[1] "ofn"        "-oTSTAD-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/STAD-TP/22507291/STAD-TP.merged_data.txt"
[1] "dfn:"
[1] "/xchip/cga/gdac-prod/tcga-gdac/jobResults/GDAC_mergedClustering/STAD-TP/22552605/STAD-TP.mergedcluster.txt"

nPatients in clinical file=443, in cluster file=443, common to both=443
[1]  10 443
[1] "CN_CNMF"
[1] 3
  1   2   3   4 
234 153  51   3 
  1   2   3   4 
234 153  51   3 
[1] "METHLYATION_CNMF"
[1] 3
  1   2   3   4   5 
 46 111  51 100  87 
  1   2   3   4   5 
 46 111  51 100  87 
[1] "RPPA_CNMF"
[1] 3
 1  2  3  4  5 
30 92 82 94 59 
 1  2  3  4  5 
30 92 82 94 59 
[1] "RPPA_CHIERARCHICAL"
[1] 3
  1   2   3   4 
140  58  79  80 
  1   2   3   4 
140  58  79  80 
[1] "MRNASEQ_CNMF"
[1] 3
 1  2  3  4  5 
94 95 94 82 50 
 1  2  3  4  5 
94 95 94 82 50 
[1] "MRNASEQ_CHIERARCHICAL"
[1] 3
  1   2   3   4 
109  83 135  88 
  1   2   3   4 
109  83 135  88 
[1] "MIRSEQ_CNMF"
[1] 3
  1   2   3   4   5   6 
 62  67  80 111  50  66 
  1   2   3   4   5   6 
 62  67  80 111  50  66 
[1] "MIRSEQ_CHIERARCHICAL"
[1] 3
  1   2   3 
245  82 109 
  1   2   3 
245  82 109 
[1] "MIRSEQ_MATURE_CNMF"
[1] 3
  1   2   3 
148 121  74 
  1   2   3 
148 121  74 
[1] "MIRSEQ_MATURE_CHIERARCHICAL"
[1] 3
  1   2   3   4   5 
103  72  45  62  61 
  1   2   3   4   5 
103  72  45  62  61 
[1] "data2feature, selection=ALL"
 [1] "YEARS_TO_BIRTH"                      
 [2] "VITAL_STATUS"                        
 [3] "DAYS_TO_DEATH"                       
 [4] "DAYS_TO_LAST_FOLLOWUP"               
 [5] "TUMOR_TISSUE_SITE"                   
 [6] "PATHOLOGIC_STAGE"                    
 [7] "PATHOLOGY_T_STAGE"                   
 [8] "PATHOLOGY_N_STAGE"                   
 [9] "PATHOLOGY_M_STAGE"                   
[10] "GENDER"                              
[11] "DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS"
[12] "RADIATION_THERAPY"                   
[13] "HISTOLOGICAL_TYPE"                   
[14] "RESIDUAL_TUMOR"                      
[15] "NUMBER_OF_LYMPH_NODES"               
[16] "RACE"                                
[17] "ETHNICITY"                           

Input Data has 17 rows and 443 columns.

[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=153,	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=226,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('FOLLOWUP', vnms) to deal with survival parameters seperately"
Variable 5:'TUMOR_TISSUE_SITE':	nDistinctValues=1,	numeric=FALSE,	binary=FALSE,	exclude=TRUE.
[1] "TUMOR_TISSUE_SITE is excluded in the analysis because there is no more than two cases of (unique non-NA values)"
Variable 6:'PATHOLOGIC_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 7:'PATHOLOGY_T_STAGE':	nDistinctValues=11,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 8:'PATHOLOGY_N_STAGE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 9:'PATHOLOGY_M_STAGE':	nDistinctValues=3,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 10:'GENDER':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 11:'DATE_OF_INITIAL_PATHOLOGIC_DIAGNOSIS':	nDistinctValues=15,	numeric=TRUE,	binary=FALSE,	exclude=TRUE.
[1] "exclude grep('DATE', vnms) to deal with survival parameters seperately"
Variable 12:'RADIATION_THERAPY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 13:'HISTOLOGICAL_TYPE':	nDistinctValues=7,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 14:'RESIDUAL_TUMOR':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 15:'NUMBER_OF_LYMPH_NODES':	nDistinctValues=33,	numeric=TRUE,	binary=FALSE,	exclude=FALSE.
Variable 16:'RACE':	nDistinctValues=4,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
Variable 17:'ETHNICITY':	nDistinctValues=2,	numeric=FALSE,	binary=FALSE,	exclude=FALSE.
[1] "## **** detect survival parameters (defined in index such as ind_OS, ind_MFS, ind_RFS, ind_RFS, ind_BCR and ind_d2ssd) *** ##"
[1] "detected survival parameters using [ind_OS, overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_OS, curated_overall_survival]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_TCGAOS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survivial parameters using [ind_MFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_RFS]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_BCR]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [ind_Progression]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using [index_additional_survival_time]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "detected survival parameters using condition: [is.null(surv.mat)&&(selection=='SURV')]"
[1] "survival parameters accumulated so far"
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "************ conversion from categorical data to rank data ********** "
[1] "PATHOLOGY_T_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_N_STAGE is converted to numeric rank data using modified categoies"
[1] "PATHOLOGY_M_STAGE is converted to rank data using modified categoies"
[1] "****** SUMMARY ***** "
Output Data has 443 columns, 1 survival variables, and 12 non-survival variables.
[1] "* survival variables: "
[1] "DAYS_TO_DEATH_OR_LAST_FUP" "VITAL_STATUS"             
[1] "* non-survival variables: "
 [1] "YEARS_TO_BIRTH"        "PATHOLOGIC_STAGE"      "PATHOLOGY_T_STAGE"    
 [4] "PATHOLOGY_N_STAGE"     "PATHOLOGY_M_STAGE"     "GENDER"               
 [7] "RADIATION_THERAPY"     "HISTOLOGICAL_TYPE"     "RESIDUAL_TUMOR"       
[10] "NUMBER_OF_LYMPH_NODES" "RACE"                  "ETHNICITY"            
YEARS_TO_BIRTH, nv=54, binary=FALSE, numeric=TRUE
PATHOLOGIC_STAGE, nv=11, binary=FALSE, numeric=FALSE
PATHOLOGY_T_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.T',vnm)"
vv
 T1  T2  T3  T4 
 23  93 198 119 
[1] "table(vv)"
vv
 T1  T2  T3  T4 
 23  93 198 119 
$ClinVariableName
[1] "PATHOLOGY_T_STAGE"

$Table
vv
 T1  T2  T3  T4 
 23  93 198 119 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 T1  T2  T3  T4 
 23  93 198 119 
PATHOLOGY_N_STAGE, nv=4, binary=FALSE, numeric=TRUE
[1] "grepl('PATHOLOGY.N',vnm)"
vv
 N0  N1  N2  N3 
132 119  86  88 
[1] "table(vv)"
vv
 N0  N1  N2  N3 
132 119  86  88 
$ClinVariableName
[1] "PATHOLOGY_N_STAGE"

$Table
vv
 N0  N1  N2  N3 
132 119  86  88 

$nClasses
[1] 4

$ClinVariableType
[1] "multiclass(4)"


 N0  N1  N2  N3 
132 119  86  88 
PATHOLOGY_M_STAGE, nv=2, binary=FALSE, numeric=TRUE
GENDER, nv=2, binary=FALSE, numeric=FALSE
RADIATION_THERAPY, nv=2, binary=FALSE, numeric=FALSE
HISTOLOGICAL_TYPE, nv=7, binary=FALSE, numeric=FALSE
RESIDUAL_TUMOR, nv=4, binary=FALSE, numeric=FALSE
NUMBER_OF_LYMPH_NODES, 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 130  92
  subtype2  81  60
  subtype3  32  17
  subtype4   3   0
subtype1 subtype2 subtype3 subtype4 
     222      141       49        3 
subtype1 subtype2 subtype3 subtype4 
      92       60       17        0 
$subtype1
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        22.98        16.24        27.35        26.93        58.03 
TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4255 TCGA-BR-4257 
       11.01         9.44         6.61        18.35         4.08         9.67 
TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6709 TCGA-BR-6803 
       17.29        13.68        19.33         9.17        12.16        31.20 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
        9.21        35.24        33.63        39.78        18.15        28.73 
TCGA-BR-7901 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 
        3.45        33.21        37.25        14.43        11.44         0.69 
TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8297 
       29.42         2.66        19.96         2.20        15.58         7.40 
TCGA-BR-8361 TCGA-BR-8369 TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8484 
       31.10        14.04        14.79         3.72         5.39        25.18 
TCGA-BR-8485 TCGA-BR-8677 TCGA-BR-8678 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 
        9.21        26.73        24.79         9.86        20.88         8.22 
TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4J6 
       10.68         7.53        34.98         1.48         0.72         0.66 
TCGA-BR-A4J7 TCGA-BR-A4PD TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-CD-5799 
       32.52        20.65        20.42         1.15        21.44        13.02 
TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 
       13.15        13.35        11.21        12.76        12.59        12.53 
TCGA-CD-8527 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8533 
        7.17        12.33        12.30        12.39        11.64        15.39 
TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48A 
       12.07        12.82         6.31        12.30        11.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4436 
       11.61        12.20        20.02         3.02        27.02         7.99 
TCGA-CG-4437 TCGA-CG-4438 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4449 
        8.05        54.08         4.01        14.01        29.98        19.07 
TCGA-CG-4466 TCGA-CG-4472 TCGA-CG-4477 TCGA-CG-5719 TCGA-CG-5724 TCGA-CG-5725 
       18.97        12.00        30.97         1.02        12.03        15.02 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5577 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        4.01        69.04        25.71        20.91        20.55        18.84 
TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 
       13.35        17.19        10.26        15.22        15.98        12.79 
TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8575 TCGA-D7-8576 
       12.36        11.31        12.33        19.50        18.21        14.66 
TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6F0 TCGA-D7-A74A 
       14.27        16.44        11.24        11.31        22.29        19.96 
TCGA-EQ-5647 TCGA-EQ-8122 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-7829 
        0.62         7.99        72.23        11.38         3.48        19.53 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A4BF 
       14.07        22.29        17.06        13.58         0.56         5.52 
TCGA-FP-A9TM TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-A4GD 
        6.21        63.06         1.51         5.92        18.15        22.75 
TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GP TCGA-HU-A4GU TCGA-HU-A4GY TCGA-HU-A4H0 
       25.81        11.77         8.98         6.58         0.26         2.10 
TCGA-HU-A4H2 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-HU-A4HD 
       12.95        23.84        23.80        21.17        15.68        33.40 
TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RJ TCGA-IN-A6RL 
       36.36        18.81         3.39        18.38        12.46        13.35 
TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A7NT TCGA-IN-A7NU TCGA-IN-AB1V 
       19.53         6.44         6.74        10.62        11.70        15.75 
TCGA-IP-7968 TCGA-KB-A6F5 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 
        2.53         5.56        37.64        36.95        14.04        45.67 
TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-R5-A805 TCGA-RD-A7BT TCGA-RD-A7BW TCGA-RD-A7C1 
       18.21         6.08         9.24         8.61         5.13        16.67 
TCGA-RD-A8MV TCGA-RD-A8MW TCGA-RD-A8N1 TCGA-RD-A8N6 TCGA-RD-A8N9 TCGA-SW-A7EB 
      122.30        37.91       115.69         8.94        35.61         5.79 
TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 
        0.92         5.46        13.25        13.02        18.48        43.36 
TCGA-VQ-A8E3 TCGA-VQ-A8P5 TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       21.73         7.73        46.26        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A8PY TCGA-VQ-A8PZ 
       17.85         1.87        13.35        64.57        14.33        73.41 
TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91X 
       18.74        20.81        32.88         1.71        42.64         9.50 
TCGA-VQ-A91Y TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D 
        9.73        55.56         9.04         4.54         5.72        66.81 
TCGA-VQ-A94O TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6B 
       21.04        42.54        18.41        43.66        38.93        32.94 
TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        54.12        26.04        27.55        12.43         0.79 

$subtype2
TCGA-CG-4460 TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4184 TCGA-BR-4187 TCGA-BR-4188 
       21.99        26.70         9.47         6.97         4.64         7.43 
TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4256 TCGA-BR-4267 TCGA-BR-4279 TCGA-BR-4280 
       30.90         4.08         9.34         6.18         9.57         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6706 
       34.68        15.95        13.87        39.12        26.10        18.05 
TCGA-BR-6707 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7703 
       19.89         8.98        30.90        44.94        21.90        36.16 
TCGA-BR-7707 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-8078 TCGA-BR-8080 TCGA-BR-8081 
       35.84        15.32         9.07        29.59         9.60        32.25 
TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8360 TCGA-BR-8363 TCGA-BR-8364 TCGA-BR-8366 
        8.05         0.56         6.18         0.26        22.19         0.95 
TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8371 TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 
       26.33         4.31        11.80        31.27        25.05         1.12 
TCGA-BR-8588 TCGA-BR-8589 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8676 
       12.79        27.12         9.34        28.14         6.28         7.53 
TCGA-BR-8680 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       31.96        34.13         6.08        27.55        28.57         8.98 
TCGA-BR-A4J4 TCGA-BR-A4J5 TCGA-BR-A4J9 TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5798 
        0.53        28.34         0.46        16.14         5.13        13.41 
TCGA-CD-8531 TCGA-CD-8536 TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4306 TCGA-CG-4462 
       12.59        12.43        11.77        12.62         1.02         0.00 
TCGA-CG-4465 TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 
        9.01         6.97         0.99         6.02         0.99       105.07 
TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5733 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8572 
       28.96        65.10        21.07        18.61        17.85        16.80 
TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YV TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A4Z0 
       17.19        20.91         5.92        36.43        13.78        14.76 
TCGA-D7-A6ET TCGA-D7-A6EY TCGA-D7-A6EZ TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B 
       26.43        11.44        20.32         8.38         4.34         7.13 
TCGA-F1-6874 TCGA-F1-A448 TCGA-FP-8209 TCGA-FP-8210 TCGA-HF-7132 TCGA-HF-7134 
       14.47        21.27        59.54         5.03        77.29        52.21 
TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 
       30.51        24.39        22.32        22.82        21.07         0.76 
TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 TCGA-HU-A4GJ TCGA-HU-A4GN 
       24.30         5.59        22.68        24.20        21.37        29.98 
TCGA-HU-A4GQ TCGA-HU-A4GT TCGA-HU-A4H8 TCGA-IN-AB1X TCGA-MX-A5UG TCGA-MX-A5UJ 
        0.10         6.51        14.07        13.51         3.72        19.73 
TCGA-R5-A7ZI TCGA-R5-A804 TCGA-RD-A7BS TCGA-RD-A8N0 TCGA-RD-A8N2 TCGA-RD-A8N4 
       74.53         4.60        11.05        40.64       116.38        71.38 
TCGA-RD-A8NB TCGA-SW-A7EA TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PB 
       16.87        19.04        38.14        37.22        30.97        34.29 
TCGA-VQ-A8PD TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ TCGA-VQ-A8PT TCGA-VQ-A91D 
       16.31         9.27        23.41        15.65        29.59        11.70 
TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91W TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A94P 
       21.83        61.22        60.85        55.43         6.58         2.66 
TCGA-VQ-AA69 TCGA-VQ-AA6I TCGA-ZA-A8F6 
       28.41        16.14        17.26 

$subtype3
TCGA-CG-5727 TCGA-FP-A8CX TCGA-KB-A93G TCGA-MX-A663 TCGA-B7-5818 TCGA-B7-A5TI 
       79.07         0.23        20.15         9.86        11.70        19.56 
TCGA-BR-6566 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-7958 TCGA-BR-8362 TCGA-BR-8365 
       32.78        25.61        40.21        29.56        13.08        17.52 
TCGA-BR-8370 TCGA-BR-8381 TCGA-BR-8486 TCGA-BR-8682 TCGA-BR-A44U TCGA-BR-A4IY 
        3.32         7.36        20.22        32.58        13.87        12.89 
TCGA-BR-A4J2 TCGA-BR-A4J8 TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-A4MG TCGA-CG-4305 
       14.17        13.51        13.18        12.10         6.58        15.95 
TCGA-CG-4469 TCGA-CG-5718 TCGA-CG-5734 TCGA-D7-5578 TCGA-D7-6518 TCGA-D7-6521 
        7.07        36.00         7.99        12.66        19.13        18.54 
TCGA-D7-8570 TCGA-D7-8578 TCGA-D7-A6F2 TCGA-HJ-7597 TCGA-HU-8249 TCGA-HU-A4G6 
       24.72        21.14        15.65        26.47        28.96        24.26 
TCGA-HU-A4GX TCGA-HU-A4H3 TCGA-IN-7808 TCGA-IN-A7NR TCGA-KB-A6F7 TCGA-R5-A7ZF 
       20.25        29.00         3.45         6.51        63.62         8.52 
TCGA-RD-A8N5 TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8PF TCGA-VQ-A91A TCGA-VQ-A923 
       57.44        48.79        37.41         2.50        39.45         2.01 
TCGA-VQ-A94T 
       11.24 

$subtype4
TCGA-CG-4455 TCGA-HU-A4GC TCGA-IN-A6RS 
       12.03         3.25        12.59 

subtype1 subtype2 subtype3 subtype4 
    0.26     0.00     0.23     3.25 
subtype1 subtype2 subtype3 subtype4 
  122.30   116.38    79.07    12.59 
subtype1 subtype2 subtype3 subtype4 
  14.025   16.800   17.520   12.030 
[1] "0.3 - 122.3 (14.0)" "0.0 - 116.4 (16.8)" "0.2 - 79.1 (17.5)" 
[4] "3.2 - 12.6 (12.0)" 
D1V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        7       19       19        22        32         2
  subtype2       1        6       16        9        13        20         1
  subtype3       0        2        6        3         5         4         0
  subtype4       0        1        0        1         0         0         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         48         31         20       22
  subtype2         26         21         14       17
  subtype3          7         10          5        5
  subtype4          0          1          0        0
D1V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        1        0        0
  STAGE IA          7        6        2        1
  STAGE IB         19       16        6        0
  STAGE II         19        9        3        1
  STAGE IIA        22       13        5        0
  STAGE IIB        32       20        4        0
  STAGE III         2        1        0        0
  STAGE IIIA       48       26        7        0
  STAGE IIIB       31       21       10        1
  STAGE IIIC       20       14        5        0
  STAGE IV         22       17        5        0
[1] 11  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  10  52 108  59
  subtype2   9  30  61  48
  subtype3   3  10  27  11
  subtype4   1   1   0   1
D1V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1       10        9        3        1
  T2       52       30       10        1
  T3      108       61       27        0
  T4       59       48       11        1
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 65 63 52 44
  subtype2 47 44 27 28
  subtype3 17 11  6 16
  subtype4  1  1  1  0
D1V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       65       47       17        1
  N1       63       44       11        1
  N2       52       27        6        1
  N3       44       28       16        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V6, binary
          cls
clus         0   1
  subtype1 209  11
  subtype2 133  14
  subtype3  44   5
  subtype4   3   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  209   11
  subtype2  133   14
  subtype3   44    5
  subtype4    3    0
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      209      133       44        3
  1       11       14        5        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V7, binary
          cls
clus         0   1
  subtype1  78 156
  subtype2  66  87
  subtype3  14  37
  subtype4   0   3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   78  156
  subtype2   66   87
  subtype3   14   37
  subtype4    0    3
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       78       66       14        0
  MALE        156       87       37        3
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V8, binary
          cls
clus         0   1
  subtype1 164  49
  subtype2 114  23
  subtype3  41   4
  subtype4   3   0
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  164   49
  subtype2  114   23
  subtype3   41    4
  subtype4    3    0
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO       164      114       41        3
  YES       49       23        4        0
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        7
  subtype2                                        3
  subtype3                                        3
  subtype4                                        0
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                    26
  subtype2                                    33
  subtype3                                    12
  subtype4                                     1
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     82
  subtype2                                                     62
  subtype3                                                     18
  subtype4                                                      1
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 9
  subtype2                                                 8
  subtype3                                                 3
  subtype4                                                 1
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                50
  subtype2                                                                26
  subtype3                                                                 6
  subtype4                                                                 0
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  5
  subtype2                                                  2
  subtype3                                                  1
  subtype4                                                  0
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               52
  subtype2                                               19
  subtype3                                                8
  subtype4                                                0
D1V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   26
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  82
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       50
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       5
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        52
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   33
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  62
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       26
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        19
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  18
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         8
                                                                   clus
vv                                                                  subtype4
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    1
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                   1
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        0
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         0
[1] 7 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 187  10  10   9
  subtype2 116   6   8  15
  subtype3  43   2   1   1
  subtype4   3   0   0   0
D1V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      187      116       43        3
  R1       10        6        2        0
  R2       10        8        1        0
  RX        9       15        1        0
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    49                         8
  subtype2    28                         3
  subtype3    10                         1
  subtype4     1                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         1   144
  subtype2                                         0   103
  subtype3                                         0    30
  subtype4                                         0     1
D1V12, multiclass
[1] "Remove cluster labels:" "subtype4"              
clus
subtype1 subtype2 subtype3 subtype4 
     202      134       41        2 
  [1] "subtype1" "subtype2" "subtype3" "subtype3" "subtype3" "subtype1"
  [7] "subtype1" "subtype1" "subtype2" "subtype2" "subtype3" "subtype3"
 [13] "subtype1" "subtype2" "subtype1" "subtype1" "subtype2" "subtype2"
 [19] "subtype2" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
 [25] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
 [31] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
 [37] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype2"
 [43] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype2"
 [49] "subtype2" "subtype1" "subtype3" "subtype3" "subtype2" "subtype2"
 [55] "subtype1" "subtype2" "subtype3" "subtype2" "subtype1" "subtype2"
 [61] "subtype2" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [67] "subtype1" "subtype1" "subtype2" "subtype1" "subtype2" "subtype1"
 [73] "subtype2" "subtype3" "subtype1" "subtype1" "subtype1" "subtype1"
 [79] "subtype1" "subtype2" "subtype2" "subtype2" "subtype2" "subtype2"
 [85] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
 [91] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype3"
 [97] "subtype2" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[103] "subtype2" "subtype1" "subtype2" "subtype3" "subtype2" "subtype1"
[109] "subtype1" "subtype1" "subtype1" "subtype3" "subtype2" "subtype2"
[115] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[121] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype1"
[127] "subtype1" "subtype1" "subtype2" "subtype3" "subtype1" "subtype2"
[133] "subtype1" "subtype1" "subtype1" "subtype2" "subtype2" "subtype3"
[139] "subtype2" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[145] "subtype1" "subtype3" "subtype2" "subtype1" "subtype1" "subtype1"
[151] "subtype1" "subtype2" "subtype2" "subtype2" "subtype1" "subtype1"
[157] "subtype3" "subtype1" "subtype1" "subtype3" "subtype1" "subtype1"
[163] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[169] "subtype1" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[175] "subtype1" "subtype1" "subtype1" "subtype1" "subtype3" "subtype1"
[181] "subtype2" "subtype2" "subtype1" "subtype3" "subtype1" "subtype3"
[187] "subtype1" "subtype1" "subtype3" "subtype2" "subtype2" "subtype1"
[193] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[199] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype2"
[205] "subtype1" "subtype1" "subtype3" "subtype2" "subtype1" "subtype1"
[211] "subtype2" "subtype2" "subtype2" "subtype2" "subtype2" "subtype1"
[217] "subtype1" "subtype2" "subtype2" "subtype1" "subtype3" "subtype2"
[223] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype2"
[229] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[235] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[241] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype2"
[247] "subtype1" "subtype3" "subtype2" "subtype2" "subtype2" "subtype2"
[253] "subtype2" "subtype2" "subtype3" "subtype2" "subtype2" "subtype1"
[259] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype2"
[265] "subtype2" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[271] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[277] "subtype1" "subtype1" "subtype3" "subtype1" "subtype1" "subtype1"
[283] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[289] "subtype3" "subtype1" "subtype1" "subtype1" "subtype2" "subtype1"
[295] "subtype1" "subtype1" "subtype2" "subtype2" "subtype1" "subtype1"
[301] "subtype1" "subtype3" "subtype2" "subtype1" "subtype2" "subtype1"
[307] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype1"
[313] "subtype2" "subtype1" "subtype2" "subtype2" "subtype3" "subtype1"
[319] "subtype1" "subtype2" "subtype2" "subtype1" "subtype1" "subtype1"
[325] "subtype1" "subtype1" "subtype1" "subtype1" "subtype1" "subtype3"
[331] "subtype2" "subtype2" "subtype1" "subtype2" "subtype2" "subtype1"
[337] "subtype2" "subtype1" "subtype1" "subtype1" "subtype1" "subtype2"
[343] "subtype2" "subtype1" "subtype2" "subtype1" "subtype1" "subtype3"
[349] "subtype2" "subtype2" "subtype2" "subtype1" "subtype1" "subtype2"
[355] "subtype1" "subtype1" "subtype1" "subtype3" "subtype1" "subtype2"
[361] "subtype1" "subtype1" "subtype1" "subtype2" "subtype1" "subtype1"
[367] "subtype1" "subtype2" "subtype1" "subtype1" "subtype1" "subtype1"
[373] "subtype2" "subtype1" "subtype1" "subtype2" "subtype1"
                                           clus
vv                                          subtype1 subtype2 subtype3
  ASIAN                                           49       28       10
  BLACK OR AFRICAN AMERICAN                        8        3        1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1        0        0
  WHITE                                          144      103       30
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D1V13, binary
          cls
clus         0   1
  subtype1   3 161
  subtype2   2 116
  subtype3   0  37
  subtype4   0   2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  161
  subtype2    2  116
  subtype3    0   37
  subtype4    0    2
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        2        0        0
  NOT HISPANIC OR LATINO      161      116       37        2
[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 25 20
  subtype2 70 37
  subtype3 34 15
  subtype4 56 41
  subtype5 49 37
subtype1 subtype2 subtype3 subtype4 subtype5 
      45      107       49       97       86 
subtype1 subtype2 subtype3 subtype4 subtype5 
      20       37       15       41       37 
$subtype1
TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-3M-AB46 TCGA-B7-A5TI TCGA-BR-7722 TCGA-BR-8370 
       16.24        27.35        58.03        19.56        15.32         3.32 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4J6 TCGA-BR-A4J8 
       31.96         9.86         8.22         7.53         0.66        13.51 
TCGA-CD-5799 TCGA-CD-5813 TCGA-CD-8532 TCGA-CD-8534 TCGA-CD-A48A TCGA-CG-5719 
       13.02        12.39        11.64        12.07        12.43         1.02 
TCGA-D7-6519 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A6EX TCGA-D7-A74A 
       20.55        18.21        14.66        14.27        11.31        19.96 
TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-8211 TCGA-HF-7133 
        0.62        14.47        11.38         3.48        13.58        63.06 
TCGA-HJ-7597 TCGA-HU-A4GX TCGA-IP-7968 TCGA-RD-A8N9 TCGA-VQ-A8E0 TCGA-VQ-A8E7 
       26.47        20.25         2.53        35.61        18.48        37.41 
TCGA-VQ-A8PS TCGA-VQ-A8PX TCGA-VQ-A91Q TCGA-VQ-A925 TCGA-VQ-A928 TCGA-VQ-A92D 
       13.35        64.57        20.81         4.54         5.72        66.81 
TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6K 
       11.24        18.41        12.43 

$subtype2
TCGA-VQ-A94U TCGA-B7-A5TJ TCGA-BR-6452 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-7703 
       26.93        11.01        34.68        19.33        32.78        36.16 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7959 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8297 
       35.84        18.15        33.21         8.05        29.42         7.40 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8362 TCGA-BR-8367 TCGA-BR-8368 TCGA-BR-8369 
        6.18        31.10        13.08        26.33         4.31        14.04 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8591 TCGA-BR-8682 TCGA-BR-A44U 
       31.27        25.05         1.12        28.14        32.58        13.87 
TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QI TCGA-BR-A4QL 
       34.98         1.48        20.42         1.15        21.44        16.14 
TCGA-BR-A4QM TCGA-CD-8524 TCGA-CD-8528 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A48C 
        5.13        12.76        12.33        12.82        12.43        11.61 
TCGA-CD-A4MG TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-5720 TCGA-CG-5724 TCGA-CG-5726 
        6.58        11.77        12.62         0.99        12.03        28.96 
TCGA-CG-5733 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6822 TCGA-D7-A4YU TCGA-D7-A4YV 
       21.07        13.35        15.22        12.33        16.44         5.92 
TCGA-D7-A4YY TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EY TCGA-F1-A448 TCGA-FP-7829 
       13.78        14.76        11.24        11.44        21.27        19.53 
TCGA-FP-8099 TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 
       17.06        11.08         5.52         6.21        77.29        52.21 
TCGA-HF-A5NB TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-A4G3 TCGA-HU-A4G8 
       30.51         1.51        24.39        22.32         5.59        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GQ TCGA-HU-A4GT 
       24.20         3.25        29.98         8.98         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-8462 
        6.58        29.00        23.84        21.17        14.07        18.81 
TCGA-IN-8663 TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS TCGA-IN-A7NU TCGA-MX-A5UJ 
        3.39         6.44         6.74        12.59        11.70        19.73 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7C1 TCGA-SW-A7EA TCGA-VQ-A8DT TCGA-VQ-A8E3 
        4.60         9.24        16.67        19.04        48.79        21.73 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PO TCGA-VQ-A8PP 
       38.14        37.22         7.73        34.29         9.27        23.41 
TCGA-VQ-A8PT TCGA-VQ-A8PY TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K 
       29.59        14.33        39.45        11.70        21.83        61.22 
TCGA-VQ-A91V TCGA-VQ-A94R TCGA-VQ-AA68 TCGA-VQ-AA6G TCGA-VQ-AA6I 
       42.64        42.54        43.66        26.04        16.14 

$subtype3
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-BR-6455 TCGA-BR-6706 TCGA-BR-6707 
       26.70        11.70         9.47        13.87        18.05        19.89 
TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7196 TCGA-BR-7958 TCGA-BR-8078 TCGA-BR-8081 
       30.90        44.94        21.90        29.56        29.59        32.25 
TCGA-BR-8285 TCGA-BR-8296 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8381 TCGA-BR-8589 
        0.56        15.58         0.26         0.95         7.36        27.12 
TCGA-BR-8676 TCGA-BR-8686 TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-CD-5801 TCGA-CD-8531 
        7.53        20.88        12.89         0.53        13.18        12.59 
TCGA-CG-4437 TCGA-CG-5722 TCGA-CG-5728 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-8570 
        8.05         0.99        65.10         7.99        25.71        24.72 
TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A6EZ TCGA-FP-7916 TCGA-FP-7998 TCGA-HU-8604 
       19.50        36.43        20.32        14.07        22.29        22.82 
TCGA-HU-8608 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4H0 TCGA-IN-A6RN TCGA-IN-AB1X 
       21.07        24.30        24.26         2.10        19.53        13.51 
TCGA-VQ-A8P8 TCGA-VQ-A8PF TCGA-VQ-A8PZ TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A924 
       30.97         2.50        73.41        60.85         2.01        55.43 
TCGA-VQ-AA69 
       28.41 

$subtype4
TCGA-CG-5727 TCGA-FP-A8CX TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-6565 TCGA-BR-6801 
       79.07         0.23         9.44        17.29         9.17        40.21 
TCGA-BR-7197 TCGA-BR-7704 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 
        9.21        35.24        33.63        39.78        28.73         3.45 
TCGA-BR-8059 TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8373 
       14.43        11.44         0.69         2.66         2.20        14.79 
TCGA-BR-8483 TCGA-BR-8484 TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8678 TCGA-BR-8690 
        5.39        25.18         9.21        20.22        24.79        10.68 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8530 
        0.72        20.65        13.15        12.59         7.17        12.39 
TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4441 TCGA-CG-5718 
       15.39         6.31        12.30        12.20        14.01        36.00 
TCGA-CG-5725 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-6520 TCGA-D7-6526 
       15.02         4.01        69.04        12.66        18.84        17.19 
TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-8572 
       10.26        15.98        12.79        12.36        11.31        16.80 
TCGA-D7-A6F0 TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-8631 TCGA-HU-8243 
       22.29        15.65         7.99        72.23         0.56         5.92 
TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H2 
       18.15        28.96        22.75        25.81        11.77        12.95 
TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A7NT 
       23.80        33.40        36.36        18.38        13.35        10.62 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7ZE 
        5.56        63.62        37.64        36.95        14.04        18.21 
TCGA-R5-A7ZR TCGA-RD-A7BT TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-VQ-A8DL TCGA-VQ-A8DU 
        6.08         8.61        37.91         8.94         0.92         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       13.25        13.02        43.36        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A91Z 
       17.85        18.74        32.88         1.71         9.50        55.56 
TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-ZA-A8F6 
        9.04        21.04        38.93        32.94        17.13        17.26 
TCGA-ZQ-A9CR 
        0.79 

$subtype5
TCGA-KB-A93G TCGA-MX-A663 TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
       20.15         9.86        15.95        13.68        39.12        26.10 
TCGA-BR-6705 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6803 TCGA-BR-7957 TCGA-BR-8058 
       25.61        12.16         8.98        31.20         9.07        37.25 
TCGA-BR-8080 TCGA-BR-8291 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8371 TCGA-BR-8384 
        9.60        19.96        22.19        17.52        11.80         3.72 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-A44T TCGA-BR-A453 
       12.79         9.34         6.28        26.73        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 
       27.55        28.57         8.98        14.17        28.34        32.52 
TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5802 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8526 
        0.46        13.41        13.35        11.21        12.10        12.53 
TCGA-CD-8529 TCGA-CD-A489 TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5723 TCGA-D7-5579 
       12.30        11.31         6.97         6.02       105.07        20.91 
TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8574 TCGA-D7-8578 
       19.13        18.54        18.61        17.85        17.19        21.14 
TCGA-D7-8579 TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-FP-8209 
       20.91        26.43         8.38         4.34         7.13        59.54 
TCGA-FP-8210 TCGA-HU-8610 TCGA-HU-A4GJ TCGA-HU-A4GY TCGA-HU-A4HB TCGA-IN-7808 
        5.03         0.76        21.37         0.26        15.68         3.45 
TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-AB1V TCGA-MX-A5UG TCGA-R5-A7O7 TCGA-R5-A7ZF 
       12.46         6.51        15.75         3.72        45.67         8.52 
TCGA-R5-A7ZI TCGA-RD-A7BS TCGA-RD-A7BW TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
       74.53        11.05         5.13       122.30        40.64       115.69 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N5 TCGA-RD-A8NB TCGA-SW-A7EB TCGA-VQ-A8PC 
      116.38        71.38        57.44        16.87         5.79        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A927 TCGA-VQ-A94P 
       16.31         1.87        15.65         9.73         6.58         2.66 
TCGA-VQ-AA6F TCGA-VQ-AA6J 
       54.12        27.55 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.62     0.10     0.26     0.23     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
   66.81    77.29    73.41    79.07   122.30 
subtype1 subtype2 subtype3 subtype4 subtype5 
  13.580   16.140   19.890   14.040   15.665 
[1] "0.6 - 66.8 (13.6)"  "0.1 - 77.3 (16.1)"  "0.3 - 73.4 (19.9)" 
[4] "0.2 - 79.1 (14.0)"  "0.3 - 122.3 (15.7)"
D2V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        1        5        5         4         2         0
  subtype2       1        7       11        5        14        17         0
  subtype3       0        1        3        3         7        10         0
  subtype4       1        3        9       10         8        17         2
  subtype5       0        3        7        6         8         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          9          8          4        7
  subtype2         16         19         14        4
  subtype3         11          8          5        3
  subtype4         23         12          7        8
  subtype5         16         15          8       11
D2V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        1        0        1        0
  STAGE IA          1        7        1        3        3
  STAGE IB          5       11        3        9        7
  STAGE II          5        5        3       10        6
  STAGE IIA         4       14        7        8        8
  STAGE IIB         2       17       10       17        9
  STAGE III         0        0        0        2        0
  STAGE IIIA        9       16       11       23       16
  STAGE IIIB        8       19        8       12       15
  STAGE IIIC        4       14        5        7        8
  STAGE IV          7        4        3        8       11
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  1 10 24 11
  subtype2 11 21 49 30
  subtype3  2  5 26 18
  subtype4  4 26 47 23
  subtype5  3 16 40 28
D2V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        1       11        2        4        3
  T2       10       21        5       26       16
  T3       24       49       26       47       40
  T4       11       30       18       23       28
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 14 10 12 10
  subtype2 40 23 23 24
  subtype3 19 13  9  9
  subtype4 28 29 20 20
  subtype5 23 26 16 20
D2V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       14       40       19       28       23
  N1       10       23       13       29       26
  N2       12       23        9       20       16
  N3       10       24        9       20       20
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V6, binary
          cls
clus         0   1
  subtype1  36   4
  subtype2 106   2
  subtype3  46   3
  subtype4  89   4
  subtype5  76  10
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   36    4
  subtype2  106    2
  subtype3   46    3
  subtype4   89    4
  subtype5   76   10
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       36      106       46       89       76
  1        4        2        3        4       10
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V7, binary
          cls
clus        0  1
  subtype1 14 32
  subtype2 39 72
  subtype3 17 34
  subtype4 35 65
  subtype5 31 56
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   14   32
  subtype2   39   72
  subtype3   17   34
  subtype4   35   65
  subtype5   31   56
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       14       39       17       35       31
  MALE         32       72       34       65       56
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V8, binary
          cls
clus        0  1
  subtype1 31 12
  subtype2 81 26
  subtype3 41  5
  subtype4 76 18
  subtype5 73 14
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   31   12
  subtype2   81   26
  subtype3   41    5
  subtype4   76   18
  subtype5   73   14
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        31       81       41       76       73
  YES       12       26        5       18       14
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        2
  subtype2                                        3
  subtype3                                        1
  subtype4                                        2
  subtype5                                        5
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                     7
  subtype2                                    13
  subtype3                                     8
  subtype4                                     5
  subtype5                                    34
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     12
  subtype2                                                     45
  subtype3                                                     20
  subtype4                                                     31
  subtype5                                                     27
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 2
  subtype2                                                 9
  subtype3                                                 0
  subtype4                                                 1
  subtype5                                                 8
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                 8
  subtype2                                                                17
  subtype3                                                                13
  subtype4                                                                28
  subtype5                                                                 7
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  1
  subtype2                                                  2
  subtype3                                                  1
  subtype4                                                  4
  subtype5                                                  0
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               13
  subtype2                                               22
  subtype3                                                8
  subtype4                                               29
  subtype5                                                6
D2V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  12
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        13
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   13
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  45
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        9
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       17
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        22
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        0
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         8
                                                                   clus
vv                                                                  subtype4
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  31
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       28
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        29
                                                                   clus
vv                                                                  subtype5
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 5
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   34
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  27
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         6
[1] 7 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 35  4  2
  subtype2 98  3  1
  subtype3 47  0  2
  subtype4 87  2  4
  subtype5 68  8  3
D2V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       35       98       47       87       68
  R1        4        3        0        2        8
  R2        2        1        2        4        3
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    11                         2
  subtype2    26                         3
  subtype3    11                         1
  subtype4    21                         5
  subtype5    20                         2
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    28
  subtype2                                         0    72
  subtype3                                         0    32
  subtype4                                         1    59
  subtype5                                         0    62
D2V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           11       26       11       21
  BLACK OR AFRICAN AMERICAN                        2        3        1        5
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           28       72       32       59
                                           clus
vv                                          subtype5
  ASIAN                                           20
  BLACK OR AFRICAN AMERICAN                        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0
  WHITE                                           62
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D2V13, binary
          cls
clus        0  1
  subtype1  1 31
  subtype2  1 83
  subtype3  1 38
  subtype4  0 69
  subtype5  2 72
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   31
  subtype2    1   83
  subtype3    1   38
  subtype4    0   69
  subtype5    2   72
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            1        1        1        0        2
  NOT HISPANIC OR LATINO       31       83       38       69       72
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(3) Variable = RPPA_CNMF
D3V1, survival
          sevent
clus2       0  1
  subtype1 18 10
  subtype2 55 33
  subtype3 42 30
  subtype4 45 44
  subtype5 32 22
subtype1 subtype2 subtype3 subtype4 subtype5 
      28       88       72       89       54 
subtype1 subtype2 subtype3 subtype4 subtype5 
      10       33       30       44       22 
$subtype1
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-5727 TCGA-KB-A93G TCGA-BR-4191 TCGA-BR-6453 
       47.05        21.99        79.07        20.15        18.35        15.95 
TCGA-BR-6565 TCGA-BR-A4J2 TCGA-BR-A4PE TCGA-CD-5800 TCGA-CG-4301 TCGA-CG-4304 
        9.17        14.17        20.42        13.15         3.02        27.02 
TCGA-CG-5721 TCGA-CG-5726 TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-A4YT TCGA-F1-A72C 
        6.02        28.96         4.01        69.04        14.27        11.38 
TCGA-IN-AB1V TCGA-SW-A7EB TCGA-VQ-A8E7 TCGA-VQ-A8PK TCGA-VQ-A8PS TCGA-VQ-A8PZ 
       15.75         5.79        37.41        17.85        13.35        73.41 
TCGA-VQ-A91X TCGA-VQ-AA6G TCGA-VQ-AA6K TCGA-ZA-A8F6 
        9.50        26.04        12.43        17.26 

$subtype2
TCGA-VQ-A8PU TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4184 TCGA-BR-4201 TCGA-BR-4257 
       27.35        26.70        11.70         6.97        30.90         9.67 
TCGA-BR-4267 TCGA-BR-4280 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7704 
        6.18         6.61         8.98        30.90        44.94        35.24 
TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8360 
       11.44        32.25         0.56        29.42        15.58         6.18 
TCGA-BR-8361 TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8676 
       31.10        25.05        25.18        27.12        28.14         7.53 
TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4J8 TCGA-BR-A4PF TCGA-BR-A4QM TCGA-CD-5799 
       10.68        13.87        13.51         1.15         5.13        13.02 
TCGA-CD-8525 TCGA-CD-8528 TCGA-CD-8529 TCGA-CD-8536 TCGA-CD-A486 TCGA-CD-A487 
       12.59        12.33        12.30        12.43         6.31        12.30 
TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4455 TCGA-CG-4469 
       12.20        20.02         7.99         8.05        12.03         7.07 
TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5728 TCGA-CG-5733 
       30.97        36.00       105.07        12.03        65.10        21.07 
TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-A4YU TCGA-D7-A4YX 
       15.98        12.36        11.31        12.33        16.44        36.43 
TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-F1-6874 TCGA-F1-A448 TCGA-HU-A4GF TCGA-HU-A4GT 
       11.24        20.32        14.47        21.27        25.81         6.51 
TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 TCGA-IN-A6RR TCGA-IN-A7NT 
       12.95        29.00        23.84        23.80         6.74        10.62 
TCGA-IN-AB1X TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-SW-A7EA 
       13.51         8.61        16.67       122.30       115.69        19.04 
TCGA-VQ-A8DL TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PC 
        0.92        18.48        21.73        37.22         7.73        46.26 
TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PO TCGA-VQ-A8PX TCGA-VQ-A91S TCGA-VQ-A91Z 
       22.19        12.79         9.27        64.57        32.88        55.56 
TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA64 TCGA-VQ-AA6D 
       66.81        42.54        18.41        17.13 

$subtype3
TCGA-EQ-A4SO TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-6452 TCGA-BR-7703 
       16.24        19.56        11.01         9.47        34.68        36.16 
TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8368 TCGA-BR-8372 
       39.78        28.73         8.05         2.20         4.31        31.27 
TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A4IV 
        9.21         9.34        24.79        20.88         8.22        28.57 
TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-CD-5801 TCGA-CD-5802 TCGA-CD-8527 TCGA-CD-A48C 
        0.72         0.53        13.18        13.35         7.17        11.61 
TCGA-CD-A4MI TCGA-CD-A4MJ TCGA-CG-4438 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4465 
       11.77        12.62        54.08        29.98        19.07         9.01 
TCGA-CG-4466 TCGA-CG-5720 TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6817 
       18.97         0.99        15.02        25.71        12.66        12.79 
TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A6F0 TCGA-F1-6875 TCGA-HF-7134 
       21.14         5.92        13.78        22.29        72.23        52.21 
TCGA-HF-A5NB TCGA-HU-A4GQ TCGA-HU-A4GU TCGA-HU-A4GX TCGA-HU-A4HD TCGA-IN-7806 
       30.51         0.10         6.58        20.25        33.40        36.36 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RI TCGA-IN-A6RL TCGA-IN-A6RN TCGA-RD-A8N0 
        3.45         3.39        18.38        13.35        19.53        40.64 
TCGA-VQ-A8DT TCGA-VQ-A8P2 TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PT TCGA-VQ-A91D 
       48.79        38.14         2.50         2.70        29.59        11.70 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A925 
       61.22        18.74         1.71        42.64        60.85         4.54 
TCGA-VQ-A94O TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6I 
       21.04        28.41        38.93        32.94        54.12        16.14 

$subtype4
TCGA-CG-4475 TCGA-VQ-A94U TCGA-B7-A5TN TCGA-BR-4183 TCGA-BR-4187 TCGA-BR-4188 
       22.98        26.93         9.44         6.61         4.64         7.43 
TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6564 
        4.08         9.34         9.57        13.68        19.33        26.10 
TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7715 
       25.61        40.21        31.20        21.90         9.21        33.63 
TCGA-BR-7717 TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8291 
       18.15        15.32         9.07        14.43         9.60        19.96 
TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8370 
        7.40        13.08        22.19        17.52        26.33         3.32 
TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8588 TCGA-BR-8592 
       11.80         3.72         5.39        20.22        12.79         6.28 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A452 TCGA-BR-A453 TCGA-BR-A4CQ 
       26.73        32.58        34.13         7.53         6.08        34.98 
TCGA-BR-A4CS TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4IZ TCGA-BR-A4J5 TCGA-BR-A4J6 
        1.48        27.55        12.89         8.98        28.34         0.66 
TCGA-BR-A4J7 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-5813 
       32.52         0.46        21.44        13.41        11.21        12.39 
TCGA-CD-8524 TCGA-CD-A489 TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-D7-5579 
       12.76        11.31        12.00         6.97         1.02        20.91 
TCGA-D7-6524 TCGA-D7-8574 TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A748 
       17.85        17.19        14.76        11.31        11.44         4.34 
TCGA-FP-7998 TCGA-HU-8610 TCGA-HU-A4GY TCGA-IN-8462 TCGA-IN-A6RS TCGA-IN-A7NR 
       22.29         0.76         0.26        18.81        12.59         6.51 
TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H TCGA-MX-A5UG TCGA-RD-A7BS TCGA-RD-A7BW 
       11.70         5.56        37.64         3.72        11.05         5.13 
TCGA-RD-A8MW TCGA-RD-A8NB TCGA-VQ-A8E2 TCGA-VQ-A8PD TCGA-VQ-A8PM TCGA-VQ-A8PP 
       37.91        16.87        43.36        16.31         1.87        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A94P 
       15.65         9.73         2.01         5.72         2.66 

$subtype5
TCGA-BR-4253 TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 
        4.08        13.87        17.29        32.78        18.05        19.89 
TCGA-BR-6709 TCGA-BR-7901 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8289 
       12.16         3.45        29.56        33.21        37.25         2.66 
TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8369 TCGA-BR-8381 TCGA-BR-8680 TCGA-BR-8683 
        0.26         0.95        14.04         7.36        31.96         9.86 
TCGA-BR-A4PD TCGA-BR-A4QL TCGA-CD-5804 TCGA-CD-8526 TCGA-CD-8530 TCGA-CD-8531 
       20.65        16.14        12.10        12.53        12.39        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8535 TCGA-CD-A48A TCGA-CD-A4MG 
       11.64        15.39        12.07        12.82        12.43         6.58 
TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-5734 TCGA-D7-6518 TCGA-D7-6519 TCGA-D7-6520 
       15.95         1.02         7.99        19.13        20.55        18.84 
TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6525 TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-8570 
       18.54        18.61        13.35        10.26        15.22        24.72 
TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-8575 TCGA-EQ-8122 TCGA-FP-7916 TCGA-HF-7132 
       16.80        19.50        18.21         7.99        14.07        77.29 
TCGA-HF-7133 TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-8608 TCGA-IP-7968 TCGA-VQ-A8DU 
       63.06        26.47        22.32        21.07         2.53         5.46 

subtype1 subtype2 subtype3 subtype4 subtype5 
    3.02     0.56     0.10     0.26     0.26 
subtype1 subtype2 subtype3 subtype4 subtype5 
   79.07   122.30    72.23    43.36    77.29 
subtype1 subtype2 subtype3 subtype4 subtype5 
  16.605   15.780   18.560   12.590   14.645 
[1] "3.0 - 79.1 (16.6)"  "0.6 - 122.3 (15.8)" "0.1 - 72.2 (18.6)" 
[4] "0.3 - 43.4 (12.6)"  "0.3 - 77.3 (14.6)" 
D3V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        2        4        3         3         2         0
  subtype2       0        1       13        8        10        12         1
  subtype3       2        5        9        3         2         9         0
  subtype4       0        3        2        8        10        13         1
  subtype5       0        0        4        7         7         8         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          4          3          1        6
  subtype2         16         16          6        4
  subtype3         17         12         13        5
  subtype4         17         11         11       14
  subtype5         13          9          1        4
D3V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        0        2        0        0
  STAGE IA          2        1        5        3        0
  STAGE IB          4       13        9        2        4
  STAGE II          3        8        3        8        7
  STAGE IIA         3       10        2       10        7
  STAGE IIB         2       12        9       13        8
  STAGE III         0        1        0        1        0
  STAGE IIIA        4       16       17       17       13
  STAGE IIIB        3       16       12       11        9
  STAGE IIIC        1        6       13       11        1
  STAGE IV          6        4        5       14        4
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  2  9 11  6
  subtype2  1 27 42 20
  subtype3  8 18 27 28
  subtype4  3  8 44 36
  subtype5  0 14 32 11
D3V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        2        1        8        3        0
  T2        9       27       18        8       14
  T3       11       42       27       44       32
  T4        6       20       28       36       11
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 13  8  4  4
  subtype2 33 21 17 17
  subtype3 19 20 19 18
  subtype4 25 28 13 24
  subtype5 19 19 12  8
D3V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       13       33       19       25       19
  N1        8       21       20       28       19
  N2        4       17       19       13       12
  N3        4       17       18       24        8
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V6, binary
          cls
clus        0  1
  subtype1 24  4
  subtype2 88  2
  subtype3 75  4
  subtype4 84  8
  subtype5 51  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   24    4
  subtype2   88    2
  subtype3   75    4
  subtype4   84    8
  subtype5   51    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       24       88       75       84       51
  1        4        2        4        8        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V7, binary
          cls
clus        0  1
  subtype1  6 24
  subtype2 35 57
  subtype3 24 58
  subtype4 35 59
  subtype5 21 38
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    6   24
  subtype2   35   57
  subtype3   24   58
  subtype4   35   59
  subtype5   21   38
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE        6       35       24       35       21
  MALE         24       57       58       59       38
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V8, binary
          cls
clus        0  1
  subtype1 21  4
  subtype2 67 18
  subtype3 52 19
  subtype4 83  7
  subtype5 42  9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   21    4
  subtype2   67   18
  subtype3   52   19
  subtype4   83    7
  subtype5   42    9
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        21       67       52       83       42
  YES        4       18       19        7        9
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        2
  subtype3                                        0
  subtype4                                        4
  subtype5                                        1
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                     2
  subtype2                                     9
  subtype3                                     9
  subtype4                                    20
  subtype5                                    12
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                      9
  subtype2                                                     34
  subtype3                                                     34
  subtype4                                                     42
  subtype5                                                     30
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 1
  subtype2                                                 4
  subtype3                                                 3
  subtype4                                                 8
  subtype5                                                 3
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                12
  subtype2                                                                25
  subtype3                                                                21
  subtype4                                                                 7
  subtype5                                                                 4
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  1
  subtype2                                                  1
  subtype3                                                  1
  subtype4                                                  1
  subtype5                                                  1
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                                2
  subtype2                                               17
  subtype3                                               13
  subtype4                                               10
  subtype5                                                8
D3V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                   9
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         2
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       25
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        17
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       21
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        13
                                                                   clus
vv                                                                  subtype4
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   20
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        8
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        10
                                                                   clus
vv                                                                  subtype5
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   12
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  30
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        4
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         8
[1] 7 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 23  1  3  2
  subtype2 77  3  2  7
  subtype3 63  3  4  4
  subtype4 73  5  4  7
  subtype5 46  3  1  5
D3V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       23       77       63       73       46
  R1        1        3        3        5        3
  R2        3        2        4        4        1
  RX        2        7        4        7        5
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1     3                         0
  subtype2    14                         2
  subtype3    16                         3
  subtype4    18                         0
  subtype5    15                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    18
  subtype2                                         1    61
  subtype3                                         0    46
  subtype4                                         0    68
  subtype5                                         0    39
D3V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                            3       14       16       18
  BLACK OR AFRICAN AMERICAN                        0        2        3        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        1        0        0
  WHITE                                           18       61       46       68
                                           clus
vv                                          subtype5
  ASIAN                                           15
  BLACK OR AFRICAN AMERICAN                        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0
  WHITE                                           39
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D3V13, binary
          cls
clus        0  1
  subtype1  0 13
  subtype2  1 62
  subtype3  0 52
  subtype4  1 75
  subtype5  0 53
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    0   13
  subtype2    1   62
  subtype3    0   52
  subtype4    1   75
  subtype5    0   53
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            0        1        0        1        0
  NOT HISPANIC OR LATINO       13       62       52       75       53
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(4) Variable = RPPA_CHIERARCHICAL
D4V1, survival
          sevent
clus2       0  1
  subtype1 71 59
  subtype2 34 15
  subtype3 49 26
  subtype4 38 39
subtype1 subtype2 subtype3 subtype4 
     130       49       75       77 
subtype1 subtype2 subtype3 subtype4 
      59       15       26       39 
$subtype1
TCGA-CG-4444 TCGA-CG-4460 TCGA-CG-4475 TCGA-CG-5727 TCGA-EQ-A4SO TCGA-VQ-A94U 
       47.05        21.99        22.98        79.07        16.24        26.93 
TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-B7-A5TK TCGA-BR-4183 TCGA-BR-4191 TCGA-BR-4253 
       19.56        11.01         9.47         6.61        18.35         4.08 
TCGA-BR-4257 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6565 TCGA-BR-6706 
        9.67        15.95        13.87        19.33         9.17        18.05 
TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 
       19.89        12.16        33.63        39.78        18.15        28.73 
TCGA-BR-8284 TCGA-BR-8295 TCGA-BR-8296 TCGA-BR-8368 TCGA-BR-8484 TCGA-BR-8485 
        8.05         2.20        15.58         4.31        25.18         9.21 
TCGA-BR-8486 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44U 
       20.22         9.34        24.79        20.88         8.22        13.87 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IV TCGA-BR-A4J1 TCGA-BR-A4J2 TCGA-BR-A4J4 
        6.08        34.98        28.57         0.72        14.17         0.53 
TCGA-BR-A4PD TCGA-BR-A4PE TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 TCGA-CD-5802 
       20.65        20.42        13.02        13.15        13.18        13.35 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8531 
       12.10        12.76        12.59         7.17        12.30        12.59 
TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-A486 TCGA-CD-A48C TCGA-CD-A4MH TCGA-CD-A4MI 
       11.64        15.39         6.31        11.61        12.20        11.77 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4306 TCGA-CG-4443 TCGA-CG-4449 
        3.02        27.02        15.95         1.02        29.98        19.07 
TCGA-CG-4465 TCGA-CG-4466 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5725 TCGA-CG-5726 
        9.01        18.97         0.99         6.02        15.02        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6519 TCGA-D7-6520 
        4.01        69.04        12.66        20.91        20.55        18.84 
TCGA-D7-6522 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-8570 TCGA-D7-8575 
       18.61        10.26        12.79        12.36        24.72        18.21 
TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6F0 TCGA-F1-6875 TCGA-F1-A72C TCGA-FP-7916 
       21.14        14.27        22.29        72.23        11.38        14.07 
TCGA-FP-7998 TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 TCGA-HJ-7597 TCGA-HU-8608 
       22.29        77.29        63.06        52.21        26.47        21.07 
TCGA-HU-A4GY TCGA-HU-A4H2 TCGA-HU-A4HD TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8663 
        0.26        12.95        33.40        36.36         3.45         3.39 
TCGA-IN-A6RI TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NT TCGA-RD-A7BS TCGA-RD-A8N0 
       18.38        19.53         6.74        10.62        11.05        40.64 
TCGA-SW-A7EB TCGA-VQ-A8DT TCGA-VQ-A8E7 TCGA-VQ-A8PF TCGA-VQ-A8PJ TCGA-VQ-A8PK 
        5.79        48.79        37.41         2.50         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PS TCGA-VQ-A8PZ TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91U 
        1.87        13.35        73.41        61.22        18.74         1.71 
TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A925 TCGA-VQ-A94O TCGA-VQ-AA6A 
       42.64        60.85         9.50         4.54        21.04        38.93 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6K 
       54.12        26.04        16.14        12.43 

$subtype2
TCGA-VQ-A8PU TCGA-B7-5816 TCGA-BR-4184 TCGA-BR-4280 TCGA-BR-6452 TCGA-BR-6566 
       27.35        26.70         6.97         6.61        34.68        32.78 
TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-8286 TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8366 
       36.16        35.24        29.42         6.18        31.10         0.95 
TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8589 TCGA-BR-8680 TCGA-BR-A4J8 TCGA-BR-A4QL 
       31.27         7.36        27.12        31.96        13.51        16.14 
TCGA-BR-A4QM TCGA-CD-8526 TCGA-CD-8535 TCGA-CD-8536 TCGA-CD-A4MG TCGA-CD-A4MJ 
        5.13        12.53        12.82        12.43         6.58        12.62 
TCGA-CG-4438 TCGA-CG-4469 TCGA-CG-5724 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-6525 
       54.08         7.07        12.03         7.99        25.71        13.35 
TCGA-D7-6528 TCGA-D7-A4YY TCGA-HF-A5NB TCGA-HU-8602 TCGA-HU-A4GQ TCGA-HU-A4GT 
       15.22        13.78        30.51        22.32         0.10         6.51 
TCGA-HU-A4GU TCGA-HU-A4GX TCGA-IP-7968 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
        6.58        20.25         2.53        21.73        38.14        37.22 
TCGA-VQ-A8PO TCGA-VQ-A8PT TCGA-VQ-A91D TCGA-VQ-A91Z TCGA-VQ-AA64 TCGA-VQ-AA69 
        9.27        29.59        11.70        55.56        18.41        28.41 
TCGA-VQ-AA6B 
       32.94 

$subtype3
TCGA-KB-A93G TCGA-B7-5818 TCGA-B7-A5TN TCGA-BR-4201 TCGA-BR-4267 TCGA-BR-4279 
       20.15        11.70         9.44        30.90         6.18         9.57 
TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8060 TCGA-BR-8081 TCGA-BR-8285 
        8.98        30.90        44.94        11.44        32.25         0.56 
TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8591 TCGA-BR-8676 
       19.96         7.40        25.05         5.39        28.14         7.53 
TCGA-BR-8677 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4IZ TCGA-BR-A4PF TCGA-CD-5813 
       26.73        10.68         7.53         8.98         1.15        12.39 
TCGA-CD-8528 TCGA-CD-8534 TCGA-CD-A487 TCGA-CG-4300 TCGA-CG-4436 TCGA-CG-4437 
       12.33        12.07        12.30        20.02         7.99         8.05 
TCGA-CG-4455 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5723 TCGA-CG-5728 TCGA-CG-5733 
       12.03        30.97        36.00       105.07        65.10        21.07 
TCGA-D7-6815 TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8573 TCGA-D7-8574 TCGA-D7-A4YU 
       15.98        11.31        12.33        19.50        17.19        16.44 
TCGA-D7-A4YX TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A748 TCGA-EQ-8122 TCGA-F1-6874 
       36.43        11.24        20.32         4.34         7.99        14.47 
TCGA-F1-A448 TCGA-HU-8610 TCGA-HU-A4GF TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H5 
       21.27         0.76        25.81        29.00        23.84        23.80 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-RD-A7BT TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 
       15.75        13.51         8.61        16.67       122.30       115.69 
TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8P5 
       19.04         0.92         5.46        18.48        43.36         7.73 
TCGA-VQ-A8PC TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PX TCGA-VQ-A91S TCGA-VQ-A92D 
       46.26        22.19        12.79        64.57        32.88        66.81 
TCGA-VQ-A94R TCGA-VQ-AA6D TCGA-ZA-A8F6 
       42.54        17.13        17.26 

$subtype4
TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-6456 TCGA-BR-6457 
        4.64         7.43         4.08         9.34        17.29        13.68 
TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
       26.10        25.61        40.21        31.20        21.90         9.21 
TCGA-BR-7722 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8058 
       15.32         3.45         9.07        29.56        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8289 TCGA-BR-8362 TCGA-BR-8363 TCGA-BR-8364 
       14.43         9.60         2.66        13.08         0.26        22.19 
TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 TCGA-BR-8371 TCGA-BR-8384 
       17.52        26.33        14.04         3.32        11.80         3.72 
TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A44T TCGA-BR-A4CS 
       12.79         6.28        32.58         9.86        34.13         1.48 
TCGA-BR-A4IU TCGA-BR-A4IY TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J9 
       27.55        12.89        28.34         0.66        32.52         0.46 
TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-8530 TCGA-CD-A489 TCGA-CD-A48A 
       21.44        13.41        11.21        12.39        11.31        12.43 
TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5719 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6524 
       12.00         6.97         1.02        19.13        18.54        17.85 
TCGA-D7-8572 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6EX TCGA-D7-A6EY TCGA-IN-8462 
       16.80         5.92        14.76        11.31        11.44        18.81 
TCGA-IN-A6RL TCGA-IN-A6RS TCGA-IN-A7NR TCGA-IN-A7NU TCGA-KB-A6F5 TCGA-KB-A93H 
       13.35        12.59         6.51        11.70         5.56        37.64 
TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8NB TCGA-VQ-A8PD TCGA-VQ-A8PP 
        3.72         5.13        37.91        16.87        16.31        23.41 
TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A94P 
       15.65         9.73         2.01         5.72         2.66 

subtype1 subtype2 subtype3 subtype4 
    0.26     0.10     0.56     0.26 
subtype1 subtype2 subtype3 subtype4 
   79.07    55.56   122.30    40.21 
subtype1 subtype2 subtype3 subtype4 
  15.485   16.140   16.670   12.790 
[1] "0.3 - 79.1 (15.5)"  "0.1 - 55.6 (16.1)"  "0.6 - 122.3 (16.7)"
[4] "0.3 - 40.2 (12.8)" 
D4V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        6       13       13         8        15         0
  subtype2       1        1        3        3         7         5         1
  subtype3       0        3       14        7         7        12         0
  subtype4       0        1        2        6        10        12         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         31         17         11       16
  subtype2         13          8          7        4
  subtype3         11         14          5        3
  subtype4         12         12          9       10
D4V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        1        0        0
  STAGE IA          6        1        3        1
  STAGE IB         13        3       14        2
  STAGE II         13        3        7        6
  STAGE IIA         8        7        7       10
  STAGE IIB        15        5       12       12
  STAGE III         0        1        0        1
  STAGE IIIA       31       13       11       12
  STAGE IIIB       17        8       14       12
  STAGE IIIC       11        7        5        9
  STAGE IV         16        4        3       10
[1] 11  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  7 33 58 38
  subtype2  3  6 29 18
  subtype3  3 27 31 17
  subtype4  1 10 38 28
D4V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        7        3        3        1
  T2       33        6       27       10
  T3       58       29       31       38
  T4       38       18       17       28
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 39 44 23 27
  subtype2 19 15 12  9
  subtype3 29 14 18 15
  subtype4 22 23 12 20
D4V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       39       19       29       22
  N1       44       15       14       23
  N2       23       12       18       12
  N3       27        9       15       20
[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"
D4V6, binary
          cls
clus         0   1
  subtype1 123  11
  subtype2  51   2
  subtype3  75   2
  subtype4  73   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  123   11
  subtype2   51    2
  subtype3   75    2
  subtype4   73    6
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0      123       51       75       73
  1       11        2        2        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"
D4V7, binary
          cls
clus        0  1
  subtype1 42 98
  subtype2 23 35
  subtype3 25 54
  subtype4 31 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   42   98
  subtype2   23   35
  subtype3   25   54
  subtype4   31   49
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       42       23       25       31
  MALE         98       35       54       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"
D4V8, binary
          cls
clus        0  1
  subtype1 96 29
  subtype2 38  9
  subtype3 59 14
  subtype4 72  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   96   29
  subtype2   38    9
  subtype3   59   14
  subtype4   72    5
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        96       38       59       72
  YES       29        9       14        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"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        6
  subtype2                                        1
  subtype3                                        2
  subtype4                                        1
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                    18
  subtype2                                     7
  subtype3                                    11
  subtype4                                    16
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     59
  subtype2                                                     26
  subtype3                                                     25
  subtype4                                                     39
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 7
  subtype2                                                 2
  subtype3                                                 3
  subtype4                                                 7
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                30
  subtype2                                                                13
  subtype3                                                                20
  subtype4                                                                 6
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  2
  subtype2                                                  1
  subtype3                                                  1
  subtype4                                                  1
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               16
  subtype2                                                8
  subtype3                                               17
  subtype4                                                9
D4V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 6
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   18
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  59
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       30
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        16
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    7
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       13
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         8
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   11
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  25
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       20
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        17
                                                                   clus
vv                                                                  subtype4
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  39
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         9
[1] 7 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 106   6   8   8
  subtype2  45   2   1   8
  subtype3  68   2   2   4
  subtype4  63   5   3   5
D4V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0      106       45       68       63
  R1        6        2        2        5
  R2        8        1        2        3
  RX        8        8        4        5
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D4V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    30                         2
  subtype2    11                         1
  subtype3    12                         2
  subtype4    13                         0
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    79
  subtype2                                         0    40
  subtype3                                         1    52
  subtype4                                         0    61
D4V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           30       11       12       13
  BLACK OR AFRICAN AMERICAN                        2        1        2        0
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        1        0
  WHITE                                           79       40       52       61
[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"
D4V13, binary
          cls
clus        0  1
  subtype1  1 93
  subtype2  0 41
  subtype3  1 54
  subtype4  0 67
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   93
  subtype2    0   41
  subtype3    1   54
  subtype4    0   67
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            1        0        1        0
  NOT HISPANIC OR LATINO       93       41       54       67
[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(5) Variable = MRNASEQ_CNMF
D5V1, survival
          sevent
clus2       0  1
  subtype1 50 37
  subtype2 41 47
  subtype3 60 30
  subtype4 47 31
  subtype5 33 13
subtype1 subtype2 subtype3 subtype4 subtype5 
      87       88       90       78       46 
subtype1 subtype2 subtype3 subtype4 subtype5 
      37       47       30       31       13 
$subtype1
TCGA-CG-4460 TCGA-CG-4475 TCGA-MX-A663 TCGA-3M-AB46 TCGA-BR-7197 TCGA-BR-7704 
       21.99        22.98         9.86        58.03         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8077 TCGA-BR-8289 
       33.63        39.78        28.73         3.45         0.69         2.66 
TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8483 TCGA-BR-8485 TCGA-BR-8676 TCGA-BR-8678 
        2.20        14.79         5.39         9.21         7.53        24.79 
TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-CD-5800 
        8.22        10.68         7.53         1.48         0.72        13.15 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8533 
       12.10        12.76        12.59        12.53         7.17        15.39 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A TCGA-CD-A4MH TCGA-CG-4440 TCGA-CG-4443 
       12.82         6.31        12.43        12.20         4.01        29.98 
TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6818 
       18.97        36.00        15.02        18.84        17.19        12.36 
TCGA-D7-6820 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A4YT TCGA-D7-A6EX 
       11.31        12.33        16.80        21.14        14.27        11.31 
TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-F1-6875 TCGA-FP-7735 TCGA-FP-8631 TCGA-HU-8243 
       22.29         7.99        72.23         3.48         0.56         5.92 
TCGA-HU-A4GD TCGA-HU-A4GH TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A7NT 
       22.75        11.77        23.80        33.40        18.38        10.62 
TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZF 
        2.53        63.62        37.64        14.04        45.67         8.52 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU 
        6.08        16.67        37.91         8.94         5.79         5.46 
TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH 
       13.25        13.02        18.48        43.36        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA64 
        2.70        17.85        55.56         9.04        21.04        18.41 
TCGA-VQ-AA6D TCGA-VQ-AA6J TCGA-ZQ-A9CR 
       17.13        27.55         0.79 

$subtype2
TCGA-KB-A93G TCGA-VQ-A94U TCGA-BR-4187 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 
       20.15        26.93         4.64         4.08         9.34         9.57 
TCGA-BR-6455 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6458 TCGA-BR-6563 TCGA-BR-6564 
       13.87        17.29        13.68        19.33        39.12        26.10 
TCGA-BR-6565 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6709 TCGA-BR-6801 TCGA-BR-6803 
        9.17        25.61        18.05        12.16        40.21        31.20 
TCGA-BR-7196 TCGA-BR-7957 TCGA-BR-7958 TCGA-BR-7959 TCGA-BR-8060 TCGA-BR-8080 
       21.90         9.07        29.56        33.21        11.44         9.60 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 
       32.25         8.05        19.96         7.40        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8384 
       22.19        17.52        26.33        14.04        11.80         3.72 
TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8686 
       12.79         9.34         6.28        26.73        32.58        20.88 
TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 
       34.13         6.08        27.55        28.57         8.98        14.17 
TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5803 
       28.34        32.52        13.51         0.46        13.41        11.21 
TCGA-CD-5813 TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8534 TCGA-CD-A489 TCGA-CD-A4MI 
       12.39        12.39        12.59        12.07        11.31        11.77 
TCGA-CG-4472 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YU 
       12.00        19.13        18.61        17.19        20.91        16.44 
TCGA-D7-A4YV TCGA-D7-A747 TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        5.92         8.38        14.07        22.29        59.54         5.03 
TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-IN-7808 TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BW 
        0.10         0.26         3.45         3.72        19.73         5.13 
TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8PQ TCGA-VQ-A91Y 
      116.38        71.38        35.61        16.87        15.65         9.73 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R TCGA-ZA-A8F6 
        5.72         2.66        42.54        17.26 

$subtype3
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-4201 TCGA-BR-4257 
       26.70        11.70         9.47         9.44        30.90         9.67 
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-8059 
       34.68        30.90        44.94        35.84        18.15        14.43 
TCGA-BR-8078 TCGA-BR-8286 TCGA-BR-8361 TCGA-BR-8366 TCGA-BR-8372 TCGA-BR-8381 
       29.59        29.42        31.10         0.95        31.27         7.36 
TCGA-BR-8382 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 TCGA-BR-8680 TCGA-BR-A4IY 
       25.05         1.12        27.12        28.14        31.96        12.89 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PE TCGA-CD-5801 TCGA-CD-8528 TCGA-CD-8536 
        0.53         0.66        20.42        13.18        12.33        12.43 
TCGA-CD-A487 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-CG-4449 TCGA-CG-4477 
       12.30        11.61         6.58        12.62        19.07        30.97 
TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5723 TCGA-CG-5724 TCGA-D7-5577 TCGA-D7-6519 
        6.97         6.02       105.07        12.03        25.71        20.55 
TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-8573 TCGA-D7-A4YX TCGA-D7-A4YY TCGA-D7-A6EY 
       17.85        13.35        19.50        36.43        13.78        11.44 
TCGA-D7-A6EZ TCGA-D7-A748 TCGA-D7-A74A TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BE 
       20.32         4.34        19.96        19.53        17.06        11.08 
TCGA-FP-A4BF TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4G6 
        5.52        30.51        26.47        22.32        22.82        24.26 
TCGA-HU-A4GN TCGA-HU-A4GU TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-8462 
       29.98         6.58         2.10        29.00        23.84        18.81 
TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-R5-A7ZE 
        3.39        12.46        11.70        15.75        13.51        18.21 
TCGA-RD-A7BS TCGA-RD-A8N5 TCGA-SW-A7EA TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8P3 
       11.05        57.44        19.04        21.73        38.14        37.22 
TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PP TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91K 
        7.73        34.29        23.41        39.45        11.70        61.22 
TCGA-VQ-A91Q TCGA-VQ-A924 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA69 TCGA-VQ-AA6K 
       20.81        55.43        66.81        11.24        28.41        12.43 

$subtype4
TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-B7-A5TI TCGA-BR-4191 TCGA-BR-4253 
       16.24         0.23        27.35        19.56        18.35         4.08 
TCGA-BR-4267 TCGA-BR-6707 TCGA-BR-7722 TCGA-BR-8058 TCGA-BR-8296 TCGA-BR-8484 
        6.18        19.89        15.32        37.25        15.58        25.18 
TCGA-BR-A4PD TCGA-CD-8529 TCGA-CD-8532 TCGA-CG-4301 TCGA-CG-4306 TCGA-CG-4437 
       20.65        12.30        11.64         3.02         1.02         8.05 
TCGA-CG-4462 TCGA-CG-5719 TCGA-CG-5722 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 
        0.00         1.02         0.99        28.96        69.04         7.99 
TCGA-D7-6521 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8575 TCGA-D7-8576 
       18.54        10.26        12.79        24.72        18.21        14.66 
TCGA-D7-A6EV TCGA-F1-A72C TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 
       11.24        11.38        13.58         6.21        77.29        63.06 
TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4G9 
       21.07         0.76        24.30         5.59        22.68        24.20 
TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H6 TCGA-HU-A4H8 
       21.37         8.98        20.25        12.95        21.17        14.07 
TCGA-HU-A4HB TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RR TCGA-IN-A7NR TCGA-KB-A93J 
       15.68        13.35        19.53         6.74         6.51        36.95 
TCGA-R5-A7ZI TCGA-R5-A805 TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-VQ-A8DT 
       74.53         9.24       122.30        40.64       115.69        48.79 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PX 
       30.97        46.26        16.31         2.50         1.87        64.57 
TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A925 
       21.83        18.74        42.64        60.85         2.01         4.54 
TCGA-VQ-A927 TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
        6.58        43.66        38.93        54.12        26.04        16.14 

$subtype5
TCGA-CG-4444 TCGA-B7-A5TJ TCGA-BR-4280 TCGA-BR-6453 TCGA-BR-6566 TCGA-BR-7703 
       47.05        11.01         6.61        15.95        32.78        36.16 
TCGA-BR-8368 TCGA-BR-8486 TCGA-BR-8683 TCGA-BR-A44U TCGA-BR-A4PF TCGA-BR-A4QI 
        4.31        20.22         9.86        13.87         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 
       16.14         5.13        13.02        27.02        15.95         7.99 
TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-5720 TCGA-D7-5578 
       54.08        14.01         9.01         7.07         0.99        12.66 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4Z0 TCGA-D7-A6F2 TCGA-F1-6874 TCGA-F1-A448 
       15.22        15.98        14.76        15.65        14.47        21.27 
TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8249 TCGA-HU-A4GC TCGA-HU-A4GF 
       52.21         1.51        24.39        28.96         3.25        25.81 
TCGA-HU-A4GT TCGA-IN-7806 TCGA-IN-A6RS TCGA-RD-A7BT TCGA-VQ-A8E7 TCGA-VQ-A8PO 
        6.51        36.36        12.59         8.61        37.41         9.27 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-AA6B 
       32.88         1.71         9.50        32.94 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.56     0.10     0.53     0.00     0.99 
subtype1 subtype2 subtype3 subtype4 subtype5 
   72.23   116.38   105.07   122.30    54.08 
subtype1 subtype2 subtype3 subtype4 subtype5 
  12.820   13.955   19.055   17.260   14.615 
[1] "0.6 - 72.2 (12.8)"  "0.1 - 116.4 (14.0)" "0.5 - 105.1 (19.1)"
[4] "0.0 - 122.3 (17.3)" "1.0 - 54.1 (14.6)" 
D5V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        3       12        7         7        10         1
  subtype2       0        0        8        7         7        17         0
  subtype3       0        4        9        8        14        14         1
  subtype4       0        4        3        5         5        10         0
  subtype5       1        5        7        2         5         5         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         21         12          7        8
  subtype2         17         14         12        7
  subtype3         16          7          9        7
  subtype4         14         15          9       13
  subtype5          6          9          0        6
D5V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           1        0        0        0        1
  STAGE IA          3        0        4        4        5
  STAGE IB         12        8        9        3        7
  STAGE II          7        7        8        5        2
  STAGE IIA         7        7       14        5        5
  STAGE IIB        10       17       14       10        5
  STAGE III         1        0        1        0        1
  STAGE IIIA       21       17       16       14        6
  STAGE IIIB       12       14        7       15        9
  STAGE IIIC        7       12        9        9        0
  STAGE IV          8        7        7       13        6
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  4 22 46 20
  subtype2  0 14 42 36
  subtype3  4 21 40 26
  subtype4  7 15 35 24
  subtype5  7 16 18  9
D5V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        4        0        4        7        7
  T2       22       14       21       15       16
  T3       46       42       40       35       18
  T4       20       36       26       24        9
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 27 26 18 17
  subtype2 29 26 13 23
  subtype3 35 26 14 15
  subtype4 15 25 20 21
  subtype5 17  9 15  6
D5V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       27       29       35       15       17
  N1       26       26       26       25        9
  N2       18       13       14       20       15
  N3       17       23       15       21        6
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V6, binary
          cls
clus        0  1
  subtype1 79  7
  subtype2 85  5
  subtype3 89  3
  subtype4 68  9
  subtype5 46  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   79    7
  subtype2   85    5
  subtype3   89    3
  subtype4   68    9
  subtype5   46    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       79       85       89       68       46
  1        7        5        3        9        3
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V7, binary
          cls
clus        0  1
  subtype1 32 62
  subtype2 39 56
  subtype3 32 62
  subtype4 29 53
  subtype5 15 35
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   32   62
  subtype2   39   56
  subtype3   32   62
  subtype4   29   53
  subtype5   15   35
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       32       39       32       29       15
  MALE         62       56       62       53       35
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V8, binary
          cls
clus        0  1
  subtype1 69 14
  subtype2 81 11
  subtype3 69 20
  subtype4 48 22
  subtype5 36  5
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   14
  subtype2   81   11
  subtype3   69   20
  subtype4   48   22
  subtype5   36    5
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        69       81       69       48       36
  YES       14       11       20       22        5
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        4
  subtype3                                        3
  subtype4                                        3
  subtype5                                        1
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                     2
  subtype2                                    30
  subtype3                                    16
  subtype4                                    16
  subtype5                                     5
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     35
  subtype2                                                     39
  subtype3                                                     42
  subtype4                                                     22
  subtype5                                                     17
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 2
  subtype2                                                 7
  subtype3                                                 6
  subtype4                                                 3
  subtype5                                                 2
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                26
  subtype2                                                                 6
  subtype3                                                                11
  subtype4                                                                18
  subtype5                                                                12
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  2
  subtype2                                                  1
  subtype3                                                  2
  subtype4                                                  1
  subtype5                                                  1
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               25
  subtype2                                                7
  subtype3                                               14
  subtype4                                               18
  subtype5                                               12
D5V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    2
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  35
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       26
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        25
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   30
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  39
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        6
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         7
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       11
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        14
                                                                   clus
vv                                                                  subtype4
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  22
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        18
                                                                   clus
vv                                                                  subtype5
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  17
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        2
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        12
[1] 7 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 74  3  4  4
  subtype2 72  4  3  7
  subtype3 78  5  1  4
  subtype4 65  4  6  4
  subtype5 41  1  3  3
D5V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       74       72       78       65       41
  R1        3        4        5        4        1
  R2        4        3        1        6        3
  RX        4        7        4        4        3
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    20                         8
  subtype2    23                         0
  subtype3    19                         1
  subtype4    16                         1
  subtype5     9                         2
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    54
  subtype2                                         0    71
  subtype3                                         0    62
  subtype4                                         0    46
  subtype5                                         1    27
D5V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           20       23       19       16
  BLACK OR AFRICAN AMERICAN                        8        0        1        1
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        0
  WHITE                                           54       71       62       46
                                           clus
vv                                          subtype5
  ASIAN                                            9
  BLACK OR AFRICAN AMERICAN                        2
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        1
  WHITE                                           27
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D5V13, binary
          cls
clus        0  1
  subtype1  2 67
  subtype2  1 86
  subtype3  0 71
  subtype4  1 46
  subtype5  1 32
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    2   67
  subtype2    1   86
  subtype3    0   71
  subtype4    1   46
  subtype5    1   32
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            2        1        0        1        1
  NOT HISPANIC OR LATINO       67       86       71       46       32
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(6) Variable = MRNASEQ_CHIERARCHICAL
D6V1, survival
          sevent
clus2       0  1
  subtype1 65 37
  subtype2 38 41
  subtype3 72 57
  subtype4 56 23
subtype1 subtype2 subtype3 subtype4 
     102       79      129       79 
subtype1 subtype2 subtype3 subtype4 
      37       41       57       23 
$subtype1
TCGA-CG-4460 TCGA-EQ-A4SO TCGA-FP-A8CX TCGA-KB-A93G TCGA-VQ-A8PU TCGA-3M-AB46 
       21.99        16.24         0.23        20.15        27.35        58.03 
TCGA-B7-A5TI TCGA-B7-A5TN TCGA-BR-4191 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4279 
       19.56         9.44        18.35         9.67         6.18         9.57 
TCGA-BR-6452 TCGA-BR-6802 TCGA-BR-7722 TCGA-BR-8058 TCGA-BR-8286 TCGA-BR-8296 
       34.68        30.90        15.32        37.25        29.42        15.58 
TCGA-BR-8484 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8687 TCGA-BR-A4PD TCGA-BR-A4PE 
       25.18        12.79         9.34         8.22        20.65        20.42 
TCGA-CD-8529 TCGA-CD-8532 TCGA-CD-8536 TCGA-CG-4301 TCGA-CG-4305 TCGA-CG-4306 
       12.30        11.64        12.43         3.02        15.95         1.02 
TCGA-CG-4437 TCGA-CG-4462 TCGA-CG-5718 TCGA-CG-5726 TCGA-CG-5732 TCGA-CG-5734 
        8.05         0.00        36.00        28.96        69.04         7.99 
TCGA-D7-6521 TCGA-D7-6524 TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-6820 TCGA-D7-8575 
       18.54        17.85        10.26        12.79        11.31        18.21 
TCGA-D7-8576 TCGA-D7-8578 TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A74A TCGA-F1-A448 
       14.66        21.14        14.76        11.24        19.96        21.27 
TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-8211 TCGA-FP-8631 TCGA-FP-A9TM TCGA-HF-7132 
       11.38         3.48        13.58         0.56         6.21        77.29 
TCGA-HF-7133 TCGA-HU-8238 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G8 
       63.06         1.51         0.76        24.30         5.59        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GP TCGA-HU-A4GX TCGA-HU-A4H2 
       24.20         3.25        21.37         8.98        20.25        12.95 
TCGA-HU-A4H4 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-A6RI TCGA-IN-A6RL 
       23.84        21.17        14.07        15.68        18.38        13.35 
TCGA-IN-A6RN TCGA-IN-A6RR TCGA-KB-A93J TCGA-MX-A5UJ TCGA-R5-A7ZI TCGA-R5-A805 
       19.53         6.74        36.95        19.73        74.53         9.24 
TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-VQ-A8DT TCGA-VQ-A8E0 
      122.30        40.64       115.69        57.44        48.79        18.48 
TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PK TCGA-VQ-A8PM TCGA-VQ-A8PX 
       30.97        46.26        16.31        17.85         1.87        64.57 
TCGA-VQ-A91A TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A925 TCGA-VQ-A927 
       39.45        21.83        18.74        42.64         4.54         6.58 
TCGA-VQ-AA68 TCGA-VQ-AA6A TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I TCGA-VQ-AA6J 
       43.66        38.93        54.12        26.04        16.14        27.55 

$subtype2
TCGA-VQ-A94U TCGA-B7-5816 TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4201 TCGA-BR-4255 
       26.93        26.70         9.47         4.64        30.90         4.08 
TCGA-BR-4256 TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 
        9.34        15.95        17.29        13.68        39.12        26.10 
TCGA-BR-6705 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8059 
       25.61        40.21        31.20         9.07        33.21        14.43 
TCGA-BR-8080 TCGA-BR-8284 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8363 
        9.60         8.05        19.96         7.40        13.08         0.26 
TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 
       22.19        17.52         0.95        26.33        14.04        11.80 
TCGA-BR-8384 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 
        3.72         6.28        26.73        32.58        34.13         6.08 
TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 
       27.55        28.57         8.98        14.17        28.34        32.52 
TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-5813 TCGA-CD-8534 
       13.51         0.46        13.41        11.21        12.39        12.07 
TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5719 TCGA-D7-6518 
       12.30        11.31        11.77        12.00         1.02        19.13 
TCGA-D7-6522 TCGA-D7-8574 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A6EY 
       18.61        17.19        20.91        16.44         5.92        11.44 
TCGA-D7-A747 TCGA-D7-A748 TCGA-FP-7916 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ 
        8.38         4.34        14.07        59.54         5.03         0.10 
TCGA-HU-A4GY TCGA-IN-7808 TCGA-MX-A5UG TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 
        0.26         3.45         3.72         5.13       116.38        71.38 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A94P TCGA-VQ-A94R 
       35.61        16.87        15.65         9.73         2.66        42.54 
TCGA-ZA-A8F6 
       17.26 

$subtype3
TCGA-CG-4475 TCGA-MX-A663 TCGA-B7-5818 TCGA-BR-4253 TCGA-BR-6455 TCGA-BR-6458 
       22.98         9.86        11.70         4.08        13.87        19.33 
TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-7196 TCGA-BR-7197 TCGA-BR-7704 
       18.05        19.89        12.16        21.90         9.21        35.24 
TCGA-BR-7715 TCGA-BR-7716 TCGA-BR-7717 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-7958 
       33.63        39.78        18.15        28.73         3.45        29.56 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8381 
       11.44         0.69         2.66         2.20        14.79         7.36 
TCGA-BR-8485 TCGA-BR-8589 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8686 TCGA-BR-A452 
        9.21        27.12         7.53        24.79        20.88         7.53 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J1 TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-CD-5800 
        1.48        12.89         0.72         0.53         0.66        13.15 
TCGA-CD-5801 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
       13.18        12.10        12.76        12.59        12.53         7.17 
TCGA-CD-8530 TCGA-CD-8531 TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A48A 
       12.39        12.59        15.39        12.82         6.31        12.43 
TCGA-CD-A48C TCGA-CD-A4MH TCGA-CG-4440 TCGA-CG-4443 TCGA-CG-4449 TCGA-CG-4466 
       11.61        12.20         4.01        29.98        19.07        18.97 
TCGA-CG-4477 TCGA-CG-5717 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 
       30.97         6.97         6.02         0.99       105.07        12.03 
TCGA-CG-5725 TCGA-D7-5577 TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6818 
       15.02        25.71        20.55        18.84        13.35        12.36 
TCGA-D7-6822 TCGA-D7-8570 TCGA-D7-8572 TCGA-D7-8573 TCGA-D7-A4YT TCGA-D7-A4YX 
       12.33        24.72        16.80        19.50        14.27        36.43 
TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-F1-6875 TCGA-FP-7998 TCGA-HU-8243 
       11.31        20.32        22.29        72.23        22.29         5.92 
TCGA-HU-8608 TCGA-HU-A4G6 TCGA-HU-A4GH TCGA-HU-A4H0 TCGA-HU-A4H5 TCGA-HU-A4HD 
       21.07        24.26        11.77         2.10        23.80        33.40 
TCGA-IN-8462 TCGA-IN-8663 TCGA-IN-A6RJ TCGA-IN-A7NR TCGA-IN-A7NT TCGA-IN-A7NU 
       18.81         3.39        12.46         6.51        10.62        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F7 TCGA-KB-A93H TCGA-MX-A666 
       15.75        13.51         2.53        63.62        37.64        14.04 
TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR TCGA-RD-A7BS TCGA-RD-A7C1 
       45.67        18.21         8.52         6.08        11.05        16.67 
TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ 
       37.91         8.94         5.79         5.46        13.25        13.02 
TCGA-VQ-A8E2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH 
       43.36        37.22         7.73        22.19         2.50        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PP TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A91Z TCGA-VQ-A922 
        2.70        23.41        20.81        60.85        55.56         9.04 
TCGA-VQ-A923 TCGA-VQ-A928 TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA69 
        2.01         5.72        21.04        11.24        18.41        28.41 
TCGA-VQ-AA6D TCGA-VQ-AA6K TCGA-ZQ-A9CR 
       17.13        12.43         0.79 

$subtype4
TCGA-CG-4444 TCGA-B7-A5TJ TCGA-BR-4280 TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6852 
       47.05        11.01         6.61         9.17        32.78        44.94 
TCGA-BR-7703 TCGA-BR-7707 TCGA-BR-8078 TCGA-BR-8081 TCGA-BR-8361 TCGA-BR-8368 
       36.16        35.84        29.59        32.25        31.10         4.31 
TCGA-BR-8372 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8591 
       31.27        25.05         5.39        20.22         1.12        28.14 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-8690 TCGA-BR-A44U TCGA-BR-A4PF TCGA-BR-A4QI 
       31.96         9.86        10.68        13.87         1.15        21.44 
TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-5799 TCGA-CD-8528 TCGA-CD-A4MG TCGA-CD-A4MJ 
       16.14         5.13        13.02        12.33         6.58        12.62 
TCGA-CG-4304 TCGA-CG-4436 TCGA-CG-4438 TCGA-CG-4441 TCGA-CG-4465 TCGA-CG-4469 
       27.02         7.99        54.08        14.01         9.01         7.07 
TCGA-CG-5720 TCGA-D7-5578 TCGA-D7-6526 TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-A4YY 
        0.99        12.66        17.19        15.22        15.98        13.78 
TCGA-D7-A6F2 TCGA-EQ-8122 TCGA-F1-6874 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-A4BE 
       15.65         7.99        14.47        19.53        17.06        11.08 
TCGA-FP-A4BF TCGA-HF-7134 TCGA-HF-A5NB TCGA-HJ-7597 TCGA-HU-8244 TCGA-HU-8249 
        5.52        52.21        30.51        26.47        24.39        28.96 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GN TCGA-HU-A4GT 
       22.32        22.82        22.75        25.81        29.98         6.51 
TCGA-HU-A4GU TCGA-HU-A4H3 TCGA-IN-7806 TCGA-IN-A6RS TCGA-RD-A7BT TCGA-SW-A7EA 
        6.58        29.00        36.36        12.59         8.61        19.04 
TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8PB TCGA-VQ-A8PO TCGA-VQ-A91D 
       21.73        37.41        38.14        34.29         9.27        11.70 
TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X TCGA-VQ-A924 TCGA-VQ-A92D 
       61.22        32.88         1.71         9.50        55.43        66.81 
TCGA-VQ-AA6B 
       32.94 

subtype1 subtype2 subtype3 subtype4 
    0.00     0.10     0.53     0.99 
subtype1 subtype2 subtype3 subtype4 
  122.30   116.38   105.07    66.81 
subtype1 subtype2 subtype3 subtype4 
  18.365   13.680   13.020   17.190 
[1] "0.0 - 122.3 (18.4)" "0.1 - 116.4 (13.7)" "0.5 - 105.1 (13.0)"
[4] "1.0 - 66.8 (17.2)" 
D6V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        4        8       11         6        15         0
  subtype2       0        0        6        5         9        12         1
  subtype3       0        6       11       10        11        16         1
  subtype4       1        6       14        3        12        13         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         17         17         11       11
  subtype2         14         12         10        7
  subtype3         30         19          9       16
  subtype4         13          9          7        7
D6V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4
  STAGE I           1        0        0        1
  STAGE IA          4        0        6        6
  STAGE IB          8        6       11       14
  STAGE II         11        5       10        3
  STAGE IIA         6        9       11       12
  STAGE IIB        15       12       16       13
  STAGE III         0        1        1        1
  STAGE IIIA       17       14       30       13
  STAGE IIIB       17       12       19        9
  STAGE IIIC       11       10        9        7
  STAGE IV         11        7       16        7
[1] 11  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  9 27 41 29
  subtype2  0 12 36 32
  subtype3  6 28 69 30
  subtype4  7 21 35 24
D6V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  T1        9        0        6        7
  T2       27       12       28       21
  T3       41       36       69       35
  T4       29       32       30       24
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 24 30 30 21
  subtype2 23 23 10 21
  subtype3 35 44 22 28
  subtype4 41 15 18 12
D6V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  N0       24       23       35       41
  N1       30       23       44       15
  N2       30       10       22       18
  N3       21       21       28       12
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V6, binary
          cls
clus         0   1
  subtype1  94   7
  subtype2  73   6
  subtype3 120  10
  subtype4  80   4
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   94    7
  subtype2   73    6
  subtype3  120   10
  subtype4   80    4
   clus
vv  subtype1 subtype2 subtype3 subtype4
  0       94       73      120       80
  1        7        6       10        4
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V7, binary
          cls
clus        0  1
  subtype1 37 72
  subtype2 36 47
  subtype3 40 95
  subtype4 34 54
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   37   72
  subtype2   36   47
  subtype3   40   95
  subtype4   34   54
        clus
vv       subtype1 subtype2 subtype3 subtype4
  FEMALE       37       36       40       34
  MALE         72       47       95       54
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V8, binary
          cls
clus         0   1
  subtype1  69  26
  subtype2  70  10
  subtype3 101  23
  subtype4  63  13
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   69   26
  subtype2   70   10
  subtype3  101   23
  subtype4   63   13
     clus
vv    subtype1 subtype2 subtype3 subtype4
  NO        69       70      101       63
  YES       26       10       23       13
[1] 2 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        4
  subtype2                                        3
  subtype3                                        2
  subtype4                                        3
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                    17
  subtype2                                    30
  subtype3                                    13
  subtype4                                     9
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     38
  subtype2                                                     28
  subtype3                                                     55
  subtype4                                                     34
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 7
  subtype2                                                 7
  subtype3                                                 3
  subtype4                                                 3
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                21
  subtype2                                                                 8
  subtype3                                                                25
  subtype4                                                                19
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  1
  subtype2                                                  0
  subtype3                                                  4
  subtype4                                                  2
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               20
  subtype2                                                6
  subtype3                                               32
  subtype4                                               18
D6V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   17
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  38
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       21
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        20
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   30
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  28
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        8
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         6
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   13
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  55
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       25
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        32
                                                                   clus
vv                                                                  subtype4
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  34
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        18
[1] 7 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1  85   6   6   7
  subtype2  61   3   3   6
  subtype3 111   5   5   5
  subtype4  73   3   3   4
D6V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4
  R0       85       61      111       73
  R1        6        3        5        3
  R2        6        3        5        3
  RX        7        6        5        4
[1] 4 4
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D6V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN
  subtype1    19                         4
  subtype2    21                         0
  subtype3    29                         5
  subtype4    18                         3
          vv
clus       NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER WHITE
  subtype1                                         0    67
  subtype2                                         0    60
  subtype3                                         0    80
  subtype4                                         1    53
D6V12, multiclass
                                           clus
vv                                          subtype1 subtype2 subtype3 subtype4
  ASIAN                                           19       21       29       18
  BLACK OR AFRICAN AMERICAN                        4        0        5        3
  NATIVE HAWAIIAN OR OTHER PACIFIC ISLANDER        0        0        0        1
  WHITE                                           67       60       80       53
[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"
D6V13, binary
          cls
clus        0  1
  subtype1  3 68
  subtype2  0 76
  subtype3  2 95
  subtype4  0 63
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   68
  subtype2    0   76
  subtype3    2   95
  subtype4    0   63
                        clus
vv                       subtype1 subtype2 subtype3 subtype4
  HISPANIC OR LATINO            3        0        2        0
  NOT HISPANIC OR LATINO       68       76       95       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(7) Variable = MIRSEQ_CNMF
D7V1, survival
          sevent
clus2       0  1
  subtype1 44 13
  subtype2 28 29
  subtype3 52 26
  subtype4 56 51
  subtype5 28 21
  subtype6 35 27
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      57       57       78      107       49       62 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
      13       29       26       51       21       27 
$subtype1
TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TJ TCGA-B7-A5TN TCGA-BR-4280 TCGA-BR-8286 
       26.93        58.03        11.01         9.44         6.61        29.42 
TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8382 TCGA-BR-8483 TCGA-BR-8486 TCGA-BR-8487 
        4.31         3.32        25.05         5.39        20.22         1.12 
TCGA-BR-8680 TCGA-BR-A4CQ TCGA-BR-A4QL TCGA-BR-A4QM TCGA-CD-8536 TCGA-CD-A48C 
       31.96        34.98        16.14         5.13        12.43        11.61 
TCGA-CD-A4MH TCGA-CG-4436 TCGA-CG-5720 TCGA-D7-6815 TCGA-D7-A4YT TCGA-D7-A4YY 
       12.20         7.99         0.99        15.98        14.27        13.78 
TCGA-D7-A6EV TCGA-D7-A6F2 TCGA-D7-A74A TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 
       11.24        15.65        19.96        72.23        19.53        17.06 
TCGA-FP-A4BE TCGA-HF-7132 TCGA-HF-7134 TCGA-HF-A5NB TCGA-HU-8244 TCGA-HU-A4G8 
       11.08        77.29        52.21        30.51        24.39        22.68 
TCGA-HU-A4G9 TCGA-HU-A4GC TCGA-HU-A4GF TCGA-HU-A4GT TCGA-HU-A4GU TCGA-HU-A4H8 
       24.20         3.25        25.81         6.51         6.58        14.07 
TCGA-IN-7808 TCGA-IN-8663 TCGA-IN-A6RP TCGA-KB-A6F5 TCGA-VQ-A8E3 TCGA-VQ-A8E7 
        3.45         3.39         6.44         5.56        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A91D TCGA-VQ-A91K TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91X 
       38.14        11.70        61.22        32.88         1.71         9.50 
TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-AA6B 
       66.81        42.54        32.94 

$subtype2
TCGA-CG-4444 TCGA-CG-4475 TCGA-CG-5727 TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-4183 
       47.05        22.98        79.07        26.70        11.70         6.61 
TCGA-BR-4184 TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4257 TCGA-BR-6452 TCGA-BR-6455 
        6.97        18.35        30.90         9.67        34.68        13.87 
TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6802 TCGA-BR-6852 
       19.33        32.78        19.89        12.16        30.90        44.94 
TCGA-BR-8078 TCGA-BR-8296 TCGA-BR-8363 TCGA-CD-5798 TCGA-CD-5799 TCGA-CD-5801 
       29.59        15.58         0.26        13.41        13.02        13.18 
TCGA-CD-5802 TCGA-CD-5813 TCGA-CG-4300 TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 
       13.35        12.39        20.02         3.02        27.02        15.95 
TCGA-CG-4306 TCGA-CG-4437 TCGA-CG-4440 TCGA-CG-4441 TCGA-CG-4443 TCGA-CG-4455 
        1.02         8.05         4.01        14.01        29.98        12.03 
TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 TCGA-CG-5718 TCGA-CG-5719 
        0.00         9.01         7.07        30.97        36.00         1.02 
TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 TCGA-CG-5730 
        6.02         0.99       105.07        12.03        28.96         4.01 
TCGA-CG-5733 TCGA-D7-5577 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6528 TCGA-EQ-5647 
       21.07        25.71        17.85        13.35        15.22         0.62 
TCGA-F1-6874 TCGA-VQ-A8PP TCGA-VQ-A924 
       14.47        23.41        55.43 

$subtype3
TCGA-EQ-A4SO TCGA-B7-A5TI TCGA-BR-4253 TCGA-BR-4267 TCGA-BR-7703 TCGA-BR-7704 
       16.24        19.56         4.08         6.18        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7717 TCGA-BR-7958 TCGA-BR-8081 TCGA-BR-8285 TCGA-BR-8360 
       35.84        18.15        29.56        32.25         0.56         6.18 
TCGA-BR-8361 TCGA-BR-8381 TCGA-BR-8484 TCGA-BR-8589 TCGA-BR-8676 TCGA-BR-A44U 
       31.10         7.36        25.18        27.12         7.53        13.87 
TCGA-BR-A4CS TCGA-BR-A4IY TCGA-BR-A4J4 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-CD-8528 
        1.48        12.89         0.53        20.42         1.15        12.33 
TCGA-CD-8531 TCGA-CD-A4MG TCGA-CD-A4MJ TCGA-D7-8570 TCGA-D7-8573 TCGA-D7-8576 
       12.59         6.58        12.62        24.72        19.50        14.66 
TCGA-D7-A4YX TCGA-D7-A6EZ TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7735 TCGA-FP-8211 
       36.43        20.32        21.27        11.38         3.48        13.58 
TCGA-FP-A4BF TCGA-HF-7133 TCGA-HU-8243 TCGA-HU-8245 TCGA-HU-8249 TCGA-HU-8602 
        5.52        63.06         5.92        18.15        28.96        22.32 
TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G6 TCGA-HU-A4GN 
       22.82        21.07         0.76        24.30        24.26        29.98 
TCGA-HU-A4H0 TCGA-HU-A4H2 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-IN-A6RS TCGA-IN-A7NU 
        2.10        12.95        29.00        23.84        12.59        11.70 
TCGA-IP-7968 TCGA-R5-A7O7 TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A804 TCGA-R5-A805 
        2.53        45.67         8.52        74.53         4.60         9.24 
TCGA-RD-A7C1 TCGA-RD-A8MV TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-SW-A7EA TCGA-VQ-A8DL 
       16.67       122.30       115.69        57.44        19.04         0.92 
TCGA-VQ-A8DT TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8PB TCGA-VQ-A8PF TCGA-VQ-A8PO 
       48.79        37.22         7.73        34.29         2.50         9.27 
TCGA-VQ-A91A TCGA-VQ-A91Q TCGA-VQ-A91W TCGA-VQ-A923 TCGA-VQ-A94T TCGA-VQ-AA69 
       39.45        20.81        60.85         2.01        11.24        28.41 

$subtype4
TCGA-MX-A663 TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4255 TCGA-BR-4256 
        9.86         9.47         4.64         7.43         4.08         9.34 
TCGA-BR-4279 TCGA-BR-6456 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 
        9.57        17.29        13.68        39.12        26.10        25.61 
TCGA-BR-6706 TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7715 TCGA-BR-7716 
       18.05        40.21        31.20        21.90        33.63        39.78 
TCGA-BR-7722 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 TCGA-BR-8059 TCGA-BR-8080 
       15.32         9.07        33.21        37.25        14.43         9.60 
TCGA-BR-8284 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8362 TCGA-BR-8364 
        8.05         2.66        19.96         7.40        13.08        22.19 
TCGA-BR-8365 TCGA-BR-8366 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8372 
       17.52         0.95        26.33        14.04        11.80        31.27 
TCGA-BR-8373 TCGA-BR-8384 TCGA-BR-8588 TCGA-BR-8590 TCGA-BR-8591 TCGA-BR-8592 
       14.79         3.72        12.79         9.34        28.14         6.28 
TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-8687 TCGA-BR-A44T 
       26.73        32.58         9.86        20.88         8.22        34.13 
TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 
        6.08        27.55        28.57         8.98        14.17        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5803 
        0.66        32.52        13.51         0.46        21.44        11.21 
TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8532 TCGA-CD-8534 
       12.10        12.76        12.30        12.39        11.64        12.07 
TCGA-CD-A489 TCGA-CD-A48A TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5717 TCGA-CG-5728 
       11.31        12.43        11.77        12.00         6.97        65.10 
TCGA-D7-5578 TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6520 TCGA-D7-6521 TCGA-D7-6522 
       12.66        20.91        19.13        18.84        18.54        18.61 
TCGA-D7-8574 TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4YU TCGA-D7-A6ET TCGA-D7-A747 
       17.19        21.14        20.91        16.44        26.43         8.38 
TCGA-D7-A748 TCGA-D7-A74B TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        4.34         7.13        14.07        22.29        59.54         5.03 
TCGA-HJ-7597 TCGA-HU-A4GQ TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ TCGA-MX-A5UG 
       26.47         0.10        36.36        18.81        12.46         3.72 
TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8PQ 
        5.13       116.38        71.38        35.61        16.87        15.65 
TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-AA6K TCGA-ZA-A8F6 
        9.73         5.72         2.66        12.43        17.26 

$subtype5
TCGA-FP-A8CX TCGA-VQ-A8PU TCGA-BR-6453 TCGA-BR-6710 TCGA-CG-5732 TCGA-CG-5734 
        0.23        27.35        15.95         8.98        69.04         7.99 
TCGA-D7-6527 TCGA-D7-6817 TCGA-D7-8575 TCGA-D7-A4YV TCGA-D7-A4Z0 TCGA-D7-A6EX 
       10.26        12.79        18.21         5.92        14.76        11.31 
TCGA-D7-A6EY TCGA-FP-A9TM TCGA-HU-8238 TCGA-HU-A4G3 TCGA-HU-A4GJ TCGA-HU-A4GP 
       11.44         6.21         1.51         5.59        21.37         8.98 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H6 TCGA-HU-A4HB TCGA-IN-A6RL TCGA-IN-A6RN 
       20.25         0.26        21.17        15.68        13.35        19.53 
TCGA-IN-A6RR TCGA-IN-A7NR TCGA-IN-AB1V TCGA-IN-AB1X TCGA-KB-A93J TCGA-MX-A5UJ 
        6.74         6.51        15.75        13.51        36.95        19.73 
TCGA-RD-A7BS TCGA-RD-A8N0 TCGA-VQ-A8E0 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD 
       11.05        40.64        18.48        30.97        46.26        16.31 
TCGA-VQ-A8PM TCGA-VQ-A8PX TCGA-VQ-A91E TCGA-VQ-A91N TCGA-VQ-A91V TCGA-VQ-A925 
        1.87        64.57        21.83        18.74        42.64         4.54 
TCGA-VQ-A927 TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6I 
        6.58        18.41        43.66        54.12        26.04        16.14 
TCGA-VQ-AA6J 
       27.55 

$subtype6
TCGA-CG-4460 TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8060 
       21.99         9.17         9.21        28.73         3.45        11.44 
TCGA-BR-8077 TCGA-BR-8295 TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8690 TCGA-BR-A452 
        0.69         2.20         9.21        24.79        10.68         7.53 
TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 
        0.72        20.65        13.15        12.59        12.53         7.17 
TCGA-CD-8533 TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CG-4438 TCGA-CG-4449 
       15.39        12.82         6.31        12.30        54.08        19.07 
TCGA-CG-4466 TCGA-CG-5725 TCGA-D7-6519 TCGA-D7-6526 TCGA-D7-6818 TCGA-D7-6820 
       18.97        15.02        20.55        17.19        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-A6F0 TCGA-EQ-8122 TCGA-FP-8631 TCGA-HU-A4GD 
       12.33        16.80        22.29         7.99         0.56        22.75 
TCGA-HU-A4GH TCGA-HU-A4H5 TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A7NT TCGA-KB-A6F7 
       11.77        23.80        33.40        18.38        10.62        63.62 
TCGA-MX-A666 TCGA-R5-A7ZE TCGA-R5-A7ZR TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB 
       14.04        18.21         6.08        37.91         8.94         5.79 
TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8DZ TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH 
        5.46        13.25        13.02        43.36        22.19        12.79 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6A 
        2.70        17.85        55.56         9.04        21.04        38.93 
TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       17.13         0.79 

subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
    0.99     0.00     0.53     0.10     0.23     0.56 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   77.29   105.07   122.30   116.38    69.04    63.62 
subtype1 subtype2 subtype3 subtype4 subtype5 subtype6 
   15.65    14.47    18.15    14.07    15.95    12.92 
[1] "1.0 - 77.3 (15.7)"  "0.0 - 105.1 (14.5)" "0.5 - 122.3 (18.1)"
[4] "0.1 - 116.4 (14.1)" "0.2 - 69.0 (15.9)"  "0.6 - 63.6 (12.9)" 
D7V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        6        7        3         7        10         1
  subtype2       0        2        7       12         5         5         0
  subtype3       0        4        8        2         9         9         0
  subtype4       0        1        8        8        13        14         1
  subtype5       0        2        1        2         5         6         0
  subtype6       1        1        9        5         2        11         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1          9          8          4        2
  subtype2         10          2          1       15
  subtype3         12         21          8        7
  subtype4         18         15         17        9
  subtype5         15          7          5        5
  subtype6         16          8          4        5
D7V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  STAGE I           1        0        0        0        0        1
  STAGE IA          6        2        4        1        2        1
  STAGE IB          7        7        8        8        1        9
  STAGE II          3       12        2        8        2        5
  STAGE IIA         7        5        9       13        5        2
  STAGE IIB        10        5        9       14        6       11
  STAGE III         1        0        0        1        0        1
  STAGE IIIA        9       10       12       18       15       16
  STAGE IIIB        8        2       21       15        7        8
  STAGE IIIC        4        1        8       17        5        4
  STAGE IV          2       15        7        9        5        5
[1] 11  6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  8 13 27 12
  subtype2  3 22 26 12
  subtype3  4 11 41 24
  subtype4  1 18 48 41
  subtype5  4 11 22 13
  subtype6  3 17 29 16
D7V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  T1        8        3        4        1        4        3
  T2       13       22       11       18       11       17
  T3       27       26       41       48       22       29
  T4       12       12       24       41       13       16
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 22 15 14  8
  subtype2 23 19 11  8
  subtype3 28 18 15 19
  subtype4 32 30 15 29
  subtype5  7 14 17 12
  subtype6 17 21 13 11
D7V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  N0       22       23       28       32        7       17
  N1       15       19       18       30       14       21
  N2       14       11       15       15       17       13
  N3        8        8       19       29       12       11
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V6, binary
          cls
clus        0  1
  subtype1 55  3
  subtype2 54 11
  subtype3 71  4
  subtype4 99  7
  subtype5 47  2
  subtype6 58  3
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   55    3
  subtype2   54   11
  subtype3   71    4
  subtype4   99    7
  subtype5   47    2
  subtype6   58    3
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  0       55       54       71       99       47       58
  1        3       11        4        7        2        3
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V7, binary
          cls
clus        0  1
  subtype1 16 46
  subtype2 33 34
  subtype3 23 57
  subtype4 39 72
  subtype5 19 31
  subtype6 25 41
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   16   46
  subtype2   33   34
  subtype3   23   57
  subtype4   39   72
  subtype5   19   31
  subtype6   25   41
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  FEMALE       16       33       23       39       19       25
  MALE         46       34       57       72       31       41
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V8, binary
          cls
clus        0  1
  subtype1 43 16
  subtype2 40  3
  subtype3 57 19
  subtype4 97 11
  subtype5 33 14
  subtype6 49 11
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   43   16
  subtype2   40    3
  subtype3   57   19
  subtype4   97   11
  subtype5   33   14
  subtype6   49   11
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  NO        43       40       57       97       33       49
  YES       16        3       19       11       14       11
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        1
  subtype2                                        0
  subtype3                                        2
  subtype4                                        4
  subtype5                                        3
  subtype6                                        1
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                     5
  subtype2                                     9
  subtype3                                    14
  subtype4                                    32
  subtype5                                     9
  subtype6                                     3
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     27
  subtype2                                                     32
  subtype3                                                     26
  subtype4                                                     45
  subtype5                                                     11
  subtype6                                                     23
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 4
  subtype2                                                 3
  subtype3                                                 4
  subtype4                                                 7
  subtype5                                                 1
  subtype6                                                 3
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                12
  subtype2                                                                18
  subtype3                                                                12
  subtype4                                                                11
  subtype5                                                                10
  subtype6                                                                16
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  0
  subtype2                                                  0
  subtype3                                                  4
  subtype4                                                  1
  subtype5                                                  1
  subtype6                                                  2
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               13
  subtype2                                                4
  subtype3                                               17
  subtype4                                               10
  subtype5                                               15
  subtype6                                               18
D7V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  27
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        13
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  32
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         4
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  26
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        17
                                                                   clus
vv                                                                  subtype4
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   32
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  45
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       11
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        10
                                                                   clus
vv                                                                  subtype5
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    9
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  11
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       10
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        15
                                                                   clus
vv                                                                  subtype6
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  23
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        3
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        18
[1] 7 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2 RX
  subtype1 50  1  0  3
  subtype2 37  4 10 12
  subtype3 67  4  0  2
  subtype4 89  6  3  6
  subtype5 47  1  2  0
  subtype6 54  2  3  2
D7V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  R0       50       37       67       89       47       54
  R1        1        4        4        6        1        2
  R2        0       10        0        3        2        3
  RX        3       12        2        6        0        2
[1] 4 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D7V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    14                         4    38
  subtype2     5                         0    32
  subtype3    21                         3    50
  subtype4    25                         0    82
  subtype5     8                         3    33
  subtype6    15                         3    38
D7V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           14        5       21       25        8
  BLACK OR AFRICAN AMERICAN        4        0        3        0        3
  WHITE                           38       32       50       82       33
                           clus
vv                          subtype6
  ASIAN                           15
  BLACK OR AFRICAN AMERICAN        3
  WHITE                           38
[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"
D7V13, binary
          cls
clus         0   1
  subtype1   1  43
  subtype2   0  37
  subtype3   3  62
  subtype4   1 101
  subtype5   0  28
  subtype6   0  46
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    1   43
  subtype2    0   37
  subtype3    3   62
  subtype4    1  101
  subtype5    0   28
  subtype6    0   46
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5 subtype6
  HISPANIC OR LATINO            1        0        3        1        0        0
  NOT HISPANIC OR LATINO       43       37       62      101       28       46
[1] 2 6
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(8) Variable = MIRSEQ_CHIERARCHICAL
D8V1, survival
          sevent
clus2        0   1
  subtype1 143  82
  subtype2  42  39
  subtype3  58  46
subtype1 subtype2 subtype3 
     225       81      104 
subtype1 subtype2 subtype3 
      82       39       46 
$subtype1
TCGA-CG-4444 TCGA-CG-4475 TCGA-EQ-A4SO TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 
       47.05        22.98        16.24        27.35        26.93        58.03 
TCGA-B7-5816 TCGA-B7-5818 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-4183 TCGA-BR-4184 
       26.70        11.70        19.56        11.01         6.61         6.97 
TCGA-BR-4191 TCGA-BR-4201 TCGA-BR-4253 TCGA-BR-4257 TCGA-BR-4267 TCGA-BR-4280 
       18.35        30.90         4.08         9.67         6.18         6.61 
TCGA-BR-6452 TCGA-BR-6453 TCGA-BR-6455 TCGA-BR-6458 TCGA-BR-6566 TCGA-BR-6707 
       34.68        15.95        13.87        19.33        32.78        19.89 
TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-7703 TCGA-BR-7704 
       12.16         8.98        30.90        44.94        36.16        35.24 
TCGA-BR-7707 TCGA-BR-7715 TCGA-BR-7722 TCGA-BR-7958 TCGA-BR-8058 TCGA-BR-8078 
       35.84        33.63        15.32        29.56        37.25        29.59 
TCGA-BR-8081 TCGA-BR-8284 TCGA-BR-8285 TCGA-BR-8286 TCGA-BR-8291 TCGA-BR-8296 
       32.25         8.05         0.56        29.42        19.96        15.58 
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8363 TCGA-BR-8366 TCGA-BR-8368 TCGA-BR-8372 
        6.18        31.10         0.26         0.95         4.31        31.27 
TCGA-BR-8382 TCGA-BR-8484 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8589 TCGA-BR-8591 
       25.05        25.18        20.22         1.12        27.12        28.14 
TCGA-BR-8676 TCGA-BR-8680 TCGA-BR-A44U TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4IY 
        7.53        31.96        13.87        34.98         1.48        12.89 
TCGA-BR-A4J4 TCGA-BR-A4J6 TCGA-BR-A4PE TCGA-BR-A4PF TCGA-BR-A4QL TCGA-BR-A4QM 
        0.53         0.66        20.42         1.15        16.14         5.13 
TCGA-CD-5799 TCGA-CD-5801 TCGA-CD-5813 TCGA-CD-8528 TCGA-CD-8531 TCGA-CD-8532 
       13.02        13.18        12.39        12.33        12.59        11.64 
TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-8536 TCGA-CD-A48C TCGA-CD-A4MG TCGA-CD-A4MJ 
       15.39        12.07        12.43        11.61         6.58        12.62 
TCGA-CG-4301 TCGA-CG-4304 TCGA-CG-4305 TCGA-CG-4436 TCGA-CG-4437 TCGA-CG-4441 
        3.02        27.02        15.95         7.99         8.05        14.01 
TCGA-CG-4443 TCGA-CG-4455 TCGA-CG-4462 TCGA-CG-4465 TCGA-CG-4469 TCGA-CG-4477 
       29.98        12.03         0.00         9.01         7.07        30.97 
TCGA-CG-5717 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5724 TCGA-CG-5726 
        6.97         0.99         6.02         0.99        12.03        28.96 
TCGA-CG-5730 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-6519 
        4.01        21.07         7.99        25.71        12.66        20.55 
TCGA-D7-6521 TCGA-D7-6525 TCGA-D7-6528 TCGA-D7-6817 TCGA-D7-8570 TCGA-D7-8573 
       18.54        13.35        15.22        12.79        24.72        19.50 
TCGA-D7-8574 TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YX TCGA-D7-A4YY 
       17.19        18.21        14.66        14.27        36.43        13.78 
TCGA-D7-A4Z0 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A6F2 TCGA-D7-A748 TCGA-D7-A74A 
       14.76        11.24        20.32        15.65         4.34        19.96 
TCGA-F1-6874 TCGA-F1-6875 TCGA-F1-A448 TCGA-F1-A72C TCGA-FP-7829 TCGA-FP-8211 
       14.47        72.23        21.27        11.38        19.53        13.58 
TCGA-FP-A4BE TCGA-FP-A4BF TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7133 TCGA-HF-7134 
       11.08         5.52         6.21        77.29        63.06        52.21 
TCGA-HJ-7597 TCGA-HU-8238 TCGA-HU-8244 TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 
       26.47         1.51        24.39        22.32        22.82        21.07 
TCGA-HU-8610 TCGA-HU-A4G2 TCGA-HU-A4G3 TCGA-HU-A4G6 TCGA-HU-A4G8 TCGA-HU-A4G9 
        0.76        24.30         5.59        24.26        22.68        24.20 
TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4GN TCGA-HU-A4GP TCGA-HU-A4GT TCGA-HU-A4GU 
        3.25        21.37        29.98         8.98         6.51         6.58 
TCGA-HU-A4GX TCGA-HU-A4GY TCGA-HU-A4H0 TCGA-HU-A4H3 TCGA-HU-A4H4 TCGA-HU-A4H6 
       20.25         0.26         2.10        29.00        23.84        21.17 
TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7806 TCGA-IN-7808 TCGA-IN-8462 TCGA-IN-8663 
       14.07        15.68        36.36         3.45        18.81         3.39 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A6RR TCGA-IN-A6RS 
       12.46        13.35        19.53         6.44         6.74        12.59 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-R5-A7ZI 
        6.51        11.70        15.75        13.51         2.53        74.53 
TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N0 TCGA-RD-A8N1 
        4.60         9.24        11.05       122.30        40.64       115.69 
TCGA-RD-A8N5 TCGA-SW-A7EA TCGA-VQ-A8DL TCGA-VQ-A8DT TCGA-VQ-A8E3 TCGA-VQ-A8E7 
       57.44        19.04         0.92        48.79        21.73        37.41 
TCGA-VQ-A8P2 TCGA-VQ-A8P3 TCGA-VQ-A8P5 TCGA-VQ-A8P8 TCGA-VQ-A8PB TCGA-VQ-A8PC 
       38.14        37.22         7.73        30.97        34.29        46.26 
TCGA-VQ-A8PD TCGA-VQ-A8PF TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PP TCGA-VQ-A8PQ 
       16.31         2.50         1.87         9.27        23.41        15.65 
TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E TCGA-VQ-A91K TCGA-VQ-A91Q 
       64.57        39.45        11.70        21.83        61.22        20.81 
TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A923 
       32.88         1.71        42.64        60.85         9.50         2.01 
TCGA-VQ-A924 TCGA-VQ-A925 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94R TCGA-VQ-A94T 
       55.43         4.54         6.58        66.81        42.54        11.24 
TCGA-VQ-AA64 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6B TCGA-VQ-AA6F TCGA-VQ-AA6G 
       18.41        43.66        28.41        32.94        54.12        26.04 
TCGA-VQ-AA6I TCGA-VQ-AA6J TCGA-VQ-AA6K 
       16.14        27.55        12.43 

$subtype2
TCGA-B7-A5TK TCGA-BR-4187 TCGA-BR-4188 TCGA-BR-4255 TCGA-BR-4256 TCGA-BR-4279 
        9.47         4.64         7.43         4.08         9.34         9.57 
TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 TCGA-BR-6801 
       13.68        39.12        26.10        25.61        18.05        40.21 
TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7717 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8080 
       31.20        21.90        18.15         9.07        33.21         9.60 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8367 TCGA-BR-8369 TCGA-BR-8370 
       13.08        22.19        17.52        26.33        14.04         3.32 
TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8592 TCGA-BR-8677 
       11.80         3.72         5.39        12.79         6.28        26.73 
TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-8686 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU 
       32.58         9.86        20.88        34.13         6.08        27.55 
TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J2 TCGA-BR-A4J5 TCGA-BR-A4J7 TCGA-BR-A4J8 
       28.57         8.98        14.17        28.34        32.52        13.51 
TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-A489 
        0.46        21.44        13.41        11.21        12.10        11.31 
TCGA-CD-A48A TCGA-CD-A4MI TCGA-CG-4472 TCGA-CG-5719 TCGA-CG-5723 TCGA-CG-5728 
       12.43        11.77        12.00         1.02       105.07        65.10 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8579 TCGA-D7-A4YU 
       20.91        19.13        18.61        17.85        20.91        16.44 
TCGA-D7-A6ET TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A747 TCGA-EQ-5647 TCGA-FP-7735 
       26.43        11.31        11.44         8.38         0.62         3.48 
TCGA-FP-7916 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ TCGA-MX-A5UG 
       14.07        22.29        59.54         5.03         0.10         3.72 
TCGA-RD-A7BW TCGA-RD-A8N2 TCGA-RD-A8N4 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A91Y 
        5.13       116.38        71.38        35.61        16.87         9.73 
TCGA-VQ-A928 TCGA-VQ-A94P TCGA-ZA-A8F6 
        5.72         2.66        17.26 

$subtype3
TCGA-CG-4460 TCGA-CG-5727 TCGA-FP-A8CX TCGA-MX-A663 TCGA-B7-A5TN TCGA-BR-6456 
       21.99        79.07         0.23         9.86         9.44        17.29 
TCGA-BR-6565 TCGA-BR-7197 TCGA-BR-7716 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8059 
        9.17         9.21        39.78        28.73         3.45        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8297 TCGA-BR-8373 
       11.44         0.69         2.66         2.20         7.40        14.79 
TCGA-BR-8381 TCGA-BR-8485 TCGA-BR-8590 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-8690 
        7.36         9.21         9.34        24.79         8.22        10.68 
TCGA-BR-A452 TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-CD-5800 TCGA-CD-5802 TCGA-CD-8524 
        7.53         0.72        20.65        13.15        13.35        12.76 
TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 TCGA-CD-8535 
       12.59        12.53         7.17        12.30        12.39        12.82 
TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4300 TCGA-CG-4306 TCGA-CG-4438 
        6.31        12.30        12.20        20.02         1.02        54.08 
TCGA-CG-4440 TCGA-CG-4449 TCGA-CG-4466 TCGA-CG-5718 TCGA-CG-5725 TCGA-CG-5732 
        4.01        19.07        18.97        36.00        15.02        69.04 
TCGA-D7-6520 TCGA-D7-6526 TCGA-D7-6527 TCGA-D7-6815 TCGA-D7-6818 TCGA-D7-6820 
       18.84        17.19        10.26        15.98        12.36        11.31 
TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A4YV TCGA-D7-A6F0 TCGA-D7-A74B 
       12.33        16.80        21.14         5.92        22.29         7.13 
TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8631 TCGA-HF-A5NB TCGA-HU-8243 TCGA-HU-8245 
        7.99        17.06         0.56        30.51         5.92        18.15 
TCGA-HU-8249 TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4H2 TCGA-HU-A4H5 
       28.96        22.75        25.81        11.77        12.95        23.80 
TCGA-HU-A4HD TCGA-IN-A6RI TCGA-IN-A7NT TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J 
       33.40        18.38        10.62         5.56        63.62        36.95 
TCGA-MX-A5UJ TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-R5-A7ZR 
       19.73        14.04        45.67        18.21         8.52         6.08 
TCGA-RD-A7C1 TCGA-RD-A8MW TCGA-RD-A8N6 TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV 
       16.67        37.91         8.94         5.79         5.46        13.25 
TCGA-VQ-A8DZ TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8PE TCGA-VQ-A8PH TCGA-VQ-A8PJ 
       13.02        18.48        43.36        22.19        12.79         2.70 
TCGA-VQ-A8PK TCGA-VQ-A91N TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-AA6A 
       17.85        18.74        55.56         9.04        21.04        38.93 
TCGA-VQ-AA6D TCGA-ZQ-A9CR 
       17.13         0.79 

subtype1 subtype2 subtype3 
    0.00     0.10     0.23 
subtype1 subtype2 subtype3 
  122.30   116.38    79.07 
subtype1 subtype2 subtype3 
  15.950   13.680   12.985 
[1] "0.0 - 122.3 (15.9)" "0.1 - 116.4 (13.7)" "0.2 - 79.1 (13.0)" 
D8V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1       15       23       15        25        31         1
  subtype2       0        0        7        6         9         7         0
  subtype3       1        1       10       11         7        17         2
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         42         35         19       22
  subtype2         16         15          9        8
  subtype3         22         11         11       13
D8V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        0        1
  STAGE IA         15        0        1
  STAGE IB         23        7       10
  STAGE II         15        6       11
  STAGE IIA        25        9        7
  STAGE IIB        31        7       17
  STAGE III         1        0        2
  STAGE IIIA       42       16       22
  STAGE IIIB       35       15       11
  STAGE IIIC       19        9       11
  STAGE IV         22        8       13
[1] 11  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  20  56 104  60
  subtype2   0  13  38  28
  subtype3   3  23  51  30
D8V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       20        0        3
  T2       56       13       23
  T3      104       38       51
  T4       60       28       30
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 80 63 51 43
  subtype2 22 23 11 22
  subtype3 27 31 23 22
D8V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       80       22       27
  N1       63       23       31
  N2       51       11       23
  N3       43       22       22
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V6, binary
          cls
clus         0   1
  subtype1 219  16
  subtype2  72   5
  subtype3  93   9
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  219   16
  subtype2   72    5
  subtype3   93    9
   clus
vv  subtype1 subtype2 subtype3
  0      219       72       93
  1       16        5        9
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V7, binary
          cls
clus         0   1
  subtype1  86 159
  subtype2  30  52
  subtype3  39  70
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   86  159
  subtype2   30   52
  subtype3   39   70
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       86       30       39
  MALE        159       52       70
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D8V8, binary
          cls
clus         0   1
  subtype1 167  49
  subtype2  73   7
  subtype3  79  18
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  167   49
  subtype2   73    7
  subtype3   79   18
     clus
vv    subtype1 subtype2 subtype3
  NO       167       73       79
  YES       49        7       18
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        7
  subtype2                                        2
  subtype3                                        2
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                    39
  subtype2                                    25
  subtype3                                     8
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     98
  subtype2                                                     31
  subtype3                                                     35
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                10
  subtype2                                                 7
  subtype3                                                 5
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                46
  subtype2                                                                 7
  subtype3                                                                26
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  3
  subtype2                                                  1
  subtype3                                                  4
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               40
  subtype2                                                8
  subtype3                                               29
D8V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 7
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   39
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  98
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       46
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        40
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   25
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  31
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        7
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         8
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  35
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       26
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       4
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        29
[1] 7 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2  RX
  subtype1 196   9  10  17
  subtype2  61   5   3   5
  subtype3  87   4   5   3
D8V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      196       61       87
  R1        9        5        4
  R2       10        3        5
  RX       17        5        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"
D8V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    43                         7   157
  subtype2    21                         1    56
  subtype3    24                         5    60
D8V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           43       21       24
  BLACK OR AFRICAN AMERICAN        7        1        5
  WHITE                          157       56       60
[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"
D8V13, binary
          cls
clus         0   1
  subtype1   3 167
  subtype2   1  74
  subtype3   1  76
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3  167
  subtype2    1   74
  subtype3    1   76
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        1
  NOT HISPANIC OR LATINO      167       74       76
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"

Clustering(9) Variable = MIRSEQ_MATURE_CNMF
D9V1, survival
          sevent
clus2       0  1
  subtype1 91 54
  subtype2 65 52
  subtype3 41 30
subtype1 subtype2 subtype3 
     145      117       71 
subtype1 subtype2 subtype3 
      54       52       30 
$subtype1
TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ TCGA-BR-7703 
       27.35        26.93        58.03        19.56        11.01        36.16 
TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7723 TCGA-BR-7958 TCGA-BR-8060 TCGA-BR-8077 
       35.24        35.84        28.73        29.56        11.44         0.69 
TCGA-BR-8078 TCGA-BR-8295 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8370 TCGA-BR-8372 
       29.59         2.20        31.10         4.31         3.32        31.27 
TCGA-BR-8485 TCGA-BR-8486 TCGA-BR-8487 TCGA-BR-8676 TCGA-BR-8678 TCGA-BR-8680 
        9.21        20.22         1.12         7.53        24.79        31.96 
TCGA-BR-8687 TCGA-BR-A452 TCGA-BR-A4CS TCGA-BR-A4J1 TCGA-BR-A4PD TCGA-BR-A4QL 
        8.22         7.53         1.48         0.72        20.65        16.14 
TCGA-BR-A4QM TCGA-CD-8527 TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8535 
        5.13         7.17        12.59        11.64        15.39        12.82 
TCGA-CD-8536 TCGA-CD-A4MH TCGA-D7-8575 TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU 
       12.43        12.20        18.21        14.66        14.27        16.44 
TCGA-D7-A4YV TCGA-D7-A6EV TCGA-D7-A6EX TCGA-D7-A6EZ TCGA-D7-A6F0 TCGA-D7-A6F2 
        5.92        11.24        11.31        20.32        22.29        15.65 
TCGA-D7-A74A TCGA-F1-6875 TCGA-FP-7829 TCGA-FP-8099 TCGA-FP-8211 TCGA-FP-8631 
       19.96        72.23        19.53        17.06        13.58         0.56 
TCGA-FP-A4BE TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-8238 TCGA-HU-8243 
       11.08         6.21        77.29        52.21         1.51         5.92 
TCGA-HU-8602 TCGA-HU-8604 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GC 
       22.32        22.82        21.07         5.59        22.68         3.25 
TCGA-HU-A4GD TCGA-HU-A4GF TCGA-HU-A4GH TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H2 
       22.75        25.81        11.77         6.51        20.25        12.95 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-A6RI 
       23.80        21.17        14.07        15.68         3.45        18.38 
TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NT TCGA-IN-AB1X TCGA-IP-7968 
       13.35        19.53         6.44        10.62        13.51         2.53 
TCGA-KB-A6F5 TCGA-KB-A6F7 TCGA-KB-A93J TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE 
        5.56        63.62        36.95        14.04        45.67        18.21 
TCGA-R5-A7ZF TCGA-R5-A7ZI TCGA-R5-A7ZR TCGA-R5-A804 TCGA-R5-A805 TCGA-RD-A7C1 
        8.52        74.53         6.08         4.60         9.24        16.67 
TCGA-RD-A8MV TCGA-SW-A7EA TCGA-SW-A7EB TCGA-VQ-A8DL TCGA-VQ-A8DU TCGA-VQ-A8DV 
      122.30        19.04         5.79         0.92         5.46        13.25 
TCGA-VQ-A8E0 TCGA-VQ-A8E2 TCGA-VQ-A8E3 TCGA-VQ-A8E7 TCGA-VQ-A8P2 TCGA-VQ-A8P5 
       18.48        43.36        21.73        37.41        38.14         7.73 
TCGA-VQ-A8PB TCGA-VQ-A8PE TCGA-VQ-A8PF TCGA-VQ-A8PH TCGA-VQ-A8PJ TCGA-VQ-A8PK 
       34.29        22.19         2.50        12.79         2.70        17.85 
TCGA-VQ-A8PM TCGA-VQ-A8PO TCGA-VQ-A8PX TCGA-VQ-A91A TCGA-VQ-A91D TCGA-VQ-A91E 
        1.87         9.27        64.57        39.45        11.70        21.83 
TCGA-VQ-A91K TCGA-VQ-A91N TCGA-VQ-A91Q TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V 
       61.22        18.74        20.81        32.88         1.71        42.64 
TCGA-VQ-A91W TCGA-VQ-A91X TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A923 TCGA-VQ-A924 
       60.85         9.50        55.56         9.04         2.01        55.43 
TCGA-VQ-A925 TCGA-VQ-A92D TCGA-VQ-A94O TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA68 
        4.54        66.81        21.04        11.24        18.41        43.66 
TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6B TCGA-VQ-AA6D TCGA-VQ-AA6F TCGA-VQ-AA6G 
       28.41        38.93        32.94        17.13        54.12        26.04 
TCGA-VQ-AA6I 
       16.14 

$subtype2
TCGA-MX-A663 TCGA-B7-A5TK TCGA-B7-A5TN TCGA-BR-6453 TCGA-BR-6456 TCGA-BR-6457 
        9.86         9.47         9.44        15.95        17.29        13.68 
TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7197 
       39.12        26.10        25.61        31.20        21.90         9.21 
TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7901 TCGA-BR-7957 TCGA-BR-7959 TCGA-BR-8058 
       33.63        18.15         3.45         9.07        33.21        37.25 
TCGA-BR-8059 TCGA-BR-8080 TCGA-BR-8286 TCGA-BR-8289 TCGA-BR-8291 TCGA-BR-8297 
       14.43         9.60        29.42         2.66        19.96         7.40 
TCGA-BR-8362 TCGA-BR-8364 TCGA-BR-8365 TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8373 
       13.08        22.19        17.52        14.04        11.80        14.79 
TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8384 TCGA-BR-8483 TCGA-BR-8588 TCGA-BR-8590 
        7.36        25.05         3.72         5.39        12.79         9.34 
TCGA-BR-8591 TCGA-BR-8592 TCGA-BR-8677 TCGA-BR-8682 TCGA-BR-8683 TCGA-BR-A44T 
       28.14         6.28        26.73        32.58         9.86        34.13 
TCGA-BR-A453 TCGA-BR-A4CQ TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ TCGA-BR-A4J5 
        6.08        34.98        27.55        28.57         8.98        28.34 
TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-BR-A4QI TCGA-CD-5798 
        0.66        32.52        13.51         0.46        21.44        13.41 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8529 
       11.21        12.10        12.76        12.59        12.53        12.30 
TCGA-CD-8530 TCGA-CD-8534 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A489 TCGA-CD-A48C 
       12.39        12.07         6.31        12.30        11.31        11.61 
TCGA-CD-A4MI TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-8572 TCGA-D7-8574 
       11.77        19.13        18.54        18.61        16.80        17.19 
TCGA-D7-8578 TCGA-D7-8579 TCGA-D7-A4Z0 TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A748 
       21.14        20.91        14.76        26.43         8.38         4.34 
TCGA-D7-A74B TCGA-EQ-8122 TCGA-FP-7735 TCGA-FP-7998 TCGA-FP-8209 TCGA-FP-8210 
        7.13         7.99         3.48        22.29        59.54         5.03 
TCGA-HU-A4GJ TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-IN-7806 TCGA-IN-8462 TCGA-IN-A6RJ 
       21.37         0.10         0.26        36.36        18.81        12.46 
TCGA-IN-A7NR TCGA-IN-A7NU TCGA-IN-AB1V TCGA-MX-A5UG TCGA-MX-A5UJ TCGA-RD-A7BS 
        6.51        11.70        15.75         3.72        19.73        11.05 
TCGA-RD-A7BW TCGA-RD-A8MW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N5 TCGA-RD-A8N6 
        5.13        37.91        40.64       115.69        57.44         8.94 
TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD 
       35.61        16.87        37.22        30.97        46.26        16.31 
TCGA-VQ-A8PQ TCGA-VQ-A91Y TCGA-VQ-A927 TCGA-VQ-A928 TCGA-VQ-A94P TCGA-VQ-A94R 
       15.65         9.73         6.58         5.72         2.66        42.54 
TCGA-VQ-AA6K TCGA-ZA-A8F6 TCGA-ZQ-A9CR 
       12.43        17.26         0.79 

$subtype3
TCGA-CG-5727 TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 
       79.07        26.70        11.70        34.68        13.87        19.33 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6706 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 
        9.17        32.78        18.05        19.89        12.16         8.98 
TCGA-BR-6801 TCGA-BR-6802 TCGA-BR-6852 TCGA-BR-8284 TCGA-BR-8296 TCGA-BR-8360 
       40.21        30.90        44.94         8.05        15.58         6.18 
TCGA-BR-8363 TCGA-BR-8690 TCGA-BR-A4IY TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
        0.26        10.68        12.89        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5813 TCGA-CD-A4MG TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-4449 
       13.35        12.39         6.58         8.05        14.01        19.07 
TCGA-CG-5717 TCGA-CG-5718 TCGA-CG-5719 TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 
        6.97        36.00         1.02         0.99         6.02         0.99 
TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5725 TCGA-CG-5726 TCGA-CG-5728 TCGA-CG-5730 
      105.07        12.03        15.02        28.96        65.10         4.01 
TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 TCGA-D7-5579 
       69.04        21.07         7.99        25.71        12.66        20.91 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6524 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6527 
       20.55        18.84        17.85        13.35        17.19        10.26 
TCGA-D7-6528 TCGA-D7-6815 TCGA-D7-6817 TCGA-D7-6818 TCGA-D7-6820 TCGA-D7-6822 
       15.22        15.98        12.79        12.36        11.31        12.33 
TCGA-D7-8570 TCGA-D7-A4YY TCGA-D7-A6EY TCGA-EQ-5647 TCGA-F1-6874 TCGA-F1-A448 
       24.72        13.78        11.44         0.62        14.47        21.27 
TCGA-HU-A4GN TCGA-HU-A4H4 TCGA-IN-8663 TCGA-VQ-A8PP TCGA-VQ-AA6J 
       29.98        23.84         3.39        23.41        27.55 

subtype1 subtype2 subtype3 
    0.56     0.10     0.26 
subtype1 subtype2 subtype3 
  122.30   115.69   105.07 
subtype1 subtype2 subtype3 
   16.67    13.68    13.87 
[1] "0.6 - 122.3 (16.7)" "0.1 - 115.7 (13.7)" "0.3 - 105.1 (13.9)"
D9V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       1        6       14        9        14        18         1
  subtype2       0        2        7        8        12        20         1
  subtype3       1        1        9       12         9         9         0
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         30         27         14       11
  subtype2         23         18         16       10
  subtype3         14          7          2        9
D9V3, multiclass
            clus
vv           subtype1 subtype2 subtype3
  STAGE I           1        0        1
  STAGE IA          6        2        1
  STAGE IB         14        7        9
  STAGE II          9        8       12
  STAGE IIA        14       12        9
  STAGE IIB        18       20        9
  STAGE III         1        1        0
  STAGE IIIA       30       23       14
  STAGE IIIB       27       18        7
  STAGE IIIC       14       16        2
  STAGE IV         11       10        9
[1] 11  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 11 23 76 38
  subtype2  2 17 58 44
  subtype3  2 32 29 11
D9V4, multiclass
    clus
vv   subtype1 subtype2 subtype3
  T1       11        2        2
  T2       23       17       32
  T3       76       58       29
  T4       38       44       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       N0 N1 N2 N3
  subtype1 45 34 38 28
  subtype2 32 34 21 30
  subtype3 26 20 15 13
D9V5, multiclass
    clus
vv   subtype1 subtype2 subtype3
  N0       45       32       26
  N1       34       34       20
  N2       38       21       15
  N3       28       30       13
[1] 4 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V6, binary
          cls
clus         0   1
  subtype1 133   8
  subtype2 106   8
  subtype3  67   6
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  133    8
  subtype2  106    8
  subtype3   67    6
   clus
vv  subtype1 subtype2 subtype3
  0      133      106       67
  1        8        8        6
[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 49 99
  subtype2 44 77
  subtype3 25 49
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   49   99
  subtype2   44   77
  subtype3   25   49
        clus
vv       subtype1 subtype2 subtype3
  FEMALE       49       44       25
  MALE         99       77       49
[1] 2 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D9V8, binary
          cls
clus         0   1
  subtype1 106  37
  subtype2 101  20
  subtype3  57   7
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1  106   37
  subtype2  101   20
  subtype3   57    7
     clus
vv    subtype1 subtype2 subtype3
  NO       106      101       57
  YES       37       20        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"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        3
  subtype2                                        4
  subtype3                                        0
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                    16
  subtype2                                    34
  subtype3                                     8
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     42
  subtype2                                                     48
  subtype3                                                     27
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 5
  subtype2                                                10
  subtype3                                                 4
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                32
  subtype2                                                                16
  subtype3                                                                19
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  3
  subtype2                                                  1
  subtype3                                                  2
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               47
  subtype2                                                8
  subtype3                                               14
D9V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 3
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   16
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  42
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        5
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       32
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        47
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   34
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  48
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                       10
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       16
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         8
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  27
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       19
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       2
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        14
[1] 7 3
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus        R0  R1  R2
  subtype1 129   4   2
  subtype2 101   6   3
  subtype3  61   4   5
D9V10, multiclass
    clus
vv   subtype1 subtype2 subtype3
  R0      129      101       61
  R1        4        6        4
  R2        2        3        5
[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"
D9V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    30                         8    94
  subtype2    28                         2    91
  subtype3     9                         2    42
D9V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3
  ASIAN                           30       28        9
  BLACK OR AFRICAN AMERICAN        8        2        2
  WHITE                           94       91       42
[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"
D9V13, binary
          cls
clus         0   1
  subtype1   3  90
  subtype2   1 109
  subtype3   1  51
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   90
  subtype2    1  109
  subtype3    1   51
                        clus
vv                       subtype1 subtype2 subtype3
  HISPANIC OR LATINO            3        1        1
  NOT HISPANIC OR LATINO       90      109       51
[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 63 37
  subtype2 39 31
  subtype3 24 19
  subtype4 31 29
  subtype5 40 20
subtype1 subtype2 subtype3 subtype4 subtype5 
     100       70       43       60       60 
subtype1 subtype2 subtype3 subtype4 subtype5 
      37       31       19       29       20 
$subtype1
TCGA-MX-A663 TCGA-VQ-A8PU TCGA-VQ-A94U TCGA-3M-AB46 TCGA-B7-A5TI TCGA-B7-A5TJ 
        9.86        27.35        26.93        58.03        19.56        11.01 
TCGA-B7-A5TK TCGA-BR-7703 TCGA-BR-7704 TCGA-BR-7707 TCGA-BR-7958 TCGA-BR-8058 
        9.47        36.16        35.24        35.84        29.56        37.25 
TCGA-BR-8078 TCGA-BR-8284 TCGA-BR-8286 TCGA-BR-8296 TCGA-BR-8362 TCGA-BR-8363 
       29.59         8.05        29.42        15.58        13.08         0.26 
TCGA-BR-8370 TCGA-BR-8372 TCGA-BR-8381 TCGA-BR-8382 TCGA-BR-8588 TCGA-BR-8591 
        3.32        31.27         7.36        25.05        12.79        28.14 
TCGA-BR-8680 TCGA-BR-8683 TCGA-BR-A4CQ TCGA-BR-A4CS TCGA-BR-A4QI TCGA-BR-A4QM 
       31.96         9.86        34.98         1.48        21.44         5.13 
TCGA-CD-8531 TCGA-CD-8532 TCGA-CD-8533 TCGA-CD-8534 TCGA-CD-A48C TCGA-D7-8570 
       12.59        11.64        15.39        12.07        11.61        24.72 
TCGA-D7-8576 TCGA-D7-A4YT TCGA-D7-A4YU TCGA-D7-A4YV TCGA-D7-A4YY TCGA-D7-A4Z0 
       14.66        14.27        16.44         5.92        13.78        14.76 
TCGA-D7-A6EX TCGA-D7-A6EY TCGA-D7-A6F2 TCGA-F1-6875 TCGA-F1-A448 TCGA-FP-7829 
       11.31        11.44        15.65        72.23        21.27        19.53 
TCGA-FP-7998 TCGA-FP-8211 TCGA-FP-A9TM TCGA-HF-7132 TCGA-HF-7134 TCGA-HU-8238 
       22.29        13.58         6.21        77.29        52.21         1.51 
TCGA-HU-8604 TCGA-HU-A4GC TCGA-HU-A4GJ TCGA-HU-A4HB TCGA-IN-7808 TCGA-IN-8462 
       22.82         3.25        21.37        15.68         3.45        18.81 
TCGA-IN-A6RJ TCGA-IN-A6RL TCGA-IN-A6RN TCGA-IN-A6RP TCGA-IN-A7NR TCGA-IN-A7NU 
       12.46        13.35        19.53         6.44         6.51        11.70 
TCGA-IN-AB1V TCGA-IN-AB1X TCGA-IP-7968 TCGA-KB-A6F5 TCGA-MX-A5UJ TCGA-R5-A804 
       15.75        13.51         2.53         5.56        19.73         4.60 
TCGA-R5-A805 TCGA-RD-A7BS TCGA-RD-A8MV TCGA-RD-A8N5 TCGA-SW-A7EA TCGA-VQ-A8DL 
        9.24        11.05       122.30        57.44        19.04         0.92 
TCGA-VQ-A8E7 TCGA-VQ-A8P3 TCGA-VQ-A8P8 TCGA-VQ-A8PC TCGA-VQ-A8PD TCGA-VQ-A8PF 
       37.41        37.22        30.97        46.26        16.31         2.50 
TCGA-VQ-A8PM TCGA-VQ-A8PP TCGA-VQ-A91A TCGA-VQ-A91K TCGA-VQ-A91Q TCGA-VQ-A923 
        1.87        23.41        39.45        61.22        20.81         2.01 
TCGA-VQ-A924 TCGA-VQ-A927 TCGA-VQ-A92D TCGA-VQ-A94T TCGA-VQ-AA64 TCGA-VQ-AA6B 
       55.43         6.58        66.81        11.24        18.41        32.94 
TCGA-VQ-AA6F TCGA-VQ-AA6G TCGA-VQ-AA6J TCGA-VQ-AA6K 
       54.12        26.04        27.55        12.43 

$subtype2
TCGA-BR-6453 TCGA-BR-6457 TCGA-BR-6563 TCGA-BR-6564 TCGA-BR-6705 TCGA-BR-6706 
       15.95        13.68        39.12        26.10        25.61        18.05 
TCGA-BR-6801 TCGA-BR-6803 TCGA-BR-7196 TCGA-BR-7715 TCGA-BR-7717 TCGA-BR-7957 
       40.21        31.20        21.90        33.63        18.15         9.07 
TCGA-BR-7959 TCGA-BR-8080 TCGA-BR-8291 TCGA-BR-8297 TCGA-BR-8364 TCGA-BR-8365 
       33.21         9.60        19.96         7.40        22.19        17.52 
TCGA-BR-8369 TCGA-BR-8371 TCGA-BR-8384 TCGA-BR-8590 TCGA-BR-8592 TCGA-BR-8677 
       14.04        11.80         3.72         9.34         6.28        26.73 
TCGA-BR-8682 TCGA-BR-A44T TCGA-BR-A453 TCGA-BR-A4IU TCGA-BR-A4IV TCGA-BR-A4IZ 
       32.58        34.13         6.08        27.55        28.57         8.98 
TCGA-BR-A4J5 TCGA-BR-A4J6 TCGA-BR-A4J7 TCGA-BR-A4J8 TCGA-BR-A4J9 TCGA-CD-5798 
       28.34         0.66        32.52        13.51         0.46        13.41 
TCGA-CD-5803 TCGA-CD-5804 TCGA-CD-A489 TCGA-CD-A4MI TCGA-CG-5719 TCGA-CG-5728 
       11.21        12.10        11.31        11.77         1.02        65.10 
TCGA-D7-5579 TCGA-D7-6518 TCGA-D7-6521 TCGA-D7-6522 TCGA-D7-6524 TCGA-D7-8574 
       20.91        19.13        18.54        18.61        17.85        17.19 
TCGA-D7-8579 TCGA-D7-A6ET TCGA-D7-A747 TCGA-D7-A748 TCGA-D7-A74B TCGA-FP-7735 
       20.91        26.43         8.38         4.34         7.13         3.48 
TCGA-FP-8209 TCGA-FP-8210 TCGA-HU-A4GQ TCGA-HU-A4GY TCGA-IN-7806 TCGA-MX-A5UG 
       59.54         5.03         0.10         0.26        36.36         3.72 
TCGA-RD-A7BW TCGA-RD-A8N0 TCGA-RD-A8N1 TCGA-RD-A8N9 TCGA-RD-A8NB TCGA-VQ-A8PQ 
        5.13        40.64       115.69        35.61        16.87        15.65 
TCGA-VQ-A91Y TCGA-VQ-A928 TCGA-VQ-A94P TCGA-ZA-A8F6 
        9.73         5.72         2.66        17.26 

$subtype3
TCGA-CG-5727 TCGA-B7-5816 TCGA-B7-5818 TCGA-BR-6452 TCGA-BR-6455 TCGA-BR-6458 
       79.07        26.70        11.70        34.68        13.87        19.33 
TCGA-BR-6565 TCGA-BR-6566 TCGA-BR-6707 TCGA-BR-6709 TCGA-BR-6710 TCGA-BR-6802 
        9.17        32.78        19.89        12.16         8.98        30.90 
TCGA-BR-6852 TCGA-BR-8486 TCGA-BR-A4IY TCGA-CD-5799 TCGA-CD-5800 TCGA-CD-5801 
       44.94        20.22        12.89        13.02        13.15        13.18 
TCGA-CD-5802 TCGA-CD-5813 TCGA-CG-4437 TCGA-CG-4441 TCGA-CG-5717 TCGA-CG-5718 
       13.35        12.39         8.05        14.01         6.97        36.00 
TCGA-CG-5720 TCGA-CG-5721 TCGA-CG-5722 TCGA-CG-5723 TCGA-CG-5724 TCGA-CG-5726 
        0.99         6.02         0.99       105.07        12.03        28.96 
TCGA-CG-5730 TCGA-CG-5732 TCGA-CG-5733 TCGA-CG-5734 TCGA-D7-5577 TCGA-D7-5578 
        4.01        69.04        21.07         7.99        25.71        12.66 
TCGA-D7-6519 TCGA-D7-6520 TCGA-D7-6525 TCGA-D7-6526 TCGA-D7-6815 TCGA-D7-6817 
       20.55        18.84        13.35        17.19        15.98        12.79 
TCGA-IN-8663 
        3.39 

$subtype4
TCGA-B7-A5TN TCGA-BR-6456 TCGA-BR-7197 TCGA-BR-7723 TCGA-BR-7901 TCGA-BR-8059 
        9.44        17.29         9.21        28.73         3.45        14.43 
TCGA-BR-8060 TCGA-BR-8077 TCGA-BR-8289 TCGA-BR-8295 TCGA-BR-8373 TCGA-BR-8483 
       11.44         0.69         2.66         2.20        14.79         5.39 
TCGA-BR-8485 TCGA-BR-8678 TCGA-BR-8687 TCGA-BR-8690 TCGA-BR-A452 TCGA-BR-A4J1 
        9.21        24.79         8.22        10.68         7.53         0.72 
TCGA-CD-8524 TCGA-CD-8525 TCGA-CD-8526 TCGA-CD-8527 TCGA-CD-8529 TCGA-CD-8530 
       12.76        12.59        12.53         7.17        12.30        12.39 
TCGA-CD-8535 TCGA-CD-A486 TCGA-CD-A487 TCGA-CD-A4MH TCGA-CG-4449 TCGA-CG-5725 
       12.82         6.31        12.30        12.20        19.07        15.02 
TCGA-D7-6818 TCGA-D7-6822 TCGA-D7-8572 TCGA-D7-8578 TCGA-D7-A6F0 TCGA-EQ-5647 
       12.36        12.33        16.80        21.14        22.29         0.62 
TCGA-EQ-8122 TCGA-FP-8099 TCGA-FP-8631 TCGA-HU-A4GD TCGA-IN-A7NT TCGA-KB-A6F7 
        7.99        17.06         0.56        22.75        10.62        63.62 
TCGA-MX-A666 TCGA-R5-A7O7 TCGA-R5-A7ZE TCGA-R5-A7ZF TCGA-RD-A8MW TCGA-RD-A8N6 
       14.04        45.67        18.21         8.52        37.91         8.94 
TCGA-SW-A7EB TCGA-VQ-A8DU TCGA-VQ-A8DV TCGA-VQ-A8E2 TCGA-VQ-A8P5 TCGA-VQ-A8PE 
        5.79         5.46        13.25        43.36         7.73        22.19 
TCGA-VQ-A8PH TCGA-VQ-A91Z TCGA-VQ-A922 TCGA-VQ-A94O TCGA-VQ-A94R TCGA-ZQ-A9CR 
       12.79        55.56         9.04        21.04        42.54         0.79 

$subtype5
TCGA-BR-8360 TCGA-BR-8361 TCGA-BR-8368 TCGA-BR-8487 TCGA-BR-8676 TCGA-BR-A4PD 
        6.18        31.10         4.31         1.12         7.53        20.65 
TCGA-BR-A4QL TCGA-CD-8536 TCGA-CD-A4MG TCGA-D7-6527 TCGA-D7-6528 TCGA-D7-6820 
       16.14        12.43         6.58        10.26        15.22        11.31 
TCGA-D7-8575 TCGA-D7-A6EV TCGA-D7-A6EZ TCGA-D7-A74A TCGA-F1-6874 TCGA-FP-A4BE 
       18.21        11.24        20.32        19.96        14.47        11.08 
TCGA-HU-8243 TCGA-HU-8602 TCGA-HU-8608 TCGA-HU-A4G3 TCGA-HU-A4G8 TCGA-HU-A4GF 
        5.92        22.32        21.07         5.59        22.68        25.81 
TCGA-HU-A4GH TCGA-HU-A4GN TCGA-HU-A4GT TCGA-HU-A4GX TCGA-HU-A4H2 TCGA-HU-A4H4 
       11.77        29.98         6.51        20.25        12.95        23.84 
TCGA-HU-A4H5 TCGA-HU-A4H6 TCGA-HU-A4H8 TCGA-IN-A6RI TCGA-KB-A93J TCGA-R5-A7ZI 
       23.80        21.17        14.07        18.38        36.95        74.53 
TCGA-R5-A7ZR TCGA-RD-A7C1 TCGA-VQ-A8E0 TCGA-VQ-A8E3 TCGA-VQ-A8P2 TCGA-VQ-A8PB 
        6.08        16.67        18.48        21.73        38.14        34.29 
TCGA-VQ-A8PJ TCGA-VQ-A8PK TCGA-VQ-A8PO TCGA-VQ-A8PX TCGA-VQ-A91D TCGA-VQ-A91E 
        2.70        17.85         9.27        64.57        11.70        21.83 
TCGA-VQ-A91N TCGA-VQ-A91S TCGA-VQ-A91U TCGA-VQ-A91V TCGA-VQ-A91W TCGA-VQ-A91X 
       18.74        32.88         1.71        42.64        60.85         9.50 
TCGA-VQ-A925 TCGA-VQ-AA68 TCGA-VQ-AA69 TCGA-VQ-AA6A TCGA-VQ-AA6D TCGA-VQ-AA6I 
        4.54        43.66        28.41        38.93        17.13        16.14 

subtype1 subtype2 subtype3 subtype4 subtype5 
    0.26     0.10     0.99     0.56     1.12 
subtype1 subtype2 subtype3 subtype4 subtype5 
  122.30   115.69   105.07    63.62    74.53 
subtype1 subtype2 subtype3 subtype4 subtype5 
  15.715   17.030   13.350   12.345   18.030 
[1] "0.3 - 122.3 (15.7)" "0.1 - 115.7 (17.0)" "1.0 - 105.1 (13.3)"
[4] "0.6 - 63.6 (12.3)"  "1.1 - 74.5 (18.0)" 
D10V2, continuous
          vv
clus       STAGE I STAGE IA STAGE IB STAGE II STAGE IIA STAGE IIB STAGE III
  subtype1       0        5        7        7         7        15         0
  subtype2       0        0        6        4        10         7         0
  subtype3       0        2        3        9         5         7         0
  subtype4       0        0        8        5         5        10         1
  subtype5       2        2        6        4         8         8         1
          vv
clus       STAGE IIIA STAGE IIIB STAGE IIIC STAGE IV
  subtype1         16         22         14        7
  subtype2         13         13          8        8
  subtype3         11          1          0        6
  subtype4         15          7          4        6
  subtype5         12          9          6        3
D10V3, multiclass
            clus
vv           subtype1 subtype2 subtype3 subtype4 subtype5
  STAGE I           0        0        0        0        2
  STAGE IA          5        0        2        0        2
  STAGE IB          7        6        3        8        6
  STAGE II          7        4        9        5        4
  STAGE IIA         7       10        5        5        8
  STAGE IIB        15        7        7       10        8
  STAGE III         0        0        0        1        1
  STAGE IIIA       16       13       11       15       12
  STAGE IIIB       22       13        1        7        9
  STAGE IIIC       14        8        0        4        6
  STAGE IV          7        8        6        6        3
[1] 11  5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       T1 T2 T3 T4
  subtype1  7 14 51 31
  subtype2  0 13 36 23
  subtype3  2 19 19  5
  subtype4  1 14 30 17
  subtype5  5 12 27 17
D10V4, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  T1        7        0        2        1        5
  T2       14       13       19       14       12
  T3       51       36       19       30       27
  T4       31       23        5       17       17
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       N0 N1 N2 N3
  subtype1 30 21 21 29
  subtype2 19 20 13 18
  subtype3 17 12 11  5
  subtype4 16 22 12 10
  subtype5 21 13 17  9
D10V5, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  N0       30       19       17       16       21
  N1       21       20       12       22       13
  N2       21       13       11       12       17
  N3       29       18        5       10        9
[1] 4 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V6, binary
          cls
clus        0  1
  subtype1 93  5
  subtype2 62  6
  subtype3 41  4
  subtype4 52  5
  subtype5 58  2
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   93    5
  subtype2   62    6
  subtype3   41    4
  subtype4   52    5
  subtype5   58    2
   clus
vv  subtype1 subtype2 subtype3 subtype4 subtype5
  0       93       62       41       52       58
  1        5        6        4        5        2
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V7, binary
          cls
clus        0  1
  subtype1 29 74
  subtype2 27 45
  subtype3 16 29
  subtype4 24 38
  subtype5 22 39
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   29   74
  subtype2   27   45
  subtype3   16   29
  subtype4   24   38
  subtype5   22   39
        clus
vv       subtype1 subtype2 subtype3 subtype4 subtype5
  FEMALE       29       27       16       24       22
  MALE         74       45       29       38       39
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V8, binary
          cls
clus        0  1
  subtype1 77 24
  subtype2 61  9
  subtype3 34  3
  subtype4 46 13
  subtype5 46 15
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1   77   24
  subtype2   61    9
  subtype3   34    3
  subtype4   46   13
  subtype5   46   15
     clus
vv    subtype1 subtype2 subtype3 subtype4 subtype5
  NO        77       61       34       46       46
  YES       24        9        3       13       15
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       STOMACH ADENOCARCINOMA, SIGNET RING TYPE
  subtype1                                        4
  subtype2                                        2
  subtype3                                        0
  subtype4                                        0
  subtype5                                        1
          vv
clus       STOMACH, ADENOCARCINOMA, DIFFUSE TYPE
  subtype1                                    14
  subtype2                                    28
  subtype3                                     5
  subtype4                                     3
  subtype5                                     8
          vv
clus       STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                     38
  subtype2                                                     25
  subtype3                                                     20
  subtype4                                                     24
  subtype5                                                     10
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE
  subtype1                                                 6
  subtype2                                                 7
  subtype3                                                 1
  subtype4                                                 4
  subtype5                                                 1
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)
  subtype1                                                                17
  subtype2                                                                 5
  subtype3                                                                12
  subtype4                                                                18
  subtype5                                                                15
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE
  subtype1                                                  1
  subtype2                                                  1
  subtype3                                                  1
  subtype4                                                  0
  subtype5                                                  3
          vv
clus       STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE
  subtype1                                               23
  subtype2                                                4
  subtype3                                                6
  subtype4                                               13
  subtype5                                               23
D10V9, multiclass
                                                                   clus
vv                                                                  subtype1
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 4
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   14
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  38
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        6
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       17
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        23
                                                                   clus
vv                                                                  subtype2
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 2
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                   28
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  25
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        7
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)        5
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         4
                                                                   clus
vv                                                                  subtype3
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    5
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  20
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       12
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       1
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                         6
                                                                   clus
vv                                                                  subtype4
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 0
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    3
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  24
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        4
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       18
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       0
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        13
                                                                   clus
vv                                                                  subtype5
  STOMACH ADENOCARCINOMA, SIGNET RING TYPE                                 1
  STOMACH, ADENOCARCINOMA, DIFFUSE TYPE                                    8
  STOMACH, ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)                  10
  STOMACH, INTESTINAL ADENOCARCINOMA, MUCINOUS TYPE                        1
  STOMACH, INTESTINAL ADENOCARCINOMA, NOT OTHERWISE SPECIFIED (NOS)       15
  STOMACH, INTESTINAL ADENOCARCINOMA, PAPILLARY TYPE                       3
  STOMACH, INTESTINAL ADENOCARCINOMA, TUBULAR TYPE                        23
[1] 7 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
          vv
clus       R0 R1 R2
  subtype1 91  4  0
  subtype2 57  6  3
  subtype3 37  1  4
  subtype4 50  3  1
  subtype5 56  0  2
D10V10, multiclass
    clus
vv   subtype1 subtype2 subtype3 subtype4 subtype5
  R0       91       57       37       50       56
  R1        4        6        1        3        0
  R2        0        3        4        1        2
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V11, continuous
          vv
clus       ASIAN BLACK OR AFRICAN AMERICAN WHITE
  subtype1    12                         4    78
  subtype2    17                         1    52
  subtype3     6                         0    23
  subtype4    14                         2    41
  subtype5    18                         5    33
D10V12, multiclass
                           clus
vv                          subtype1 subtype2 subtype3 subtype4 subtype5
  ASIAN                           12       17        6       14       18
  BLACK OR AFRICAN AMERICAN        4        1        0        2        5
  WHITE                           78       52       23       41       33
[1] 3 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
D10V13, binary
          cls
clus        0  1
  subtype1  3 71
  subtype2  0 66
  subtype3  0 29
  subtype4  1 47
  subtype5  1 37
[1] "tbl2"
          cls
clus       [,1] [,2]
  subtype1    3   71
  subtype2    0   66
  subtype3    0   29
  subtype4    1   47
  subtype5    1   37
                        clus
vv                       subtype1 subtype2 subtype3 subtype4 subtype5
  HISPANIC OR LATINO            3        0        0        1        1
  NOT HISPANIC OR LATINO       71       66       29       47       37
[1] 2 5
[1] TRUE
[1] "dimension of contingency table is larger than 2 by 2 --- so will do fisher test with simulate.p.value=TRUE"
