA-UZ-A9PU TCGA-UZ-A9PV 
       26.47        48.30        60.03         0.53        30.67        25.68 
TCGA-WN-A9G9 TCGA-Y8-A897 TCGA-Y8-A8RZ 
       26.01        18.05         6.74 

$subtype2
TCGA-2Z-A9J2 TCGA-2Z-A9JK TCGA-2Z-A9JN TCGA-2Z-A9JO TCGA-4A-A93Y TCGA-A4-7585 
       59.01        38.99        24.33        31.20        11.57        35.18 
TCGA-A4-8312 TCGA-A4-8518 TCGA-A4-A57E TCGA-A4-A5Y1 TCGA-AL-3466 TCGA-AL-7173 
       23.28        19.73         8.48        12.99         9.63        44.61 
TCGA-B1-A47O TCGA-B1-A656 TCGA-B3-8121 TCGA-B9-A44B TCGA-B9-A69E TCGA-BQ-5876 
       16.87         0.46        12.46         2.10        14.86        19.27 
TCGA-BQ-5877 TCGA-BQ-5880 TCGA-BQ-5881 TCGA-BQ-5882 TCGA-BQ-5883 TCGA-BQ-5884 
        8.88        43.20        47.80        21.63        40.83        26.04 
TCGA-BQ-5887 TCGA-BQ-5888 TCGA-BQ-5889 TCGA-BQ-5892 TCGA-BQ-7045 TCGA-BQ-7048 
       25.35        13.25        10.88        11.97        48.26        93.34 
TCGA-BQ-7049 TCGA-BQ-7050 TCGA-BQ-7053 TCGA-BQ-7056 TCGA-BQ-7058 TCGA-BQ-7061 
       44.84        61.28        49.84        20.12        11.28         7.17 
TCGA-DW-7834 TCGA-DW-7838 TCGA-DZ-6131 TCGA-DZ-6132 TCGA-DZ-6134 TCGA-EV-5903 
      129.86        24.46        79.86        80.88        61.02        24.89 
TCGA-F9-A97G TCGA-G7-6789 TCGA-G7-6793 TCGA-G7-6796 TCGA-G7-7501 TCGA-G7-7502 
        0.43         4.01        11.05        34.82        13.68        25.84 
TCGA-G7-A8LD TCGA-GL-6846 TCGA-GL-A4EM TCGA-GL-A9DD TCGA-IA-A83S TCGA-IA-A83T 
       16.90       194.79         1.05        11.21        85.78        88.24 
TCGA-IZ-8195 TCGA-J7-8537 TCGA-KV-A6GD TCGA-MH-A857 TCGA-P4-AAVK TCGA-P4-AAVL 
       22.26         0.13        11.97        21.44        52.27        16.01 
TCGA-PJ-A5Z8 TCGA-Q2-A5QZ TCGA-SX-A7SM TCGA-SX-A7SO TCGA-SX-A7SP TCGA-UZ-A9PN 
       12.85        14.07        11.93        38.63        16.31        21.93 
TCGA-UZ-A9PQ TCGA-WN-AB4C TCGA-Y8-A898 TCGA-Y8-A8S1 
       86.27        29.00        15.62        13.28 

$subtype3
TCGA-2Z-A9J9 TCGA-2Z-A9JJ TCGA-A4-7287 TCGA-A4-7915 TCGA-B3-4104 TCGA-BQ-5879 
       75.42        35.67        19.63         0.23        34.49        22.92 
TCGA-BQ-5893 TCGA-BQ-5894 TCGA-F9-A4JJ TCGA-F9-A8NY TCGA-GL-7966 TCGA-P4-A5E8 
        7.92         2.76        10.68         1.18         3.68        42.94 
TCGA-P4-A5EA 
        6.61 

$subtype4
TCGA-2Z-A9JQ TCGA-4A-A93W TCGA-A4-7734 TCGA-AL-3472 TCGA-AT-A5NU TCGA-B1-A47N 
       25.58         0.13         0.89        30.35         2.20        24.56 
TCGA-B1-A654 TCGA-B1-A657 TCGA-B9-A5W9 TCGA-DW-5560 TCGA-DW-5561 TCGA-DW-7836 
        3.55         6.58         0.16        11.61        13.61        35.93 
TCGA-DW-7842 TCGA-G7-A4TM TCGA-G7-A8LE TCGA-GL-7773 TCGA-HE-A5NJ TCGA-IZ-8196 
        3.02         6.38        80.65        12.92        56.75        21.34 
TCGA-MH-A854 TCGA-MH-A856 TCGA-O9-A75Z TCGA-P4-A5E7 TCGA-PJ-A5Z9 TCGA-SX-A71S 
        0.36        25.97        15.48        87.22        17.75        47.44 
TCGA-SX-A7SU TCGA-UZ-A9PR TCGA-UZ-A9PX TCGA-Y8-A8RY TCGA-Y8-A8S0 
       43.76        38.86        27.39        25.28         6.02 

subtype1 subtype2 subtype3 subtype4 
    0.46     0.13     0.23     0.13 
subtype1 subtype2 subtype3 subtype4 
  123.62   194.79    75.42    87.22 
subtype1 subtype2 subtype3 subtype4 
  25.680   21.535   10.680   17.750 
[1] "0.5 - 123.6 (25.7)" "0.1 - 194.8 (21.5)" "0.2 - 75.4 (10.7)" 
[4] "0.1 - 87.2 (17.8)" 
D10V2, continuous
          vv
clus       STAGE I STAGE II STAGE III STAGE IV
  subtype1      62        9        14        1
  subtype2      36        3        20        9
  subtype3       3        3         6        3
  subtype4      27        0         1        0
D10V3, multiclass
           clus
vv          subtype1 subtype2 subtype3 subtype4
  STAGE I         62       36        3       27
  STAGE II         9        3        3        0
  STAGE III       14       20        6        1
  STAGE IV         1        9        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"
          vv
clus       T1 T2 T3+T4
  subtype1 65 11    14
  subtype2 37  3    26
  subtype3  4  3     8
  subtype4 28  1     1
D10V4, multiclass
       clus
vv      subtype1 subtype2 subtype3 subtype4
  T1          65       37        4       28
  T2          11        3        3        1
  T3+T4       14       26        8        1
[1] 3 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2
  subtype1 15  3  0
  subtype2 17 11  4
  subtype3  1  7  0
  subtype4  4  0  0
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       15       17        1        4
  N1        3       11        7        0
  N2        0        4        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"
D10V6, binary
          cls
clus        0  1
  subtype1 28  0
  subtype2 29  5
  subtype3  6  3
  subtype4 10  0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   28    0
  subtype2   29    5
  subtype3    6    3
  subtype4   10    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       28       29        6       10
  1        0        5        3        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"
D10V7, binary
          cls
clus        0  1
  subtype1 17 75
  subtype2 23 48
  subtype3 10  5
  subtype4  8 22
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   17   75
  subtype2   23   48
  subtype3   10    5
  subtype4    8   22
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       17       23       10        8
  MALE         75       48        5       22
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, continuous
[1] "Remove cluster labels:" "subtype3"              
clus
subtype1 subtype2 subtype3 subtype4 
      23       20        1        8 
 [1] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
 [7] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype4"
[13] "subtype4" "subtype2" "subtype4" "subtype1" "subtype2" "subtype1"
[19] "subtype1" "subtype4" "subtype1" "subtype1" "subtype2" "subtype1"
[25] "subtype2" "subtype2" "subtype2" "subtype2" "subtype4" "subtype1"
[31] "subtype1" "subtype2" "subtype4" "subtype1" "subtype1" "subtype1"
[37] "subtype2" "subtype2" "subtype2" "subtype1" "subtype4" "subtype1"
[43] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype2"
[49] "subtype1" "subtype1" "subtype4"
D10V9, continuous
D10V10, continuous
          vv
clus       AMERICAN INDIAN OR ALASKA NATIVE ASIAN BLACK OR AFRICAN AMERICAN
  subtype1                                2     1                        14
  subtype2                                0     3                        16
  subtype3                                0     1                         4
  subtype4                                0     0                         5
          vv
clus       WHITE
  subtype1    72
  subtype2    50
  subtype3     8
  subtype4    23
D10V11, multiclass
                                  clus
vv                                 subtype1 subtype2 subtype3 subtype4
  AMERICAN INDIAN OR ALASKA NATIVE        2        0        0        0
  ASIAN                                   1        3        1        0
  BLACK OR AFRICAN AMERICAN              14       16        4        5
  WHITE                                  72       50        8       23
[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"
D10V12, binary
          cls
clus        0  1
  subtype1  2 77
  subtype2  4 54
  subtype3  1 11
  subtype4  3 26
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   77
  subtype2    4   54
  subtype3    1   11
  subtype4    3   26
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            2        4        1        3
  NOT HISPANIC OR LATINO       77       54       11       26
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
